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Sample records for repetto turbidite sequences

  1. 优雅舞者 Repetto

    Institute of Scientific and Technical Information of China (English)

    Kitten Miao

    2008-01-01

    <正>或许你还不太了解这个品牌,但当你在它的使用者名单上发现一长串好莱坞大牌明星时,当你在它的设计者名单里找到不胜枚举的时尚大师时,相信你的好奇心已然爆棚。六十年来芭蕾便鞋的鼻祖,代表法国式优雅的Repetto,已经势不可挡地杀回时尚舞台——

  2. Estimating Inland Ground Motions from Lake Turbidite Sequences, Northern Cascadia margin, USA.

    Science.gov (United States)

    Goldfinger, C.; Hausmann, R. B.; Black, B.; Romsos, C. G.; Beeson, J. W.; Galer, S.; Collins, T.

    2016-12-01

    Using cores collected from lakes in northern Oregon and Washington, we are attempting to estimate ground motions from plate boundary earthquakes at inland paleoseismic sites. Paleoseismic evidence in Cascadia comes largely from coastal and offshore sites, while population the main population centers of Seattle, Victoria, Vancouver and Portland are 100-180 km inland. Cores from Leland Lake on the Olympic Peninsula, Lake Sawyer, near Seattle, and Bull Run Lake, 65 km east of Portland contain sequences of event beds that are interpreted as internal lake turbidites. The number, timing based on 14C constrained age models, sequencing, and individual event characteristics correlated with physical properties and CT data are compatible with onshore and offshore paleoseismic records of plate boundary earthquakes. The likely correlative turbidite sequence at Bull Run is well-matched to the nearest offshore turbidite sequences at Hydrate Ridge and Oceanus Basin (see also Hausmann et al. this meeting). Similarly, the Washington lake sequences are well matched to the offshore Washington sequences (Goldfinger et al. 2016), with the likely inclusion of a single Seattle Fault earthquake 1000 cal BP. Bull Run Lake has several ashes, but otherwise, additional event beds related to crustal faulting or other events are not observed. Our strategy is to investigate lakes that have low sensitivity to subaquatic slope failures in order to explore the limits of stability. In this case, the minimum ground shaking required for slope failure will approach actual ground motions as stability increases. We mapped failure zones within the lakes, and collected shear vane measurements to estimate sediment cohesion. We then computed minimum ground motions for these sites. For Leland Lake, there are no mappable failures, indicating internal lake turbidites likely were generated by thin surface failures below mapping resolution. For Sawyer and Bull Run, the most stable failure sites require 0.2-0.3g

  3. Sequence stratigraphic setting of turbidite-related petroleum fields, Green Canyon and Ewing Bank lease areas, northern Gulf of Mexico

    Energy Technology Data Exchange (ETDEWEB)

    Weimer, P.; Pulham, A.J. [Univ. of Colorado, Boulder, CO (United States)

    1996-08-01

    The Green Canyon (GC) and Ewing Bank (EW) OCS lease areas have 17 discoveries/fields, primarily from bathyal turbidite systems. Salt has played a significant role in the formation of the intraslope basins that the turbidite systems were deposited in, by influencing the flows of turbidities throughout the basin, in the subsequent trap formation, and, in some cases, as a seal. Nearly every field/discovery is associated with a seismic amplitude anomaly. Fields generally have multiple pay zones, with up to 22 in GC 184 (Jolliet). To date, eight of the fields are producing: EB 826, EB 873 (Lobster), GC 6 (Kodiak), GC 18, GC 53/54 (Marquette), GC 65/110 (Bullwinkle), GC 184 (Jolliet), and GC 205 (Vancouver). Other fields expected to be developed are GC 72/116 (Popeye), GC 254 (Allegheny), GC 200/244 (Olivella), GC and GC 166 (Bison). Other discoveries that were produced and then abandoned include GC 19, and GC29. Producing reservoir facies are highly variable across the area. Turbidite reservoir geometries in Pliocene sands (>1.6 Ma) consist of sheets and amalgamated sheet sands. Pleistocene sands are characterized primarily from channel-levee systems and related deposits. These sands tend to more compartmentalized with separate oil/water or gas/water contacts. Most reservoir sands occur within 100 ft overlying a sequence boundary, indicating the eustatic control on the timing of reservoir sand deposition.

  4. New constraints on the origin of the ophiolitic rocks within sinorogenic turbiditic sequences at Cilento region (southern Italy)

    Energy Technology Data Exchange (ETDEWEB)

    Mazzeo, F.C.; Vita, P. de; Aulinas, M.; Arienzo, I.; Cirillo, G.; Iovine, R.S.; Spari, D.

    2016-07-01

    Mafic igneous rocks (pillow lavas and gabbros) embedded as olistoliths within Miocene turbiditic sequences crop out in the Cilento area at the Mount Centaurino (Campania region, Southern Italy). The concentration of major oxides, as well as trace element ratios (Nb/Yb, Nb/Ta, Th/Nb) and the chondrite-normalized Rare Earth Elements (REE) patterns suggest a tholeiitic character with Mid Oceanic Ridge Basalts (MORB) affinity. The chemical composition of pillow lavas is consistent with magmas generated by 10% degrees of non-modal fractional partial melting, of a spinel-bearing MORB-type asthenospheric mantle. Regarding gabbros, the calculated composition of parental melts in equilibrium with the clinopyroxenes show a wide compositional range, and there are very different from the pillow basalts of the Mount Centaurino, suggesting that the clinopyroxenes might have derived from more evolved melts compared to those that produced the basalts. The origin of these olistoliths is not yet understood. Here we suggest that these rocks represent fragment of a dismantled accretionary wedge embedded during the deposition of the Cilento group sedimentary successions in a thrust top basin. (Author)

  5. Lower Cretaceous turbidites of the Moray Firth: sequence stratigraphical framework and reservoir distribution

    Energy Technology Data Exchange (ETDEWEB)

    Jeremiah, J.M. [Nederlandse Ardolie Maatschappij B.V., Assen (Netherlands)

    2000-11-01

    Lower Cretaceous depositional systems of the Moray Firth are influenced by eustatic sea-level oscillations which have been dramatically overprinted by two major phases of pulsed tectonism, the Late Cimmerian and Austrian. The biostratigraphical resolution obtained has allowed the timing and differentiation of distinct tectonic/sequence boundaries, some of which are utilized as important seismo-stratigraphic markers. The construction of detailed facies maps for individual sequences has, in parallel, allowed an insight into the tectonic history of the main source areas during the Early Cretaceous. (Author)

  6. Recognition of cyclic steps in sandy and gravelly turbidite sequences and consequences for the Bouma facies model

    NARCIS (Netherlands)

    Postma, George; Kleverlaan, K.; Cartigny, Matthieu

    2014-01-01

    Preservation of cyclic steps contrasts markedly with that of subcritical-flow bedforms, because cyclic steps migrate upslope eroding their lee face and preserving their stoss side. Such bedforms have not been described from turbidite outcrops and cores as yet. A conceptual block diagram for recognit

  7. Problems in turbidite research: A need for COMFAN

    Science.gov (United States)

    Normark, W.R.; Mutti, E.; Bouma, A.H.

    1984-01-01

    Comparison of modern submarine fans and ancient turbidite sequences is still in its infancy, mainly because of the incompatibility of study approaches. Research on modern fan systems mainly deals with morphologic aspects and surficial sediments, while observations on ancient turbidite formations are mostly directed to vertical sequences. The lack of a common data set also results from different scales of observation. To review the current status of modern and ancient turbidite research, an international group of specialists formed COMFAN (Committee on Fans) and met in September 1982 at the Gulf Research and Development Company research facilities in Pennsylvania. ?? 1984 Springer-Verlag New York Inc.

  8. Fine-Grained Turbidites: Facies, Attributes and Process Implications

    Science.gov (United States)

    Stow, Dorrik; Omoniyi, Bayonle

    2016-04-01

    Within turbidite systems, fine-grained sediments are still the poor relation and sport several contrasting facies models linked to process of deposition. These are volumetrically the dominant facies in deepwater and, from a resource perspective, they form important marginal and tight reservoirs, and have great potential for unconventional shale gas, source rocks and seals. They are also significant hosts of metals and rare earth elements. Based on a large number of studies of modern, ancient and subsurface systems, including 1000s of metres of section logging, we define the principal genetic elements of fine-grained deepwater facies, present a new synthesis of facies models and their sedimentary attributes. The principal architectural elements include: non-channelised slope-aprons, channel-fill, channel levee and overbank, turbidite lobes, mass-transport deposits, contourite drifts, basin sheets and drapes. These comprise a variable intercalation of fine-grained facies - thin-bedded and very thin-bedded turbidites, contourites, hemipelagites and pelagites - and associated coarse-grained facies. Characteristic attributes used to discriminate between these different elements are: facies and facies associations; sand-shale ratio, sand and shale geometry and dimensions, sand connectivity; sediment texture and small-scale sedimentary structures; sediment fabric and microfabric; and small-scale vertical sequences of bed thickness. To some extent, we can relate facies and attribute characteristics to different depositional environments. We identify four distinct facies models: (a) silt-laminated mud turbidites, (b) siliciclastic mud turbidites, (c) carbonate mud turbidites, (d) disorganized silty-mud turbidites, and (e) hemiturbidites. Within the grainsize-velocity matrix turbidite plot, these all fall within the region of mean size < 0.063mm, maximum grainsize (one percentile) <0.2mm, and depositional velocity 0.1-0.5 m/s. Silt-laminated turbidites and many mud

  9. Spatially limited mud turbidites on the Cascadia margin: segmented earthquake ruptures?

    Directory of Open Access Journals (Sweden)

    C. Goldfinger

    2013-08-01

    Full Text Available A series of 23 thin, mostly mud-silt turbidites are found interspersed between larger, well-dated and regionally correlated paleoseismic sandy turbidites that extend along most of the Cascadia margin, northwestern United States. Investigation of the structure, distribution, and sedimentology of these thin mud-silt units supports the interpretation of these units as turbidites originating on the continental slope. Interpretation of mud turbidites is inhibited by bioturbation and lower response to analytical and imaging techniques; nevertheless most of the 23 interpreted beds exhibit most of the characteristics of coarser turbidites. These characteristics include sharp bases, fining upward sequences, darker color, increased gamma and CT density and magnetic susceptibility relative to the hemipelagic background, sparse microfossils, high lithic content, and evidence of transport from marine sources on the continental slope. New core data from sites south of Rogue Apron indicate that sandy and muddy turbidites may be correlated at least 150 km south to Trinidad Plunge Pool for the period ~ 4800 yr BP to present. Many of the mud turbidites initially described at Rogue Apron coarsen southward, becoming sandy turbidites. High-resolution Chirp seismic profiles reveal that turbidite stratigraphy along the base of the southern Cascadia continental slope is continuous, with little variation for at least 240 km along strike. The Chirp data show that turbidites along the Cascadia base of slope are ubiquitous, and likely not sourced solely from submarine canyon mouths, but may also have been delivered to the proximal abyssal plain as sheet flows from the open continental slope and coalescing local sources. Regional stratigraphy reveals that hemipelagic sedimentation rates and total Holocene turbidite thickness and mass are similar at widely separated sites, yet the total thickness of the Holocene section is greater by a factor of two in southern Cascadia

  10. Is the turbidite facies association scheme valid for interpreting ancient submarine fan environments?

    Science.gov (United States)

    Shanmugam, G.; Damuth, J. E.; Moiola, R. J.

    1985-04-01

    Although turbidite facies reflect only processes of deposition, turbidite facies associations are routinely used to identify ancient submarine-fan subenvironments (e.g., upper fan, channel, lobe, etc.). The assumption that process of deposition also reflects environment of deposition may not be valid for the following reasons: (1) Mutti and Ricci Lucchi's facies association scheme for submarine fans has been developed exclusively from ancient turbidite sequences; however, the true relationship between such turbidite facies associations and related fan subenvironments has not been confirmed from modern fans; (2) individual channel-levee systems of many modern submarine fans are in many cases large enough to contain the entire ancient fan systems on which these facies associations are based; (3) large channel-levee systems comparable to those of modern fans have not been recognized in outcrops. Consequently, the validity of turbidite facies associations for interpreting ancient submarine-fan subenvironments must be considered tenuous until confirmed in modern fans.

  11. Middle Miocene reworked turbidites in the Baiyun Sag of the Pearl River Mouth Basin, northern South China Sea margin: Processes, genesis, and implications

    Science.gov (United States)

    Gong, Chenglin; Wang, Yingmin; Zheng, Rongcai; Hernández-Molina, F. Javier; Li, Yun; Stow, Dorrik; Xu, Qiang; Brackenridge, Rachel E.

    2016-10-01

    Our understanding of reworked turbidites is still in its infancy, and their flow processes and genesis still remain understudied. Core data from the middle Miocene Zhujiang Formation in the Pearl River Mouth Basin allow us to differentiate reworked turbidites, yielding two main contributions. Firstly, reworked turbidites are distinguished from turbidites by the association of traction structures and tidal signatures, which occur in discrete units rather than forming a classic "Bouma Sequence" for turbidites. Sedimentological characteristics of reworked turbidites proposed here will help to obtain a robust set of diagnostic criteria for the recognition of deep-water non-turbidite deepwater units as reservoirs. Secondly, our results suggest that, in the down-slope direction, classic detritus carried in turbidity flows would synchronously be bidirectionally reworked by internal tides and waves, resulting in tidal signatures seen in the interpreted reworked turbidites. In the along-slope direction, upper parts of dilute turbidity currents would mix vertically with seawater, and muddy fines would be winnowed away by contour currents, whereas lower parts of dilute turbidity currents would probably drop their coarse particles, resulting in traction structures recognized in the documented reworked turbidites. Our work highlights the influence of bottom currents on the development and modification of turbidites and suggests that reworked turbidites were created by the combined action of down-slope transport and reworking and along-slope winnowing and sorting, helping to better understand flow processes and genesis of non-turbidite reservoirs with a great economic interest.

  12. Feasibility of Optimizing and Reserves from a Mature and Geological Complex Multiple Turbidite Offshore California Reservoir Through the Drilling and Completion of a Trilateral Horizontal Well.

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-06-01

    The main objective of this project is to devise an effective re- development strategy to combat producibility problems related to the Repetto turbidite sequences of the Carpinteria Field. The lack of adequate reservoir characterization, high-water cut production, and scaling problems have in the past contributed to the field`s low productivity. To improve productivity and enhance recoverable reserves, the following specific goals were proposed: (1) Develop an integrated database of all existing data from work done by the former ownership group. (2) Expand reservoir drainage and reduce sand problems through horizontal well drilling and completion. (3) Operate and validate reservoir`s conceptual model by incorporating new data from the proposed trilateral well. (4) Transfer methodologies employed in geologic modeling and drilling multilateral wells to other operators with similar reservoirs. Pacific Operators Offshore, Inc. with the cooperation of its team members; the University of Southern California; Schlumberger; Baker Oil Tools; Halliburton Energy Services and Coombs and Associates undertook a comprehensive study to reexamine the reservoir conditions leading to the cent field conditions and to devise methodologies to mitigate the producibility problems. A computer based data retrieval system was developed to convert hard copy documents containing production, well completion and well log data into easily accessible on-line format. To ascertain the geological framework of the reservoir, a thorough geological modeling and subsurface mapping of the Carpinteria field was developed. The model is now used to examine the continuity of the sands, characteristics of the sub-zones, nature of water influx and transition intervals in individual major sands. The geological model was then supplemented with a reservoir engineering study of spatial distribution of voidage in individual layers using the production statistics and pressure surveys. Efforts are continuing in

  13. Turbidite plays` immaturity means big potential remains

    Energy Technology Data Exchange (ETDEWEB)

    Pettingill, H.S. [Repsol Exploracion SA, Madrid (Spain)

    1998-10-05

    The international exploration and production industry is increasingly focusing on deepwater plays. Turbidites are not the only reservoir type that occurs in deepwater frontiers, but they are the primary reservoir type of those plays. A worldwide data base assembled from published information on 925 fields and discoveries with deepwater clastic reservoirs (turbidites sensu lato) has been employed to investigate the large-scale exploration and production trends. Coverage of the Former Soviet Union, China, and the Indian subcontinent has been minor, but with the large data base of fields and discoveries from the rest of the world, the broad conclusions should remain valid. This article describes the global turbidite play in terms of: (1) basins of the world where turbidite fields have been discovered; (2) the five largest basins in terms of total discovered resources; and (3) a summary of trap type, which is a critical geological factor in turbidite fields. The second article will summarize a population of the world`s 43 largest turbidite fields and discoveries.

  14. Selected highlights of a half-century of academic and industry studies of turbidite systems

    Science.gov (United States)

    Nelson, C. H.

    2012-04-01

    From more than 50 years of research on modern turbidite systems and considering this bias (e.g. experimental and modeling research not included in this summary), the following are my suggested landmarks for interplay between academic and industry research on turbidite systems: 1.In the 1960´s, the outcrop research of the Bouma sequence showed immediate relevance for the characterization of proximal to distal depositional environments of modern Astoria Fan (e.g. a&b structures in proximal channels, c-e in levees, a-e in lobes, d&e in basin plains), and for identification of turbidites in industry boreholes. 2.In the 1970´s, Mutti and Ricchi Lucchís facies assemblages from outcrops correlated well with Nelson and Nilseńs comparison of modern and ancient turbidite systems. The emerging models from this and other outcrop and modern system studies of Walker and Normark provided early guidelines for industry exploration. 3.In the 1980´s, the new high-resolution sidescan sonar studies on modern systems revealed the complex morphology of channel and lobe systems. These new details interplayed with the major contribution of seismic sequence stratigraphy from industry, which had important implications for outcrop studies, modern system research, and an emerging variety of improved fan models that considered the depositional elements defined by Mutti and Normark. The maturity of studies at this point outlined the key tectonic, sediment supply and climate/sea level factors controlling the development of a wide variety of turbidite system depositional patterns. 4.In the 1990´s, the 3D seismic studies of industry and high-resolution seismic and coring studies on modern systems provided detailed new insight into a complex variety of turbidite systems, particularly for slope environments. The close comparison of these data confirmed the relevance of present-day turbidite systems as a key to past outcrop and subsurface systems. 5.In the new millennium, seismic geomorphology

  15. Bacterial Diversity Across a Turbidite-Stranded Sediment-Water Interface, La Jolla Canyon, CA

    Science.gov (United States)

    Harrison, B. K.; Flood, B.; Myrbo, A.; Bailey, J.

    2016-12-01

    The emplacement of gravity-driven sediment flows imposes a significant physical and geochemical impact on underlying sediment and microbial communities. Although previous studies have established lasting mineralogical (e.g., McKay and Pederson, 2014) and biological signatures (e.g., Anschutz et al., 2002) of turbidite deposition, the response of prokaryotes within and beneath debris flows remains poorly constrained. Both bacterial cells associated with the underlying sediment and allocthonous material must respond to substantially altered selective pressures. As a consequence, turbidites and underlying sediments provide an exceptional opportunity to examine 1) microbial community response to sedimentation 2) preservation and identification of microbial dispersal mechanisms. We collected Illumina MiSeq sequence libraries across an intact marine turbidite boundary at 25cm sediment depth in La Jolla canyon off the coast of California. 16S rRNA gene signatures of relict and active bacterial populations exhibit persistent differences attributable to turbidite deposition. In particular, the sedimentary boundary is sharply demarcated at the cm scale by the diversity and abundance of Chloroflexi, Planctomycetes, and Actinobacteria. Variations in the abundance of putative dissimilatory sulfate-reducing Deltaproteobacteria across the stranded sediment-water interface reflect persistent turbidite-induced changes to the geochemical environment. This work raises the possibility that abrupt sedimentological events may alter the microbial community in a manner that persists with burial.

  16. XRF analysis of turbidites in the Japan Trench: Evidences of provenances?

    Science.gov (United States)

    Schwestermann, Tobias; Fink, Hiske G.; Wefer, Gerold; Fleischmann, Timo; McHugh, Cecilia M.; Ikehara, Ken; Kanamatsu, Toshiya; Kioka, Arata; Strasser, Michael

    2017-04-01

    Since the Mw 9 Tohoku-oki earthquake in 2011, intensive research is going on, in order to analyse earthquake-related changes and fingerprints in the sedimentological record of the Japan Trench. Many turbidites were detected within small depositional trench basins in the central part of the trench by means of high-resolution sub-bottom profiles and sediment cores. There, distinct thick turbidite sequences have been dated by tephra and radiocarbon analyses and correlated to historic earthquakes. However, information on the turbiditeś source areas and, thus, inferences on their causing earthquake characteristics, is so far lacking. For this purpose, this study performs turbidite provenance analyses by detailed petrographic and XRF core scanning analysis on cores retrieved during cruises of R/V Sonne SO-219A and R/V Sonne SO-251A, covering the entire along-strike extent of the Japan Trench from 36° to 40.3°N. Cores were measured on the Avaatech x-ray fluorescence (XRF) core scanner at MARUM, Bremen, with a sampling interval of 1cm with 10kV and 30kV for the elements Al, Si, K, Ca, Ti, Mn, Fe and Rb, Sr, Zr, respectively. First results show distinctly different chemical fingerprints of the various spatially and temporally distributed turbidite sequences. In particular, the fine grained (silt to clay) upper parts of the turbidite sequences have partly distinct trends in elemental ratios, indicating either (i) various source areas, (ii) sorting processes along the turbidités pathways and/or (iii) post-depositional alteration processes. Furthermore, also the coarser basal sequences (mostly composed of multiple fine sand layers and beds) show various trends of elemental ratios. In particular the Fe/Rb vs. density trends can be indicative for the event deposits in the central part of the trench, which have been linked to historic earthquakes. Although, XRF core scanning data from the sand fraction needs to be interpreted with care, also sediment petrographic data (heavy

  17. Late precambrian outer-fan turbidites from Namibia - vertical and lateral characteristics

    Science.gov (United States)

    Swart, Roger

    1994-01-01

    Little is known about the lateral dimensions of distal (outer-fan to fan-fringe) ancient turbidites because of outcrop limitations. The Zebrapüts and Brak River Formations of the Zerrissene turbidite system, well exposed in hyper-arid Namib Desert of south-western Africa, provide a good opportunity of examining facies types, facies associations, vertical sequences and lateral continuity of distal turbidites. The two formations are characterised by sequences of Mutti and Ricci Lucchi facies B 1, C 2, D 1, D 2, F, G and a glacial facies. Facies F represents small scale slumps related to the glacial facies, and not slumping from shelf areas. Four facies associations have been recognised (designated 1 to 4) and these represent lobe sandstone, fan-fringe, glacial-marine/turbidite and basin plain facies. No large scale thinning- or thickening-upward sequences are present, but minor (compensation) cycles have been recognized. In only one instance are these statistically significant. Individual units are laterally continuous for at least several kilometres. One shallow channel has been identified in the lobe sandstones.

  18. Turbidite event history--Methods and implications for Holocene paleoseismicity of the Cascadia subduction zone

    Science.gov (United States)

    Goldfinger, Chris; Nelson, C. Hans; Morey, Ann E.; Johnson, Joel E.; Patton, Jason R.; Karabanov, Eugene; Gutierrez-Pastor, Julia; Eriksson, Andrew T.; Gracia, Eulalia; Dunhill, Gita; Enkin, Randolph J.; Dallimore, Audrey; Vallier, Tracy; Kayen, Robert; Kayen, Robert

    2012-01-01

    Turbidite systems along the continental margin of Cascadia Basin from Vancouver Island, Canada, to Cape Mendocino, California, United States, have been investigated with swath bathymetry; newly collected and archive piston, gravity, kasten, and box cores; and accelerator mass spectrometry radiocarbon dates. The purpose of this study is to test the applicability of the Holocene turbidite record as a paleoseismic record for the Cascadia subduction zone. The Cascadia Basin is an ideal place to develop a turbidite paleoseismologic method and to record paleoearthquakes because (1) a single subduction-zone fault underlies the Cascadia submarine-canyon systems; (2) multiple tributary canyons and a variety of turbidite systems and sedimentary sources exist to use in tests of synchronous turbidite triggering; (3) the Cascadia trench is completely sediment filled, allowing channel systems to trend seaward across the abyssal plain, rather than merging in the trench; (4) the continental shelf is wide, favoring disconnection of Holocene river systems from their largely Pleistocene canyons; and (5) excellent stratigraphic datums, including the Mazama ash and distinguishable sedimentological and faunal changes near the Pleistocene-Holocene boundary, are present for correlating events and anchoring the temporal framework. Multiple tributaries to Cascadia Channel with 50- to 150-km spacing, and a wide variety of other turbidite systems with different sedimentary sources contain 13 post-Mazama-ash and 19 Holocene turbidites. Likely correlative sequences are found in Cascadia Channel, Juan de Fuca Channel off Washington, and Hydrate Ridge slope basin and Astoria Fan off northern and central Oregon. A probable correlative sequence of turbidites is also found in cores on Rogue Apron off southern Oregon. The Hydrate Ridge and Rogue Apron cores also include 12-22 interspersed thinner turbidite beds respectively. We use 14C dates, relative-dating tests at channel confluences, and

  19. Turbidite megabeds in an Oceanic Rift Valley recording jokulhlaups of late Pleistocene glacial lakes of the western United States

    Science.gov (United States)

    Zuffa, G.G.; Normark, W.R.; Serra, F.; Brunner, C.A.

    2000-01-01

    Escanaba Trough is the southernmost segment of the Gorda Ridge and is filled by sandy turbidites locally exceeding 500 m in thickness. New results from Ocean Drilling Program (ODP) Sites 1037 and 1038 that include accelerator mass spectrometry (AMS) 14C dates and revised petrographic evaluation of the sediment provenance, combined with high-resolution seismic-reflection profiles, provide a lithostratigraphic framework for the turbidite deposits. Three fining-upward units of sandy turbidites from the upper 365 m at ODP Site 1037 can be correlated with sediment recovered at ODP Site 1038 and Deep Sea Drilling Program (DSDP) Site 35. Six AMS 14C ages in the upper 317 m of the sequence at Site 1037 indicate that average deposition rates exceeded 10 m/k.yr. between 32 and 11 ka, with nearly instantaneous deposition of one ~60-m interval of sand. Petrography of the sand beds is consistent with a Columbia River source for the entire sedimentary sequence in Escanaba Trough. High-resolution acoustic stratigraphy shows that the turbidites in the upper 60 m at Site 1037 provide a characteristic sequence of key reflectors that occurs across the floor of the entire Escanaba Trough. Recent mapping of turbidite systems in the northeast Pacific Ocean suggests that the turbidity currents reached the Escanaba Trough along an 1100-km-long pathway from the Columbia River to the west flank of the Gorda Ridge. The age of the upper fining-upward unit of sandy turbidites appears to correspond to the latest Wisconsinan outburst of glacial Lake Missoula. Many of the outbursts, or jokulhlaups, from the glacial lakes probably continued flowing as hyperpycnally generated turbidity currents on entering the sea at the mouth of the Columbia River.

  20. Sedimentology, petrology, and gas potential of the Brallier Formation: upper Devonian turbidite facies of the Central and Southern Appalachians

    Energy Technology Data Exchange (ETDEWEB)

    Lundegard, P.D.; Samuels, N.D.; Pryor, W.A.

    1980-03-01

    The Upper Devonian Brallier Formation of the central and southern Appalachian basin is a regressive sequence of siltstone turbidites interbedded with mudstones, claystones, and shales. It reaches 1000 meters in thickness and overlies basinal mudrocks and underlies deltaic sandstones and mudrocks. Facies and paleocurrent analyses indicate differences between the depositional system of the Brallier Formation and those of modern submarine fans and ancient Alpine flysch-type sequences. The Brallier system is of finer grain size and lower flow intensity. In addition, the stratigraphic transition from turbidites to deltaic sediments is gradual and differs in its facies succession from the deposits of the proximal parts of modern submarine fans. Such features as massive and pebbly sandstones, conglomerates, debris flows, and massive slump structures are absent from this transition. Paleocurrents are uniformly to the west at right angles to basin isopach, which is atypical of ancient turbidite systems. This suggests that turbidity currents had multiple point sources. The petrography and paleocurrents of the Brallier Formation indicate an eastern source of sedimentary and low-grade metasedimentary rocks with modern relief and rainfall. The depositional system of the Brallier Formation is interpreted as a series of small ephemeral turbidite lobes of low flow intensity which coalesced in time to produce a laterally extensive wedge. The lobes were fed by deltas rather than submarine canyons or upper fan channel systems. This study shows that the present-day turbidite facies model, based mainly on modern submarine fans and ancient Alpine flysch-type sequences, does not adequately describe prodeltaic turbidite systems such as the Brallier Formation. Thickly bedded siltstone bundles are common features of the Brallier Formation and are probably its best gas reservoir facies, especially when fracture porosity is well developed.

  1. Complexities within distal sheet turbidite deposits: case study 160,000ka Icod Turbidite, Moroccan Turbidite System

    Science.gov (United States)

    Hunt, James; Wynn, Russell

    2010-05-01

    The Icod landslide from the northern flank of Tenerife not only generated a debris avalanche phase (Watts & Masson, 1995; Masson et al. 2002), but produced a volcaniclastic turbidite that spans three interconnected basins. The Icod turbidite (160,000ka) was reported and correlated during work in the Madeira Abyssal Plain (Pearce & Jarvis, 1992; Rothwell, Pearce & Weaver, 1992). Here it forms a series of vertically stacked sand bodies accumulating into a single event bed. However, the Madeira Abyssal Plain is fed from the Agadir Basin by a series of channels, thus invoking a level of complexity to the deposit with the flow exiting channels at different times. The Icod turbidite can be found deposited more proximally to source in the Agadir Basin as a 0.3-0.6m stacked sand with accompanying 0.2-1.5m mudcap. With this stacked sand facies present here a number of other mechanisms can still be viable: (1) multistage retrogressive landslide failure, (2) flow reflection and (3) internal waves. Geochemical methodologies including ICP-AES, ICP-MS, XRF, ITRAX micro-XRF, SEM EDS and laser-diffraction grain-size analysis have been employed here to investigate the potential of a retrogressive failure at source being the driver of this facies. Evidence suggests that this stacked sand facies in this case is derived from the failure mechanism at source. Five vertical sand packages have been identified and correlated through the Agadir Basin, with the initial basal package representing the thickest. However, this amalgamated sand displays degrees of complexity with correlated internal erosional surfaces marked by sand-sand grain-size breaks. There are also sand-sand grain-size breaks found at the transition between facies associated with flow properties i.e. Bouma Tb parallel laminations and Bouma Tc ripple laminations. Each of the stacked sand intervals also has a sand-mud grain-size break present at the top of the package. This sand-mud break could possibly indicate (1) bypass of

  2. The late Proterozoic Amis River Formation of Namibia—a turbidite system developed by vertical accretion

    Science.gov (United States)

    Swart, Roger

    1990-04-01

    Vertical facies changes form the fundamental basis of interpretation of many submarine turbidite systems. Some systems, however, do not show major vertical cyclicity over thicknesses of hundreds of metres, but rather display significant lateral changes. The late Proterozoic Amis River Formation of Namibia, which contains the facies typical of submarine turbidite systems, shows little vertical variation but has major lateral changes. In the west of the exposed area the sequence consists predominantly of bundles of facies C 2 and D 1 (facies scheme of Mutti and Ricci Lucchi, 1975) with interbedded packages of facies B 1 beds, which become more common upwards. Only minor vertical cyclicity is observed, beds are laterally continuous for many kilometres and the sandstone: shale ratio is high. In the east largely thin-bedded facies D 2 beds occur with a much lower sandstone: shale ratio than in the west. This system is interpreted here as developing largely by vertical accretion rather than progradation.

  3. Ooid turbidites from the Central Western continental margin of India

    Digital Repository Service at National Institute of Oceanography (India)

    Rao, P.S.

    revealed that the turbidites are mainly composed of ooids, shell fragments, and shallow water benthic foraminifera. Bioclastic sediments of the outer shelf and upper slope regions are considered the source of the debris flows/turbidity deposits. It appears...

  4. Turbidite systems: State of the art and future directions

    Science.gov (United States)

    Normark, W.R.; Posamentier, H.; Mutti, E.

    1993-01-01

    The study of turbidite systems covering a wide range of physical scales has led to confus ion regarding the use of certain key terms and hence a breakdown in communication between workers involved in turbidite research. There are three fundamentally different scales and types of observations derived from the study of outcrop data (ancient systems), high-resolution seismic reflection and side scan sonar data (modern systems), and multichannel seismic reflection data (modern and older buried systems). Despite the variability of scale the same terms are used to describe features that may have little in common. Consequently, turbidite system terminology has become imprecise and even misleading in some cases, thus providing impediments to developing useful predictive models for processes, depositional environments, and lateral and vertical distribution of sand bodies within turbidite systems. To address this concern, we review the principal elements critical to deepwater systems: slump scars, submarine canyons, channels, channel fill deposits, overbank deposits, and lobes and discuss some of their recognition criteria with each different type of data base. Local and regional tectonic setting, relative sea level variations, and bottom current activity are probably the main factors that control size, external geometry, internal stratal configuration, and facies characteristics of both modern and ancient turbidite systems. These factors ultimately control the timing and bounding characteristics between stages of growth of deepwater systems. If comparison of elements from different turbidite deposits using various data types is carried out at similar physical and temporal scales, predictive models eventually may be improved.

  5. Recurrent uranium relocations in distal turbidites emplaced in pelagic conditions

    Science.gov (United States)

    Colley, S.; Thomson, J.

    1985-11-01

    The sediments of the Madeira Abyssal Plain, east of Great Meteor Seamount, are dominated by distal turbidite deposition. While the turbidites exhibit a wide compositional range (25-80% CaCO 3), individual examples can be correlated over a wide area and are relatively homogenous. Organic C oxidation, by bottom water oxygen, proceeds from the turbidite tops downwards after emplacement in pelagic conditions, and the progress of this oxidation front is marked by a sharp colour contrast in the sediments ( WILSONet al., 1985). In turbidites with C org ≫ 0.5%, redistribution of authigenic U occurs to form a concentration peak (4-9 ppm U), just below the oxidation front or colour change. Several tens μg U/cm 2 may be mobilised, and in all examples studied ≫60% of the remobilised U is relocated into the peak. Following burial by subsequent turbidites, such U concentration peaks are persistent as relict indicators of their extinct oxidation fronts for at least 2 × 10 5 years. In the case of thin turbidites where labile C org is almost exhausted, the U peaks may be located in underlying sedimentary units because of their relationship to the oxidation front. A redox mechanism for U peak formation is suggested from these data rather than a complexation with organic matter.

  6. Seismic Shaking, Tsunami Wave Erosion And Generation of Seismo-Turbidites in the Ionian Sea

    Science.gov (United States)

    Polonia, Alina; Nelson, Hans; Romano, Stefania; Vaiani, Stefano Claudio; Colizza, Ester; Gasparotto, Giorgio; Gasperini, Luca

    2016-04-01

    support a scenario of synchronous deposition of the HAT in an area as wide as 150.000 km2, which suggests basin-scale sediment remobilization processes. The HAT in our cores is made up of a base to top sequence of stacked and graded sand/silt units with different compositions related to the Malta, Calabria and Sicilian margin locations. This composition suggests multiple synchronous slope failures typical of seismo-turbidites; however, the Crete earthquake source is too distant from the Italian margins to cause sediment failures by earthquake shaking. Consequently, because our present evidence suggests shallow-water sediment sources, we reinforce previous interpretations that the HAT is a deep-sea "tsunamite" deposit. Utilizing the expanded stratigraphy of the HAT, together with the heterogeneity of the sediment sources of the Ionian margins, we are trying to unravel the relative contribution of seismic shaking (sediment failures, MTDs, turbidity currents) and of tsunami wave processes (overwash surges, backwash flows, turbidity currents) for seismo-turbidite generation.

  7. Comprehensive constraint on the tectono-sedimentary setting of Late Paleozoic turbidites of the Kamuste area,eastern Junggar, Xinjiang

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Petrography and geochemistry, combined with sedimentation analyses allow for a thorough evaluation of the tectono-sedimentary setting of late Paleozoic turbidites of the Kamuste area eastern Junggar. Sandstones of the Alabiye1) Formation are composed mostly of volcanic and sedimentary detritus with lesser amounts of plagioclase and quartz. They were derived from an undissected magmatic-arc provenance. The geochemistry of sandstone-mudrock suites indicates a fesic-intermediate igneous provenance, and constrains the Alabiye Formation to have derived from a differentiated oceanic-continental margin island-arc tectonic setting. Likewise, geochemistry and sandstone petrography of the Kamuste Formation reflect a mixed provenance signature dominated by magmatic arc, basement uplift, and subduction-complex sources of a differentiated continental-island arc. Sedimentation analysis indicates that the Alabiye and Kamuste formations are two sets of turbidite sequences deposited on a submarine slope and a submarine fan and basin plain respectively. In conclusion, submarine slope turbidite deposition of the Alabiye Formation records the main sedimentary response to the development of early Devonian back-arc basins of the northern Junggar tectonic belt. Submarine fan and basin plain turbidite and background hemipelagic deposition of the Kamuste Formation record the main sedimentary response to the late Early Carboniferous development of an inter-arc relict ocean basin of the eastern Junggar composite terrane.

  8. Turbidite Megabeds in an Oceanic Rift Valley Recording Jökulhlaups of Late Pleistocene Glacial Lakes of the Western United States.

    Science.gov (United States)

    Zuffa; Normark; Serra; Brunner

    2000-05-01

    Escanaba Trough is the southernmost segment of the Gorda Ridge and is filled by sandy turbidites locally exceeding 500 m in thickness. New results from Ocean Drilling Program (ODP) Sites 1037 and 1038 that include accelerator mass spectrometry (AMS) 14C dates and revised petrographic evaluation of the sediment provenance, combined with high-resolution seismic-reflection profiles, provide a lithostratigraphic framework for the turbidite deposits. Three fining-upward units of sandy turbidites from the upper 365 m at ODP Site 1037 can be correlated with sediment recovered at ODP Site 1038 and Deep Sea Drilling Program (DSDP) Site 35. Six AMS 14C ages in the upper 317 m of the sequence at Site 1037 indicate that average deposition rates exceeded 10 m/k.yr. between 32 and 11 ka, with nearly instantaneous deposition of one approximately 60-m interval of sand. Petrography of the sand beds is consistent with a Columbia River source for the entire sedimentary sequence in Escanaba Trough. High-resolution acoustic stratigraphy shows that the turbidites in the upper 60 m at Site 1037 provide a characteristic sequence of key reflectors that occurs across the floor of the entire Escanaba Trough. Recent mapping of turbidite systems in the northeast Pacific Ocean suggests that the turbidity currents reached the Escanaba Trough along an 1100-km-long pathway from the Columbia River to the west flank of the Gorda Ridge. The age of the upper fining-upward unit of sandy turbidites appears to correspond to the latest Wisconsinan outburst of glacial Lake Missoula. Many of the outbursts, or jökulhlaups, from the glacial lakes probably continued flowing as hyperpycnally generated turbidity currents on entering the sea at the mouth of the Columbia River.

  9. Archean deep-water depositional system: interbedded and banded iron formation and clastic turbidites in the Barberton Greenstone Belt, South Africa

    Science.gov (United States)

    Zentner, Danielle; Lowe, Donald

    2013-04-01

    The 3.23 billion year old sediments in the Barberton greenstone belt, South Africa include some of the world's oldest known deep-water deposits. Unique to this locality are turbidites interbedded with banded iron formation (BIF) and banded ferruginous chert (BFC). This unusual association may provide clues for reconstructing Archean deep-water depositional settings. For our study we examined freshly drilled core in addition to measuring ~500 m of outcrop exposures along road cuts. The stacking pattern follows an overall BIF to BFC to amalgamated turbidite succession, although isolated turbidites do occur throughout the sequence. The turbidites are predominately massive, and capped with thin, normally graded tops that include mud rip-ups, chert plates, and ripples. The lack of internal stratification and the amalgamated character suggests emplacement by surging high-density turbidity currents. Large scours and channels are absent and bedding is tabular: the flows were collapsing with little turbulence reaching the bed. In contrast, field evidence indicates the BIF and BFC most likely precipitated directly out of the water column. Preliminary interpretations indicate the deposits may be related to a pro-deltaic setting. (1) Deltaic systems can generate long-lived, high volume turbidity currents. (2) The contacts between the BIF, BFC, and turbidite successions are gradual and inter-fingered, possibly representing lateral facies relationships similar to modern pro-delta environments. (3) Putative fan delta facies, including amalgamated sandstone and conglomerate, exist stratigraphically updip of the basinal sediments.

  10. The thick-bedded tail of turbidite thickness distribution as a proxy for flow confinement: Examples from tertiary basins of central and northern Apennines (Italy)

    Science.gov (United States)

    Marini, Mattia; Felletti, Fabrizio; Milli, Salvatore; Patacci, Marco

    2016-07-01

    This study reviews the thickness statistics of non-channelized turbidites from four tertiary basins of Central-Northern Apennines (Italy), where bed geometry and sedimentary character have been previously assessed. Though very different in terms of size and, arguably, character of feeder system, these basins share a common stratigraphic evolution consisting in transition from an early ponded to a late unconfined setting of deposition. Based on comparison of thickness subsets from diverse locations and stratigraphic heights within the studied turbidite fills, this paper seeks to answer the following questions: i) how data collection procedures and field operational constraints (e.g. measure location, outcrop quality, use of thicknesses data from single vs. multiple correlative sections, stratigraphic thickness of the study interval) can affect statistics of sample data? ii) how depositional controls of confined vs. unconfined turbidite basins can result in different thickness-frequency distributions?; and iii) is there in thickness statistics a 'flow confinement' signature which can be used to distinguish between confined and unconfined turbidites? Results suggest that: i) best practices of data collection are crucial to a meaningful interpretation of sample data statistics, especially in presence of stratigraphic and spatial trends of turbidite bed thickness; ii) a systematic bias against cm-thick Tcd Bouma sequence turbidites exists in sample data, which can result in the low-end tail of empirical thickness-frequency distributions to depart significantly from the actual distribution of turbidite thickness; and iii) thickness statistics of beds starting with a basal Ta/Tb Bouma division bear a coherent relationship to the transition from ponded to unconfined depositional settings, consisting in reduction of variance and mean and, consequently, parameters, or even type, of best fit model distribution. This research highlights the role of flow stripping, sediment by

  11. Were the 2.1-Gyr fossil colonial organisms discovered in the Francevillian basin (Palaeoproterozoic, Gabon) buried by turbidites?

    Science.gov (United States)

    Parize, Olivier; Feybesse, Jean-Louis; Guillocheau, François; Mulder, Thierry

    2013-02-01

    The Francevillian series (Gabon) in which the Earth's oldest large colonial organisms were recently discovered (El Albani et al., 2010) were deposited 2 Gyr ago. These series are usually interpreted as a fining-upward basin-fill sequence composed by five superimposed lithological terms noted FA to FE. New studies initiated by AREVA, allowed new data to be collected on the southwestern edge of the Francevillian basin, particularly on newly excavated outcrops. Facies interpretations show that the Poubara sandstones and associated shales and black shales (upper part of FB,FB2a), correspond to turbidites deposited on an upper slope rather than one a shelf, submitted to tidal currents or storm wave action. These new interpretations based on facies association, sedimentary geometries, and basin evolution show that the depositional environment could be a turbidite lobe set at a palaeobathymetry deeper than 200 m.

  12. Intrabasinal and extrabasinal turbidites: Origin and distinctive characteristics

    Science.gov (United States)

    Zavala, Carlos; Arcuri, Mariano

    2016-05-01

    The discovery of turbidites represents perhaps the major genuine advance of sedimentology during the twentieth century. Turbidites are the deposits of turbidity currents and were originally related to the gravitational instability and re-sedimentation of previously accumulated shallow water sediments into deep waters. As these flows originate and entirely evolve within a marine or lacustrine basin, their associated deposits are here termed intrabasinal turbidites. Controversially, increasing evidences support that turbidity currents can also be originated by the direct discharge of sediment-water mixtures by rivers in flood (hyperpycnal flows). Since these flows are originated in the continent, their associated deposits are here termed extrabasinal turbidites. Deposits related to these two different turbidity currents are often confused in the literature although they display diagnostic features that allow a clear differentiation between them. Intrabasinal turbidites are mostly related to surge-like (unsteady) flows that initiate from a cohesive debris flow that accelerates along the slope and evolves into a granular and finally a turbulent flow. Its flow behavior results on the accumulation of normally graded beds and bedsets that lacks terrestrial phytodetritus and lofting rhythmites. Extrabasinal turbidites, on the contrary, are deposits related to fully turbulent flows having interstitial freshwater and sustained by a relatively dense and long-lived river discharge. According to the grain size of suspended materials, hyperpycnal flows can be muddy or sandy. Sandy hyperpycnal flows (with or without associated bedload) often accumulate sandy to gravelly composite beds in prodelta to inner basin areas. Their typical deposits show sharp to gradual internal facies changes and recurrence, with abundant plant remains. In marine waters, the density reversal induced by freshwater results in the accumulation of lofting rhythmites at flow margin areas. Muddy hyperpycnal

  13. Experimental studies of supercritical bedforms applied to coarse-grained turbidite deposits of the Tabernas Basin (SE Spain, late Miocene)

    Science.gov (United States)

    Cartigny, Matthieu; Postma, George; Kleverlaan, Kick

    2014-05-01

    Modern submarine canyon floors are often covered with bedform patterns linked to supercritical turbidity currents, while recognition of sedimentary structures associated with such bedforms in outcrops are rare. On the basis of experimental work on bed morphodynamics and flow structure of high-density turbidity currents, a 3-dimensional bedform stability diagram and related sedimentary facies diagram have been constructed. To allow scaling of this diagram to natural flows, four non-dimensional parameters are used: 1) densimetric Froude number, 2) modified mobility parameter, 3) dimensionless grain size and 4) basal sediment concentration. Each bedform and basal sediment concentration is then linked to a characteristic facies type. Numerical and theoretical models from the literature and observations from modern turbidite depositional systems are used to estimate characteristic sizes of the bedforms for different flow types. The model is applied to the turbidite fan systems of the Tabernas Basin (SE Spain, late Miocene) and discussed along existing classical models of high density turbidity current deposits. It is concluded that the vertical sequence of supercritical bedforms have been described in these models, yet to date have never been recognized as bedforms in outcrop, presumably because of their large size that easily exceeds the dimensions of commonly available outcrop. On the basis both experimental work and outcrop studies in the Tabernas Basin (SE Spain) a conceptual three-dimensional bedform diagram for recognition of cyclic steps in outcrop is constructed. Experimental data indicates that depositional processes on the stoss-side of a cyclic step are controlled by hydraulic jump, which temporarily stalls the flow and by subsequent waxing of the flow up to supercritical again. The hydraulic jump produces large scours with soft sediment deformation (flames) preserved in Bouma Ta, while near horizontal, massive to stratified top-cut-out turbidite beds are

  14. A Comparison of Disturbance Events in Cascadia Lakes to Marine Seismogenic Turbidites

    Science.gov (United States)

    Morey, A. E.; Goldfinger, C.; Briles, C.; Gavin, D. G.; Colombaroli, D.; Kusler, J.

    2012-12-01

    Lacustrine sedimentary sequences have been successfully used to develop earthquake chronologies and seismic hazard assessments in a variety of settings, however most of these lakes are large (> 10 km2), deep, and in close proximity to an active fault. The recent discovery of disturbance in small (0.04 - 1.20 km2) southern Cascadia inland lakes with similar characteristics and timing as compared to marine seismogenic turbidites prompted us to investigate the nature of these deposits and compare to the marine record. For this study we investigated lacustrine records from four lakes: Sanger and Bolan Lakes (both predominantly spring-fed, cirque lakes) and Upper Squaw Lake (a stream-fed, landslide-dammed lake), are from the Klamath Mountains of northern California and southern Oregon 24-100 km from the coast. Triangle Lake (a stream-fed, landslide dammed lake), is from the central Oregon Coast Range 43 km from the coast. Lacustrine disturbance event characteristics differ as a result of the type and availability of sediment, size of lake, drainage area, terrain near the lake shore, location of core with respect to lake bathymetry, and distance from the coast. The disturbance events are typically coarser-grained, fining-upward deposits higher in mineral content as compared to background sedimentation. Physical property (magnetic susceptibility, gamma and CT density) and particle size data through these disturbance events show similarities to contemporaneous deposits in the marine turbidite record, except where the concentration of organic matter attenuates the signal. Even with these differences in composition between lake and marine settings, these disturbance events can be correlated spatially using deposit and sequence characteristics, and associated radiocarbon ages. Geochemical analyses through one disturbance event (dated at 1520(1280-1830) BP) from the Upper Squaw Lake core revealed evidence of a manganese oxide profile which suggests instantaneous deposition

  15. Hydrocarbon Accumulation in Lacustrine Turbidite in the Rift Basin, Bohai Bay

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Three types of turbidites are identified in the studied area, including proximal turbidite along the northern steep slope (alluvial fans, fan delta, and subaqueous fans via short-distance transportation), distal turbidites along the southern gentle slope (stacked sliding of delta and fan delta front), and fluxoturbidite in the central depression. Detailed studies of several case histories and the relationship between sedimentary facies and faults suggest a significant role of tectonic setting and faults in the development of turbidite, which created source areas, effected slope topography, controlled the climate and paleo-environment, and formed enough slope angle and slope break for sedimentary instabilities and massive block movement to form turbidite. According to statistics, 0-86%, with an average value of 40.3%, of the trap volumes in the 69 identified Tertiary lacustrine turbidites in the Jiyang Superdepression in the Bohai Bay Basin are filled with oil. The porosity and permeability of turbidite sands vary widely. The productive reservoirs are generally those from the braided channels of both distal and proximal turbidite, and from the main channel of proximal turbidite, with a low carbonate content and the porosity and permeability higher than 12% and 1 mD respectively. Most of the lithologic oil pools in the Jiyang Superdepression are enveloped by the effective source rocks, and the percentage of the trap volume generally increases with the hydrocarbon expulsion intensity of source rocks. This is in contrast with structural-lithologic traps (i.e. proximal turbidite along the steep slope and distal turbidite along the gentle slope), in which, graben-boundary faults play an important role in oil migration, as the turbidites are not in direct contact with effective hydrocarbon source rocks.

  16. Marine and Lacustrine Turbidite Records: Testing Linkages and Estimating Ground Motions, Central Cascadia Margin, USA

    Science.gov (United States)

    Hausmann, R. B.; Goldfinger, C.; Black, B.; Collins, T.; Romsos, C. G.; Medeiros, L.; Mutschler, M.; Galer, S.; Raymond, R.; Morey, A. E.

    2015-12-01

    We are investigating a potential paleoseismic record at Bull Run Lake, 165 km inland and 280 km landward of the tip of the plate boundary thrust, at the latitude of Portland, Oregon, central Cascadia margin. Bull Run is a landslide dammed lake in a cirque basin on the western flanks of Mt. Hood. Bull Run is potentially a good paleoseismic site, with no major stream inputs and a small catchment basin. The watershed and lake are faulted, and may contain ashes and evidence of crustal faulting. The lake was investigated by Raymond (1983), who cored the lake and found an orderly stratigraphic sequence with a number of minerogenic disturbance events (turbidites) and the Mazama Ash. The bulk ages of several of the disturbance events dated in Raymond's cores overlap well-known Cascadia earthquakes, including the AD 1700 event and several prior earthquakes, suggesting potential for this site. We collected full coverage high-resolution multibeam and backscatter data, along with a high resolution grid of CHIRP sub-bottom profiles, and seven new sediment gravity cores. We find that the turbidite record in the lake is well imaged in the high-resolution chirp data, and is found throughout the lake, including at least one basin isolated from the main basin. The continuity of the turbidite record shows little or no relationship to the minor stream inlets, suggesting the disturbance beds are not likely to be storm related. Many faint laminae may contain a storm record. Subtle channels from north and south sides of the lake feed an axial channel that terminates at the eastern shore. Lake sidewall failures are evident on the north and south walls, and occur with and without imageable tabular blocky slide debris where sedimented slopes exceed ~ 22-25 deg. Smaller failures visible in backscatter data are found on slopes as low as 12 degrees. We conducted diver investigations of several of the landslide areas, collecting hand push core samples and in-situ vane shear torquemeter

  17. New sedimentary-core records and a recent co-seismic turbidite help to unravel the paleoseismicity of the Hikurangi Subduction Zone, New Zealand

    Science.gov (United States)

    Barnes, Philip; Orpin, Alan; Howarth, Jamie; Patton, Jason; Lamarche, Geoffroy; Woelz, Susanne; Hopkins, Jenni; Gerring, Peter; Mitchell, John; Quinn, Will; McKeown, Monique; Ganguly, Aratrika; Banks, Simon; Davidson, Sam

    2017-04-01

    The Hikurangi margin straddles the convergent boundary between the Pacific and Australia tectonic plates and is New Zealand's potentially largest earthquake and tsunami hazard. The 3000 m-deep Hikurangi Trough, off eastern Marlborough, Wairarapa, Hawkes Bay, and East Cape, marks the location where the Pacific plate is subducting beneath the eastern continental margin of the North Island and northeastern South Island. To date the Hikurangi margin has a short historical record relative to the recurrence of great earthquakes and tsunami, and consequently the associated hazard remains poorly constrained. In October 2016 a new, international, 5-year project commenced to evaluate the pre-historic earthquake history of the margin. In November 2016 a RV Tangaroa voyage acquired 50 sediment cores up to 5.5 m long from sites on the continental margin between the Kaikoura coast and Poverty Bay. Core sites were selected using available 30 kHz multibeam bathymetry and backscatter data, sub-bottom acoustic profiles, archived sediment samples, and results from numerical modelling of turbidity currents. Sites fell into three general categories: turbidite distributary systems; small isolated slope-basins; and Hikurangi Channel, levees, and trough. Typical of the margin, the terrigenous-dominated sequence included layers of gravel, sand, mud, and volcanic ash. Many of these layers are turbidites, some of which may have been triggered by strong shaking associated with earthquakes (subduction megathrust and other coastal faults). Some cores contain up to 25 individual turbidites. This library of turbidites may provide the basis of new paleoseismic records that span several hundred kilometres of strike along the plate boundary. During the voyage the 14th November 2016 (NZDT) Mw 7.8 Kaikoura Earthquake occurred, causing strong ground shaking beneath the Kaikoura Canyon region. Sampling with a multicorer within five days of the earthquake, we recovered what appeared to be a very recently

  18. Enhanced Seismic Imaging of Turbidite Deposits in Chicontepec Basin, Mexico

    Science.gov (United States)

    Chavez-Perez, S.; Vargas-Meleza, L.

    2007-05-01

    We test, as postprocessing tools, a combination of migration deconvolution and geometric attributes to attack the complex problems of reflector resolution and detection in migrated seismic volumes. Migration deconvolution has been empirically shown to be an effective approach for enhancing the illumination of migrated images, which are blurred versions of the subsurface reflectivity distribution, by decreasing imaging artifacts, improving spatial resolution, and alleviating acquisition footprint problems. We utilize migration deconvolution as a means to improve the quality and resolution of 3D prestack time migrated results from Chicontepec basin, Mexico, a very relevant portion of the producing onshore sector of Pemex, the Mexican petroleum company. Seismic data covers the Agua Fria, Coapechaca, and Tajin fields. It exhibits acquisition footprint problems, migration artifacts and a severe lack of resolution in the target area, where turbidite deposits need to be characterized between major erosional surfaces. Vertical resolution is about 35 m and the main hydrocarbon plays are turbidite beds no more than 60 m thick. We also employ geometric attributes (e.g., coherent energy and curvature), computed after migration deconvolution, to detect and map out depositional features, and help design development wells in the area. Results of this workflow show imaging enhancement and allow us to identify meandering channels and individual sand bodies, previously undistinguishable in the original seismic migrated images.

  19. Pre-lithification structures, deformation mechanisms, and fabric ellipsoids in slumped turbidites from the Pigeon Point Formation, California

    Science.gov (United States)

    Paterson, Scott R.; Tobisch, Othmar T.

    1993-06-01

    Paterson, S.R. and Tobisch, O.T. 1993. Pre-lithification structures, deformation mechanisms, and fabric ellipsoids in slumped turbidites from the Pigeon Point Formation, California. Tectonophysics, 222: 135-149. Quantitative fabric, structural, and microstructural analyses of pre-lithification folds, foliations, and lineations formed by slumping of turbidite sequences in the Cretaceous Pigeon Point Formation, California, provide a useful comparison with strain and microstructures developed in lithified and tectonically deformed turbidites. Our results indicate the following: (1) multiple generations of folds, cleavages, and lineations can develop prior to any post-lithification tectonic deformation (2) individual grains in sandstones have variable axial ratios, but the ratios and orientations of large populations of grains define fabric ellipsoids with small axial ratios ( ave. = 1.25:1.13:1) (3) phyllosilicate grains define moderate flattening fabrics (reflecting 20-40% shortening or volume loss), with the intensity of alignment partly controlled by the percent of quartz and feldspar grains (4) the fabric ellipsoids in sand-rich layers largely reflect deposition and slumping: pre- and post-slump compactions did not occur, in sand-rich units but did align clay particles in mud-siltstone units, and (5) intra-grain microstructures in quartz and feldspar (e.g., undulose extinction, subgrains) are inherited or recycled features rather than representing effects of post-lithification strains. Our data also suggest that prelithification slumping occurred by pervasive grain rotation and grain boundary sliding in saturated sands with some local movement of material along bedding horizons. A likely model for the folding and associated fabrics is that buckling and fold-hinge flattening drove fluid expulsion, which in turn caused local grain-scale realignment, transposition of bedding, and the development of an axial planar cleavage in the hinge zones. Continued fluid flow was

  20. Depositional Patterns and Oil/Gas Accumulation Features of Sha-3 Member Turbidites in Dongying Depression, Bohai Bay Basin

    Institute of Scientific and Technical Information of China (English)

    BaiGuoping; ZhangShanwen

    2004-01-01

    Recent exploration results indicate that a significant exploration potential remains in the Dongying Depression of the Bohai Bay Basin and the undiscovered oil and gas are largely reservoired in subtle traps including turbidite litholigeal traps of the Sha-3 Member. In order to effectively guide the exploration program targeting turbidites, this study will focus on the depositional models of the Sha-3 Member turbidites and oil/gas accumulation characteristics in these turbidites. Two corresponding relationships were found. One is that the East African Rift Valley provides a modem analog for the depositionai systems in the Dongying Depression. The other is that the depositional models of line-sourced slope aprons, single point-source submarine fan and multiple source romp turbidite, established for deep.sea turbidites, can be applied to interpret the depositional features of the turbidite fans of three differant origins: slope turbidite aprons, lake floor turbidite fans and delia-fed turbidite fans in the Sha-3 Member. Updip sealing integrity is the key factor determining whether oil/gas accumulates or not in the slope aprons and lake floor fans. The factors controlling oil/gas migration and accumulation in the delta-ted turbidite fans are not very clear. Multiple factors rather than a single factor probably played significant roles in these processes.

  1. Deepwater turbidite system analysis : From outcrops studies to basin scale depositional elements. Key learnings for reservoir occurence and characterisation.

    Science.gov (United States)

    Navarre, J.-C.; Dattilo, P.; Crumeyrolle, P.

    2012-04-01

    Decisions on exploration and production in the deepwater domain rely mostly on seismic data (2D or 3D) with limited amount of well geological data. This limited information has to be supplemented by models derived from analogues at different scales, in order to derisk the reservoir presence and infer the reservoir architecture within a larger stratigraphic framework from shelf to deep basin. The fundamental outcrop analysis carried in the 70's and the 80's contributed to identify and characterize the main deep water depositional elements. Outcrop observations are the best way to appraise the architectural and faciological complexity of the subsurface depositional systems within their stratigraphic framework. The lessons learned in the Earth surface provide the key to the subsurface data understanding: core analysis, well-logs correlations and detailed 3D seismic interpretations. Subsurface data is in turn bringing key insights on large scale depositional system; 3D geometry and sediment nature of the depositional elements and processes. Research derived from 3D seismic subsurface data interpretations with tentative continuity between shelf to basin improved the understanding of shelf to deep basin sediment transfer mechanisms. In particular, it has been accompanied by a renewal of interest in the processes associated with hyperpycnal flows in the various deepwater settings. Outcrop and Subsurface integration appears as a powerful tool to characterize and predict reservoir occurence. A seismic based approach on the recognition of depositional elements defined at different scales honoring the stratigraphical architecture of turbidites deposits is systematically applied in our evaluations at a similar scale than the elementary depositional sequences recognized by Mutti (1994). Despite common depositional processes, a large diversity of systems and geobodies will be illustrated from regional scale to reservoir scale from a worldwide portfolio of assets in turbidite

  2. Upslope deposition of extremely distal turbidites: an example from the Tiburon Rise, west-central Atlantic

    Science.gov (United States)

    Dolan, J.; Beck, C.; Ogawa, Y.

    1989-01-01

    These terrigenous silt and sand turbidities represent an unprecedented example of upslope turbidite deposition in an extremely distral setting. Flow thickness was the dominant control on deposition of these beds, rather than true upslope flow. -from Authors

  3. Great earthquakes along the Western United States continental margin: implications for hazards, stratigraphy and turbidite lithology

    Directory of Open Access Journals (Sweden)

    C. H. Nelson

    2012-11-01

    Full Text Available We summarize the importance of great earthquakes (Mw ≳ 8 for hazards, stratigraphy of basin floors, and turbidite lithology along the active tectonic continental margins of the Cascadia subduction zone and the northern San Andreas Transform Fault by utilizing studies of swath bathymetry visual core descriptions, grain size analysis, X-ray radiographs and physical properties. Recurrence times of Holocene turbidites as proxies for earthquakes on the Cascadia and northern California margins are analyzed using two methods: (1 radiometric dating (14C method, and (2 relative dating, using hemipelagic sediment thickness and sedimentation rates (H method. The H method provides (1 the best estimate of minimum recurrence times, which are the most important for seismic hazards risk analysis, and (2 the most complete dataset of recurrence times, which shows a normal distribution pattern for paleoseismic turbidite frequencies. We observe that, on these tectonically active continental margins, during the sea-level highstand of Holocene time, triggering of turbidity currents is controlled dominantly by earthquakes, and paleoseismic turbidites have an average recurrence time of ~550 yr in northern Cascadia Basin and ~200 yr along northern California margin. The minimum recurrence times for great earthquakes are approximately 300 yr for the Cascadia subduction zone and 130 yr for the northern San Andreas Fault, which indicates both fault systems are in (Cascadia or very close (San Andreas to the early window for another great earthquake.

    On active tectonic margins with great earthquakes, the volumes of mass transport deposits (MTDs are limited on basin floors along the margins. The maximum run-out distances of MTD sheets across abyssal-basin floors along active margins are an order of magnitude less (~100 km than on passive margins (~1000 km. The great earthquakes along the Cascadia and northern California margins

  4. Sub-decadal turbidite frequency during the early Holocene: Eel Fan, offshore northern California

    Science.gov (United States)

    Paull, Charles K.; McGann, Mary L.; Sumner, Esther J; Barnes, Philip M; Lundsten, Eve M; Anderson, Krystle; Gwiazda, Roberto; Edwards, Brian D.; Caress, David W

    2014-01-01

    Remotely operated and autonomous underwater vehicle technologies were used to image and sample exceptional deep sea outcrops where an ∼100-m-thick section of turbidite beds is exposed on the headwalls of two giant submarine scours on Eel submarine fan, offshore northern California (USA). These outcrops provide a rare opportunity to connect young deep-sea turbidites with their feeder system. 14C measurements reveal that from 12.8 ka to 7.9 ka, one turbidite was being emplaced on average every 7 yr. This emplacement rate is two to three orders of magnitude higher than observed for turbidites elsewhere along the Pacific margin of North America. The turbidites contain abundant wood and shallow-dwelling foraminifera, demonstrating an efficient connection between the Eel River source and the Eel Fan sink. Turbidite recurrence intervals diminish fivefold to ∼36 yr from 7.9 ka onward, reflecting sea-level rise and re-routing of Eel River sediments.

  5. Ice-sheet sourced juxtaposed turbidite systems in Labrador Sea

    Science.gov (United States)

    Hesse, R.; Klaucke, I.; Ryan, William B. F.; Piper, D.J.W.

    1997-01-01

    Ice-sheet sourced Pleistocene turbidite systems of the Labrador Sea are different from non-glacially influenced systems in their facies distribution and depositional processes. Two large-scale sediment dispersal systems are juxtaposed, one mud-dominated and associated with the Northwest Atlantic Mid-Ocean Channel (NAMOC), the other sand-dominated and forming a huge submarine braided sandplain. Co-existence of the two systems reflects grain-size separation of the coarse and fine fractions on an enormous scale, caused by sediment winnowing at the entrance points of meltwater from the Laurentide Ice Sheet (LIS) to the sea (Hudson Strait, fiords) and involves a complex interplay of depositional and redepositional processes. The mud-rich NAMOC system is multisourced and represents a basinwide converging system of tributary canyons and channels. It focusses its sand load to the central trunk channel in basin centre, in the fashion of a "reverse" deep-sea fan. The sand plain received its sediment from the Hudson Strait by turbidity currents that were generated either by failure of glacial prodelta slopes at the ice margin, or by direct meltwater discharges with high bedload concentration. We speculate that the latter might have been related to subglacial-lake outburst flooding through the Hudson Strait, possibly associated with ice-rafting (Heinrich) events.

  6. Deep-water turbidites as Holocene earthquake proxies: the Cascadia subduction zone and Northern San Andreas Fault systems

    Directory of Open Access Journals (Sweden)

    J. E. Johnson

    2003-06-01

    Full Text Available New stratigraphic evidence from the Cascadia margin demonstrates that 13 earthquakes ruptured the margin from Vancouver Island to at least the California border following the catastrophic eruption of Mount Mazama. These 13 events have occurred with an average repeat time of ?? 600 years since the first post-Mazama event ?? 7500 years ago. The youngest event ?? 300 years ago probably coincides with widespread evidence of coastal subsidence and tsunami inundation in buried marshes along the Cascadia coast. We can extend the Holocene record to at least 9850 years, during which 18 events correlate along the same region. The pattern of repeat times is consistent with the pattern observed at most (but not all localities onshore, strengthening the contention that both were produced by plate-wide earthquakes. We also observe that the sequence of Holocene events in Cascadia may contain a repeating pattern, a tantalizing look at what may be the long-term behavior of a major fault system. Over the last ?? 7500 years, the pattern appears to have repeated at least three times, with the most recent A.D. 1700 event being the third of three events following a long interval of 845 years between events T4 and T5. This long interval is one that is also recognized in many of the coastal records, and may serve as an anchor point between the offshore and onshore records. Similar stratigraphic records are found in two piston cores and one box core from Noyo Channel, adjacent to the Northern San Andreas Fault, which show a cyclic record of turbidite beds, with thirty- one turbidite beds above a Holocene/.Pleistocene faunal «datum». Thus far, we have determined ages for 20 events including the uppermost 5 events from these cores. The uppermost event returns a «modern» age, which we interpret is likely the 1906 San Andreas earthquake. The penultimate event returns an intercept age of A.D. 1664 (2 ?? range 1505- 1822. The third event and fourth event

  7. Block faulted turbidites: an Upper Jurassic-Lower Cretaceous subtle play-potential in the Central Graben

    Energy Technology Data Exchange (ETDEWEB)

    Gregersen, U.; Rasmussen, E.S.

    1998-10-01

    The Gertrud Graben, in the Danish Central Graben, was formed during Early Volgain by extensional block rotation, bounded by a series of NW-SE trending normal faults. The post-rift topography, formed after the Early Volgian rift pulse, controlled the depocenteres of Volgian-Ryazanian turbidites. The turbidites are interbedded in the Farsund Formation. Seismic correlation to basin marginal turbidite sand in the Jeppe-1 and Gwen-2 wells suggest, that high amplitude horizons and high acoustic impedance values in the depocenter of the turbidites probably reflect accumulation of sand-rich turbidites. The high amplitude and impedance values, calculated from seismic inversion, are locally concentrated in minor closures. A short flat impedance horizon within the turbidite depocenter and below a closure possible indicates hydrocarbon accumulation, adjacent to a well-known Jurassic source-rock (the `Hot Unit`) in the Central Graben area. The turbidites seem to have been transported mainly from the north, possibly from the Mandal High or Piggvar Terrace areas. Subsequent Late Ryazanian block faulting and local compressional tectonics caused erosional truncation of upper parts of the turbidites on footwall blocks, but preserved parts of the basin axial turbidites from erosion in the hanging wall positions. (au) 23 fig., 22 refs.

  8. Sedimentology of seismo-turbidites off the Cascadia and northern California active tectonic continental margins, Pacific Ocean

    Science.gov (United States)

    Gutierrez Pastor, Julia; Nelson, Hans; Goldfinger, Chris; Escutia, Carlota

    2013-04-01

    Holocene turbidites from turbidite channel systems along the active tectonic continental margins of the Cascadia subduction zone (offshore Vancouver Island to Mendocino Triple Junction) and the northern San Andreas Transform Fault (the Triple Junction to San Francisco Bay), have been analyzed for sedimentologic features related to their seismic origin. Centimeter thick silt/sand beds (turbidite base) capped by mud layers (turbidite tail) and interbedded with hemipelagic silty clay intervals with high biogenic content have been characterized by visual core descriptions, grain-size analysis, X-ray radiographs and physical properties. Along the northern California margin in upstream single tributary canyons and channels, most turbidites are uni-pulsed (classic fining up) whereas downstream below multiple tributary canyon and channel confluences, most deposits are stacked turbidites. Because each set of stacked turbidites has no hemipelagic sediment between each turbidite unit and each unit has a distinct mineralogy from a different tributary canyon, we interpret that a stacked turbidite is deposited by several coeval turbidity currents fed by multiple tributary canyons and channels with synchronous triggering from a single San Andreas Fault earthquake. The Cascadia margin is characterized by individual multi-pulsed turbidites that contain multiple coarse-grained sub-units without hemipelagic sediment between pulses. Because the number and character of multiple coarse-grained pulses for each correlative multi-pulsed turbidite is almost always constant both upstream and downstream in different channel systems for 600 km along the margin,we interpret that the earthquake shaking or aftershock signature is usually preserved, for the much stronger Cascadia (≥9 Mw) compared to weaker California (≥8Mw) earthquakes, which result in upstream uni-pulsed turbidites and downstream stacked turbidites. Consequently, both the strongest (≥9 Mw) great earthquakes and downstream

  9. Upper Jurassic basin axial turbidites within the Gertrud Graben, Danish Central Graben

    Energy Technology Data Exchange (ETDEWEB)

    Rasmussen, E.S.; Jepsen, A.M.; Maver, K.G.

    1998-10-01

    Fore more than twenty years, the Jurassic succession in the Danish Central Graben has been subject to intense exploration for hydrocarbons. Approximately 43 wildcats have been drilled and most of these tested were structural traps located on footwall crests. The reservoirs encountered were Middle and Upper Jurassic sandstones deposited mainly in near shore depositional environments. Some of these wells penetrated thin turbidites of Late Jurassic to Early Cretaceous age. Within the Gertrud Graben distinct seismic anomalies indicate the presence of basin floor turbidites, which can be correlated to fan fringe turbites encountered in the Jeppe-1, Gwen-2 and Mona-1 wells. Within the Gertrud Graben, seismic anomalies characterized by high amplitude reflections with in an otherwise transparent reflection pattern have been recognized. The zone with high amplitude reflections correlates with thin turbidites with oil shows encountered in the Jeppe-1 well. The turbiditic sandstone succession has a gross thickness of 25 m and a net to gross of 75%, with porosity up to 10%. The presence of oil shows in the thin turbiditic sandstones in the Jeppe-1 well, drilled on a footwall crest, suggests the possibility of thicker sandstones in the basinal areas. The aim of this study is to map the distribution of the seismic anomalies by performing seismic inversion. Seismic inversion is used to derive acoustic impedance as a lithology indicator and to establish a geological model that is a likely prediction of the lithology and architecture of the depositional system. (EG) 2 fig., 17 refs.

  10. Quantitative estimation of lithofacies from seismic data in a tertiary turbidite system in the North Sea

    Energy Technology Data Exchange (ETDEWEB)

    Joerstad, A.K.; Avseth, P.Aa; Mukerji, T.; Mavko, G.; Granli, J.R.

    1998-12-31

    Deep water clastic systems and associated turbidite reservoirs are often characterized by very complex sand distributions and reservoir description based on conventional seismic and well-log stratigraphic analysis may be very uncertain in these depositional environments. There is shown that reservoirs in turbidite systems have been produced very inefficiently in conventional development. More than 70% of the mobile oil is commonly left behind, because of the heterogeneous nature of these reservoirs. In this study there is examined a turbidite system in the North Sea with five available wells and a 3-D seismic near and far offset stack to establish most likely estimates of facies and pore fluid within the cube. 5 figs.

  11. Sediment composition and texture of Pleistocene deep-sea turbidites in the eastern Nankai Trough gas hydrate field

    Science.gov (United States)

    Egawa, K.; Nishimura, O.; Izumi, S.; Ito, T.; Konno, Y.; Yoneda, J.; Jin, Y.; Kida, M.; Suzuki, K.; Nakatsuka, Y.; Nagao, J.

    2013-12-01

    In the 2012 JOGMEC/JAPEX pressure coring operation, we collected a totally 60-m-long core sample from the interval of gas hydrate concentration zone at the planned site of the world's first offshore production test of natural gas hydrates in the eastern Nankai Trough area. In this contribution, the cored sediments were sedimentologically, mineralogically, and paleontologically analyzed to know sediment composition and texture of reservoir formation, which are known to provide useful geological information to discuss sedimentation, diagenesis, and permeability. The targeted interval belongs to a Middle Pleistocene deep-sea turbidite sequence distributed around the Daini Atsumi Knoll, east of the Kumano forearc basin, and consists of the lower (thick sand-dominant), middle (thin-bedded sand-and-mud alteration), and upper (mud-dominant) formations in ascending order. X-ray powder diffraction analysis and scanning electron microscopic observation revealed that pore space in turbidite sands is commonly filled with clay fractions (mostly phyllosilicates) in the lower formation. Such a pore filling of clay fractions is reflected in particle size distribution showing high standard deviation and clay content, and thus is expected to have an impact on permeability. There is the older Pliocene to Early Pleistocene fossil coccolith record in the middle formation, indicating sediment reworking probably induced by submarine landslide. The coexistence of authigenic siderite and framboidal pyrite in the middle formation strongly suggests anoxic microbial activity under methane oxidation and sulfide reduction conditions at least before the hydrate cementation. This contribution was financially supported by the Research Consortium for Methane Hydrate Resources in Japan (MH21 Research Consortium) planned by the Ministry of Economy, Trade and Industry (METI).

  12. Upper Jurassic - Lower Cretaceous turbidite sandstones in the Central Graben, North Sea; with special focus on the Danish Gertrud Graben

    Energy Technology Data Exchange (ETDEWEB)

    Johannessen, P.

    1998-10-01

    Thick Late Jurassic - Early cretaceous turbidite sandstone successions in the Central Graben are uncommon except from the Moray Firth and Viking Graven north of the Central Graben, where several important hydrocarbon producing turbidite sandstone fields are known. The only hydrocarbon producing turbidite reservoir sandstones in the Central Graben is the up to 55 m thick Ribble Sandstone Member located in the British South-west Central Graben, where it is lying above thick shoreface reservoir sandstones of the Fulmar Formation, separated by offshore claystones of the Kimmeridge Clay Formation. The turbidite sandstones of the Ribble Sandstone Member derived from the more proximal thick reservoir sandstones of the Fulmar Formation located near the Mid North Sea High. It has not yet been possible to correlate thick shoreface sandstones of the Norwegian Ula Formation or the Danish Heno Formation to more distal thick turbidite sandstones derived from the shoreface sandstones. (au) 60 fig., 85 refs.

  13. Significance of organic matter in Eocene turbidite sediments (SE Pyrenees, Spain)

    Science.gov (United States)

    Caja, M. A.; Permanyer, A.

    2008-11-01

    Although turbidite deposits are classically considered to be good reservoir rocks for oil and gas, there are no reports concerning their source rock potential in the literature. The sediments from the Vallfogona Formation in the South-Eastern Pyrenees present numerous organic matter-rich levels interbedded in sandstones and coarse turbidite deposits. Two types of organic matter deposits were differentiated on the basis of organic geochemistry and petrography: type A and type B. Type A was deposited in a carbonate marine environment under hypersaline conditions as indicated mainly by even/odd n-alkane predominance, pristane and phytane ratio (Pr/Ph) 1. Type B was deposited in a more mud-rich marine environment evidenced by the predominance of odd n-alkane, Pr/Ph ≥ 1, Ts/Tm diasteranes. Turbidite facies can be regarded as an environment where organic matter sedimentation is heterogeneous in type and amount. This study suggests that turbidite deposits with interbedded organic matter-rich levels may act as a combined source reservoir system.

  14. Sedimentology and paleogeography of an Upper Cretaceous turbidite basin in the South-Central Pyrenees, Spain

    NARCIS (Netherlands)

    Hoorn, van B.

    1970-01-01

    The present study deals with the primary lithology, sedimentary structures, depositional history and paleogeography of an Upper Cretaceous turbidite basin in the south-central Pyrenees, and presents a brief review of the lithology and depositional environment of surrounding contemporaneous deposits.

  15. Flow dynamics at the origin of thin clayey sand lacustrine turbidites: Examples from Lake Hazar, Turkey

    KAUST Repository

    Hage, Sophie

    2017-04-18

    Turbidity currents and their deposits can be investigated using several methods, i.e. direct monitoring, physical and numerical modelling, sediment cores and outcrops. The present study focuses on thin clayey sand turbidites found in Lake Hazar (Turkey) occurring in eleven clusters of closely spaced thin beds. Depositional processes and sources for three of those eleven clusters are studied at three coring sites. Bathymetrical data and seismic reflection profiles are used to understand the specific geomorphology of each site. X-ray, thin sections and CT-scans imagery combined with grain-size, geochemical and mineralogical measurements on the cores allow characterisation of the turbidites. Turbidites included in each cluster were produced by remobilization of surficial slope sediment, a process identified in very few studies worldwide. Three types of turbidites are distinguished and compared with deposits obtained in flume studies published in the literature. Type 1 is made of an ungraded clayey silt layer issued from a cohesive flow. Type 2 is composed of a partially graded clayey sand layer overlain by a mud cap, attributed to a transitional flow. Type 3 corresponds to a graded clayey sand layer overlain by a mud cap issued from a turbulence-dominated flow. While the published experimental studies show that turbulence is damped by cohesion for low clay content, type 3 deposits of this study show evidence for a turbulence dominated mechanism despite their high clay content. This divergence may in part relate to input variables such as water chemistry and clay mineralogy that are not routinely considered in experimental studies. Furthermore, the large sedimentological variety observed in the turbidites from one coring site to another is related to the evolution of a sediment flow within a field scale basin made of a complex physiography that cannot be tackled by flume experiments.

  16. Geometry and petrophysical parameters of a calcarenitic turbidite lobe (Barremian-Aptian, Pas-de-la-Cluse, France)

    Science.gov (United States)

    Savary, Bérengère; Ferry, Serge

    2004-06-01

    Several bioclastic resedimentation systems, late Barremian to early Aptian in age, outcrop in southeastern France. The upslope portion of a calcarenitic turbidite lobe outcrops as a cliff, 2.3 km wide and up to 45 m high, oriented roughly perpendicular to the direction of palaeoflow. It has been studied through 31 sections. The studied body is point-sourced and corresponds to a channel/lobe transition located at the toe-of-slope of a Urgonian carbonate platform on the western edge of the Vocontian Trough (French Subalpine Chains). The internal geometry of the lobe is the result of repeated erosion and filling of channels, creating well-defined stacked units. Filling phases result in lobe-shaped morphology. Units evolve from base to top in an ordered way. First, the sediments exported from the platform and deposited in the basin are represented by decimetre-thick, sheet-like and fine-grained Bouma a-e and ab-e sequences. In this first unit, erosion is limited and represented by shallow and symmetrical channels. This initial phase of deposition corresponds to the formation of a lobe with a positive morphology. The next phase of system development is more erosional and this is dominated by migrating, sinuous channels several metres deep filled with coarse-grained, poorly graded turbidites. These channels are first filled through lateral accretion and then sediment spills over to create a sub-lobe. The mixture of channel and lobe features could be considered as a carbonate equivalent of the channel-levee system of siliciclastic deposits. Finally, the system ends with the deposition of a flat-based unit. This unit extends for more than 2 km and is composed of the southwards lateral accretion of hundreds of metres wide sequences each composed of a debris-flow deposit capped by a coarse-grained calcarenite bed. These sigmoidal bodies could be the ultimate forms of a spreading out phenomenon of the lobe. Overall, the Pas-de-la-Cluse system is a coarsening-upward body. As

  17. Lowstand Turbidites and Delta Systems of the Itararé Group in the Vidal Ramos region (SC, southern Brazil

    Directory of Open Access Journals (Sweden)

    Carla Gimena Puigdomenech

    Full Text Available Turbidites have captioned the attention of sedimentologists during the last decades due their importance as hydrocarbon reservoirs. However, their relationship to delta systems still deserves further studies. This paper presents examples from a late deglacial to early post-glacial deltaic and turbidite strata exposed in the surroundings of Vidal Ramos (Santa Catarina State, Brazil, southern portion of the Paraná Basin. There, the uppermost part of the Mafra Formation and the Rio do Sul Formation onlap the Proterozoic basement and comprises an up to 360 m thick package. It includes (base to top black shales, mass transport deposits (MTD and sandy turbidites (Mafra Formation as well as thin bedded turbidites (tbt, including one interval of black shales and sandy turbidites, overlain by proximal delta front sandstones (Rio do Sul Formation. The analysis of the succession shows two more than 150 m thick coarsening-upwards deltaic successions composed of turbidite sand sheets at their base (prodelta, followed by partially collapsed thin bedded turbidites (delta slope wedge and delta front sandstones. Both turbidite sand-sheets abruptly overlay black shale intervals related to maximum flooding surfaces and therefore record correlative conformities. A detailed stratigraphic section elaborated from the correlation of four logs (1/100 suggests that distal delta front sands includes both thin bedded turbidites and wave reworked sands whereas the proximal delta front was dominated by long-lived underflows (hyperpycnal flows. The succession suggests that the most expressive turbidite beds (base of the delta systems have resulted from relative sea-level falls (early lowstand whereas the thin-bedded turbidites were related to the development of the late lowstand wedge. Black shales represent the transgressive systems tract and HST were not deposited or preserved in the area. High sediment supply associated with lowstand tracts could explain the occasional

  18. Geochemical insights into the provenance of large scale North Atlantic turbidites

    Science.gov (United States)

    Watts, Millie; Hunt, James; Talling, Peter; Allin, Josh; Pope, Ed

    2015-04-01

    The North Atlantic margin has been subject to several very large (>100 km3) submarine landslides. Motion of some of these slides has been shown to generate damaging tsunamis, which travelled long distances across the ocean, such as that generated by the Storegga slide at 8.15 ka BP. If such a tsunami occurred again, it would pose a major hazard to northern European coastlines. Therefore identifying the source and age of past slide deposits is important to quantifying the risk to UK and the rest of coastal Europe. In this study we analyse the distal deposits of slides (turbidites) to assess their provenance. We present initial results from a new shallow piston core dataset from the Storegga slide, Trænadjupet slide, Lofoten Drift and basin, and the outer edge of the Voring plateau. Turbidite mudcaps were analysed using both the non-destructive, semi-quantitative Itrax micro-XRF core scanner at BOSCORF for major elements. In addition ICP-MS was used to determine the rare earth element (REE) abundances, allowing the relationship of distal turbidite deposits to be established. REEs are a good source discriminator due to the stability and immobility of lanthanide group elements, and the preservation of elemental ratios during transport. Due to hydraulic fractionation only the finest mud fraction was analysed to avoid the bias associated with heavy mineral concentrations . Clusters of distinct elemental ratios indicate different provenances for the distal turbidites, notably the Eu/Eu* anomaly and (Gd/Yb)N. The clusters demonstrate each deposit has a unique geochemical signature and provide insights into the history of past large-volume slides in the region and the influence of contour current-reworking of deep-water deposits. The Norwegian margin has a long record of large-scale landslides, which are commonly linked to glacial-interglacial transitions. This margin is also an important location of deep-water formation, with strong currents capable of transporting

  19. Long-term (17 Ma) turbidite record of the timing and frequency of large flank collapses of the Canary Islands

    Science.gov (United States)

    Hunt, J. E.; Talling, P. J.; Clare, M. A.; Jarvis, I.; Wynn, R. B.

    2014-08-01

    turbidites on the Madeira Abyssal Plain provide a record of large-volume volcanic island flank collapses from the Canary Islands. This long-term record spans 17 Ma, and comprises 125 volcaniclastic beds. Determining the timing, provenance and volumes of these turbidites provides key information about the occurrence of mass wasting from the Canary Islands, especially the western islands of Tenerife, La Palma and El Hierro. These turbidite records demonstrate that landslides often coincide with protracted periods of volcanic edifice growth, suggesting that loading of the volcanic edifices may be a key preconditioning factor for landslide triggers. Furthermore, the last large-volume failures from Tenerife coincide with explosive volcanism at the end of eruptive cycles. Many large-volume Canary Island landslides also occurred during periods of warmer and wetter climates associated with sea-level rise and subsequent highstand. However, these turbidites are not serially dependent and any association with climate or sea level change is not statistically significant.

  20. Stratigraphie séquentielle du Carbonifère inférieur du Haut Atlas central et des Jebilet (Maroc): un exemple de bassins à turbidites contrôlées par la tectonique

    Science.gov (United States)

    Izart, Alain; Beauchamp, Jacques; Vachard, Daniel; Tourani, Abdel-Ilah; Essamani, Mohammed

    1997-05-01

    Marine deposits of Visean age are well exposed in the Marrakesh area. Two third order sequences are identified in the central High Atlas and Jebilet: SA, which is of Middle Visean age (CM); SB of Upper Visean age (Cf6αβγ); and a complex with olistoliths of Upper Visean-Lower Namurian age (Cf6δ-Cf7). The SA and SIB sequences consist of a relative low-lying system tract with turbidites, a retrograde transgressive system tract and a prograde high-lying system tract. The relative low level comprises a turbiditic fan fed by tectonic uplift, which does not strictly coincide with eustatic processes. The transgressive system tract retrogrades firstly on the slope during tectonic reactivation with slumps, channels and silty levees, secondly on the shelf edge with a mixture of turbiditic and storm deposits and finally on the shelf with storm deposits and reef building. The high level system tract progrades on the shelf by a delta fan. This model is similar to sequences described in Spain and Italy by Mutti (1992), where tectonism is dominant. Nevertheless, eustasy, as described by Vail et al. (1977) played a part, since the same sequences are found in the chart of Ross and Ross (1987): S1, which of Middle Visean age (Cf5) and S2 which is of Upper Visean age (Cf6αβγ). Only the comparison between regional sequences described in Morocco and the sequences of the European platform allow tectonics and eustasy to be taken into consideration.

  1. Characterization of Turbiditic Oil Reservoirs Based on Geophysical Models of their Formation

    Energy Technology Data Exchange (ETDEWEB)

    Roger Bonnecaze

    2006-01-15

    Models are developed and solved to describe the flow of and deposition from low and high concentration turbidity currents. The shallow water equations are amended to include particle transport to describe the low concentration turbidity currents. The suspension balance model is used to describe the high concentration turbidity currents. Numerical simulations are developed to solve the highly non-linear, free boundary problems associated with these models. Simpler, algebraic scaling relationships are also developed for these models. The models are successfully validated against field observations of turbidites. With these models, one can take seismic information on the shape of the turbiditic deposit and estimate the particle size, which can be used to determine the porosity and permeability.

  2. CATS - A process-based model for turbulent turbidite systems at the reservoir scale

    Science.gov (United States)

    Teles, Vanessa; Chauveau, Benoît; Joseph, Philippe; Weill, Pierre; Maktouf, Fakher

    2016-09-01

    The Cellular Automata for Turbidite systems (CATS) model is intended to simulate the fine architecture and facies distribution of turbidite reservoirs with a multi-event and process-based approach. The main processes of low-density turbulent turbidity flow are modeled: downslope sediment-laden flow, entrainment of ambient water, erosion and deposition of several distinct lithologies. This numerical model, derived from (Salles, 2006; Salles et al., 2007), proposes a new approach based on the Rouse concentration profile to consider the flow capacity to carry the sediment load in suspension. In CATS, the flow distribution on a given topography is modeled with local rules between neighboring cells (cellular automata) based on potential and kinetic energy balance and diffusion concepts. Input parameters are the initial flow parameters and a 3D topography at depositional time. An overview of CATS capabilities in different contexts is presented and discussed.

  3. Continental Growth and Recycling in Convergent Orogens with Large Turbidite Fans on Oceanic Crust

    Directory of Open Access Journals (Sweden)

    Ben D. Goscombe

    2013-07-01

    Full Text Available Convergent plate margins where large turbidite fans with slivers of oceanic basement are accreted to continents represent important sites of continental crustal growth and recycling. Crust accreted in these settings is dominated by an upper layer of recycled crustal and arc detritus (turbidites underlain by a layer of tectonically imbricated upper oceanic crust and/or thinned continental crust. When oceanic crust is converted to lower continental crust it represents a juvenile addition to the continental growth budget. This two-tiered accreted crust is often the same thickness as average continental crustal and is isostatically balanced near sea level. The Paleozoic Lachlan Orogen of eastern Australia is the archetypical example of a tubidite-dominated accretionary orogeny. The Neoproterozoic-Cambrian Damaran Orogen of SW Africa is similar to the Lachlan Orogen except that it was incorporated into Gondwana via a continent-continent collision. The Mesozoic Rangitatan Orogen of New Zealand illustrates the transition of convergent margin from a Lachlan-type to more typical accretionary wedge type orogen. The spatial and temporal variations in deformation, metamorphism, and magmatism across these orogens illustrate how large volumes of turbidite and their relict oceanic basement eventually become stable continental crust. The timing of deformation and metamorphism recorded in these rocks reflects the crustal thickening phase, whereas post-tectonic magmatism constrains the timing of chemical maturation and cratonization. Cratonization of continental crust is fostered because turbidites represent fertile sources for felsic magmatism. Recognition of similar orogens in the Proterozoic and Archean is important for the evaluation of crustal growth models, particularly for those based on detrital zircon age patterns, because crustal growth by accretion of upper oceanic crust or mafic underplating does not readily result in the addition of voluminous zircon

  4. Turbidites as indicators of paleotopography, Upper Miocene Lake Pannon, Western Mecsek Mountains (Hungary)

    OpenAIRE

    Sztanó Orsolya; Sebe Krisztina; Csillag Gábor; Magyar Imre

    2015-01-01

    The floor of Lake Pannon covering the Pannonian Basin in the Late Miocene had considerable relief, including both deep sub-basins, like the Drava Basin, and basement highs, like the Mecsek Mts, in close proximity. The several km thick lacustrine succession in the Drava Basin includes profundal marls, basin-center turbidites, overlain by shales of basin-margin slopes, coarsening-upward deltaic successions and alluvial deposits. Along the margin of the Mecsek Mts locally derived shoreface sands...

  5. Submarine paleoseismology of the northern Hikurangi subduction margin of New Zealand as deduced from Turbidite record since 16 ka

    Science.gov (United States)

    Pouderoux, Hugo; Proust, Jean-Noël; Lamarche, Geoffroy

    2014-01-01

    Paleoseismic studies seek to characterise the signature of pre-historical earthquakes by deriving quantitative information from the geological record such as the source, magnitude and recurrence of moderate to large earthquakes. In this study, we provide a ˜16,000 yr-long paleo-earthquake record of the 200 km-long northern Hikurangi Margin, New Zealand, using cm-thick deep-sea turbidites identified in sediment cores. Cores were collected in strategic locations across the margin within three distinct morphological re-entrants - the Poverty, Ruatoria and Matakaoa re-entrants. The turbidite facies vary from muddy to sandy with evidence for rare hyperpycnites interbedded with hemipelagites and tephra. We use the Oxal probabilistic software to model the age of each turbidite, using the sedimentation rate of hemipelagite deduced from well-dated tephra layers and radiocarbon ages measurements on planktonic foraminifera.

  6. Reservoir evaluation of thin-bedded turbidites and hydrocarbon pore thickness estimation for an accurate quantification of resource

    Science.gov (United States)

    Omoniyi, Bayonle; Stow, Dorrik

    2016-04-01

    One of the major challenges in the assessment of and production from turbidite reservoirs is to take full account of thin and medium-bedded turbidites (succession, they can go unnoticed by conventional analysis and so negatively impact on reserve estimation, particularly in fields producing from prolific thick-bedded turbidite reservoirs. Field development plans often take little note of such thin beds, which are therefore bypassed by mainstream production. In fact, the trapped and bypassed fluids can be vital where maximising field value and optimising production are key business drivers. We have studied in detail, a succession of thin-bedded turbidites associated with thicker-bedded reservoir facies in the North Brae Field, UKCS, using a combination of conventional logs and cores to assess the significance of thin-bedded turbidites in computing hydrocarbon pore thickness (HPT). This quantity, being an indirect measure of thickness, is critical for an accurate estimation of original-oil-in-place (OOIP). By using a combination of conventional and unconventional logging analysis techniques, we obtain three different results for the reservoir intervals studied. These results include estimated net sand thickness, average sand thickness, and their distribution trend within a 3D structural grid. The net sand thickness varies from 205 to 380 ft, and HPT ranges from 21.53 to 39.90 ft. We observe that an integrated approach (neutron-density cross plots conditioned to cores) to HPT quantification reduces the associated uncertainties significantly, resulting in estimation of 96% of actual HPT. Further work will focus on assessing the 3D dynamic connectivity of the low-pay sands with the surrounding thick-bedded turbidite facies.

  7. Techniques used in the exploration of turbidite reservoirs in a frontier setting - Helland Hansen setting, Voering Basin, offshore Mid Norway

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez-Ferrer, F.; James, S.D.; Lak, B.; Evans, A.M.

    1998-12-31

    In the 15th Norwegian licensing round there was awarded operation of the Helland Hansen deep water license. Subsurface interpretation commenced towards the end of 1996, following completion of a 1540 km{sup 2} 3-D seismic survey. The main exploration target comprise Turonian to Coniacian turbidite sands within a large fault-bound dip closure. This presentation describes various techniques applied in the exploration of this new turbidite play, with emphasis on the study of the reservoir potential. A methodology of integrated analysis is presented. Through these efforts, a greater understanding of the lithological and depositional models in this non-calibrated area has progressively been achieved. 5 refs., 11 figs.

  8. Measured sections and discussion of the main turbidite member, Middle Pennsylvanian Minturn Formation, northern Sangre de Cristo Range, Custer and Saguache counties, Colorado

    Science.gov (United States)

    Soulliere, S.J.; DeAngelis, B.L.; Lindsey, D.A.

    1984-01-01

    Turbidites are sediments deposited by turbid density currents. The turbidites described here are interpreted as prodelta deposits that formed in front of fan deltas and alluvial fans during the uplift of the ancestral Rocky Mountains in Pennsylvanian time. Laterally extensive, lenticular sand bodies deposited by turbidity flows crop out in the Middle Pennsylvanian Minturn Formation in the northern Sangre de Crísto Range, Custer and Saguache Counties, Colo. (figs. 1, 2). One of the turbidite-bearing intervals, informally designated the "main turbidite member," lies 90.6 m above the base of the Minturn; it reaches 150 m in thickness and extends more than 13 km along strike. The internal stratigraphy and sedimentary structures of the main turbidite member are described from the measured sections presented here.

  9. The geochemistry of volcanic, plutonic and turbiditic rocks from Sumba, Indonesia

    Science.gov (United States)

    Lytwyn, J.; Rutherford, E.; Burke, K.; Xia, C.

    2001-06-01

    Rocks that reveal the geology of Sumba for times before the Later Miocene (˜16 Ma) are relatively few and are not particularly well exposed. This has led to uncertainty about the nature of the basement rocks of the island and especially about whether Sumba originated as a fragment of Australia, or of that part of southeastern Eurasia which many authors have called Sundaland. A third possibility is that Sumba is underlain by arc material generated on the ocean floor and is not a fragment of either continent. We have studied the geochemistry of volcanic, plutonic and turbiditic rocks collected from Sumba in an attempt to provide additional insight into the island's origin and history between Late Cretaceous (˜86 Ma) and Early Miocene (˜16 Ma) times. Late Cretaceous to Early Oligocene (˜31 Ma) volcanic rocks on Sumba range compositionally from basalts to andesites, and are of typical oceanic island-arc affinity, exhibiting geochemical characteristics similar to those of high-Al basalts and their derivatives. Compositions indicate evolution along both calc-alkaline and tholeiitic trends. Some samples show indications of possible modifications by slab-derived melts and/or related fluids and also of contamination by turbiditic sediments. Gabbros and diorites collected from the Paleocene Tanadaro intrusion are compositionally similar to the associated volcanic rocks and, we consider, represent the plutonic equivalents of high-Al basalt. The geochemistry of Cretaceous turbiditic sedimentary rocks on Sumba indicates close proximity to an intra-oceanic island-arc environment. These results are consistent with the geochemical, sedimentological, stratigraphic, paleontological and paleomagnetic results of other investigators which together indicate that: (1) Late Cretaceous to Early Oligocene volcanic, plutonic and volcaniclastic rocks of Sumba are island-arc- and forearc-related; (2) the arc involved appears to have been what we refer to as the Great Indonesian Volcanic

  10. Late Quaternary climatic events and sea-level changes recorded by turbidite activity, Dakar Canyon, NW Africa

    Science.gov (United States)

    Pierau, Roberto; Hanebuth, Till J. J.; Krastel, Sebastian; Henrich, Rüdiger

    2010-03-01

    The relationship of sea-level changes and short-term climatic changes with turbidite deposition is poorly documented, although the mechanisms of gravity-driven sediment transport in submarine canyons during sea-level changes have been reported from many regions. This study focuses on the activity of the Dakar Canyon off southern Senegal in response to major glacial/interglacial sea-level shifts and variability in the NW-African continental climate. The sedimentary record from the canyon allows us to determine the timing of turbidite events and, on the basis of XRF-scanning element data, we have identified the climate signal at a sub-millennial time scale from the surrounding hemipelagic sediments. Over the late Quaternary the highest frequency in turbidite activity in the Dakar Canyon is confined to major climatic terminations when remobilisation of sediments from the shelf was triggered by the eustatic sea-level rise. However, episodic turbidite events coincide with the timing of Heinrich events in the North Atlantic. During these times continental climate has changed rapidly, with evidence for higher dust supply over NW Africa which has fed turbidity currents. Increased aridity and enhanced wind strength in the southern Saharan-Sahelian zone may have provided a source for this dust.

  11. Building an 18 000-year-long paleo-earthquake record from detailed deep-sea turbidite characterisation in Poverty Bay, New Zealand

    Science.gov (United States)

    Pouderoux, H.; Lamarche, G.; Proust, J.-N.

    2012-06-01

    Two ~20 m-long sedimentary cores collected in two neighbouring mid-slope basins of the Paritu Turbidite System in Poverty Bay, east of New Zealand, show a high concentration of turbidites (5 to 6 turbidites per meter), interlaid with hemipelagites, tephras and a few debrites. Turbidites occur as both stacked and single, and exhibit a range of facies from muddy to sandy turbidites. The age of each turbidite is estimated using the statistical approach developed in the OxCal software from an exceptionally dense set of tephrochronology and radiocarbon ages (~1 age per meter). The age, together with the facies and the petrophysical properties of the sediment (density, magnetic susceptibility and P-wave velocity), allows the correlation of turbidites across the continental slope (1400-2300 m water depth). We identify 73 synchronous turbidites, named basin events, across the two cores between 819 ± 191 and 17 729 ± 701 yr BP. Compositional, foraminiferal and geochemical signatures of the turbidites are used to characterise the source area of the sediment, the origin of the turbidity currents, and their triggering mechanism. Sixty-seven basin events are interpreted as originated from slope failures on the upper continental slope in water depth ranging from 150 to 1200 m. Their earthquake trigger is inferred from the heavily gullied morphology of the source area and the water depth at which slope failures originated. We derive an earthquake mean return time of ~230 yr, with a 90% probability range from 10 to 570 yr. The earthquake chronology indicates cycles of progressive decrease of earthquake return times from ~400 yr to ~150 yr at 0-7 kyr, 8.2-13.5 kyr, 14.7-18 kyr. The two 1.2 kyr-long intervals in between (7-8.2 kyr and 13.5-14.7 kyr) correspond to basin-wide reorganisations with anomalous turbidite deposition (finer deposits and/or non deposition) reflecting the emplacement of two large mass transport deposits much more voluminous than the "classical" earthquake

  12. Immediate propagation of deglacial environmental change to deep-marine turbidite systems along the Chile convergent margin

    Science.gov (United States)

    Bernhardt, Anne; Schwanghart, Wolfgang; Hebbeln, Dierk; Stuut, Jan-Berend W.; Strecker, Manfred R.

    2017-09-01

    Understanding how Earth-surface processes respond to past climatic perturbations is crucial for making informed predictions about future impacts of climate change on sediment fluxes. Sedimentary records provide the archives for inferring these processes, but their interpretation is compromised by our incomplete understanding of how sediment-routing systems respond to millennial-scale climate cycles. We analyzed seven sediment cores recovered from marine turbidite depositional sites along the Chile continental margin. The sites span a pronounced arid-to-humid gradient with variable relief and related sediment connectivity of terrestrial and marine environments. These sites allowed us to study event-related depositional processes in different climatic and geomorphic settings from the Last Glacial Maximum to the present day. The three sites reveal a steep decline of turbidite deposition during deglaciation. High rates of sea-level rise postdate the decline in turbidite deposition. Comparison with paleoclimate proxies documents that the spatio-temporal sedimentary pattern rather mirrors the deglacial humidity decrease and concomitant warming with no resolvable lag times. Our results let us infer that declining deglacial humidity decreased fluvial sediment supply. This signal propagated rapidly through the highly connected systems into the marine sink in north-central Chile. In contrast, in south-central Chile, connectivity between the Andean erosional zone and the fluvial transfer zone probably decreased abruptly by sediment trapping in piedmont lakes related to deglaciation, resulting in a sudden decrease of sediment supply to the ocean. Additionally, reduced moisture supply may have contributed to the rapid decline of turbidite deposition. These different causes result in similar depositional patterns in the marine sinks. We conclude that turbiditic strata may constitute reliable recorders of climate change across a wide range of climatic zones and geomorphic

  13. Three-dimensional modelling of stacked turbidite channels in West Africa: impact on dynamic reservoir simulations

    Energy Technology Data Exchange (ETDEWEB)

    Labourdette, Richard; Poncet, Jerome; Seguin, Julien; Temple, Francois [Total, Geoscience Technologies, Pau, 64 (France); Hegre, JoAnn; Irving, Alan [Total E and P UK plc, Geoscience Research Centre, Aberdeen (United Kingdom)

    2006-07-01

    The examination of production history from hydrocarbon fields composed of turbidite deposits indicates that fluid flow behaviour is often more complex than expected. The cause is commonly linked to the presence of fine-scale sedimentary heterogeneities, which complicate the reservoir. This is especially true in the case of turbiditic submarine channel complexes with final channel-filling stages composed of lateral migration deposits. These fine-scale heterogeneities are usually below seismic resolution and are rarely represented in initial reservoir models designed for such fields. Thus, it is difficult to match the production history or identify methods to improve production and reduce associated risks. The various depositional patterns recognized in channel migration and aggradation packages from the Oligocene Malembo Formation of the Congo Basin, offshore Angola, exhibit different dynamic responses when modelled in a reservoir simulator. These dynamic differences are related to the different preservation rates of bank collapse sediments within isolated channel bodies, hereafter referred to as 'elementary channels'. According to these preservation differences, the vertical stacking pattern of channels results in better connectivity than the true lateral migration. This effect has been incorporated into a full-field simulation model by applying petrophysical upscaling methods. The recognition and modelling of detailed sedimentological heterogeneities, and their distribution along full-field models produces a better history match when the inherent uncertainties have been taken into account. Incorporating all available data and concepts to define reservoir architecture is essential in understanding the impact that fine-scale heterogeneities have on reservoir management. As the lateral extent and areal distribution of heterogeneities is still unknown, our modelling workflow incorporates uncertainty in the form of multiple realizations to identify and

  14. Provenance analysis of the Oligocene turbidites (Andaman Flysch), South Andaman Island: A geochemical approach

    Indian Academy of Sciences (India)

    P C Bandopadhyay; Biswajit Ghosh

    2015-07-01

    The Oligocene-aged sandstone-shale turbidites of the Andaman Flysch are best exposed along the east coast of the South Andaman Island. Previously undocumented sandstone-shale geochemistry, investigated here, provides important geochemical constraints on turbidite provenance. The average 70.75 wt% SiO2, 14.52 wt% Al2O3, 8.2 wt% Fe2O$^{\\text{t}}_{3}$+MgO and average 0.20 Al2O3/SiO2 and 1.08 K2O/Na2O ratios in sandstones, compare with quartzwackes. The shale samples have average 59.63 wt% SiO2, 20.29 wt% Al2O3, 12.63 wt% Fe2O$^{\\text{t}}_{3}$+MgO and average 2.42 K2O/Na2O and 0.34 Al2O3/SiO2 ratios. Geochemical data on CaO–Na2O–K2O diagram fall close to a granite field and on K2O/Na2O–SiO2 diagram within an active continental margin tectonic setting. The range and average values of Rb and Rb/Sr ratios are consistent with acid-intermediate igneous source rocks, while the values and ratios for Cr and Ni are with mafic rocks. Combined geochemical, petrographic and palaeocurrent data indicate a dominantly plutonic-metamorphic provenance with a lesser contribution from sedimentary and volcanic source, which is possibly the Shan–Thai continental block and volcanic arc of the north-eastern and eastern Myanmar. Chemical index of alteration (CIA) values suggests a moderate range of weathering of a moderate relief terrane under warm and humid climate.

  15. Turbidites as indicators of paleotopography, Upper Miocene Lake Pannon, Western Mecsek Mountains (Hungary

    Directory of Open Access Journals (Sweden)

    Sztanó Orsolya

    2015-08-01

    Full Text Available The floor of Lake Pannon covering the Pannonian Basin in the Late Miocene had considerable relief, including both deep sub-basins, like the Drava Basin, and basement highs, like the Mecsek Mts, in close proximity. The several km thick lacustrine succession in the Drava Basin includes profundal marls, basin-center turbidites, overlain by shales of basin-margin slopes, coarsening-upward deltaic successions and alluvial deposits. Along the margin of the Mecsek Mts locally derived shoreface sands and deltaic deposits from further away have been mapped so far on the surface. Recent field studies at the transition between the two areas revealed a succession that does not fit into either of these environments. A series of sandstone a few meters thick occurs above laminated to bioturbated clayey siltstone. The sandstone show normal grading, plane lamination, flat erosional surfaces, soft-sediment deformations (load and water-escape structures and sharp-based beds with small reverse faults and folds. These indicate rapid deposition from turbidity currents and their deformation as slumps on an inclined surface. These beds are far too thick and may reveal much larger volumes of mass wasting than is expected on the 20–30 m high delta slopes; however, regional seismic lines also exclude outcropping of deep-basin turbidites. We suggest that slopes with transitional size (less than 100 m high may have developed on the flank of the Mecsek as a consequence of lake-level rise. Although these slopes were smaller than the usually several hundred meter high clinoforms in the deep basins, they could still provide large enough inertia for gravity flows. This interpretation is supported by the occurrence of sublittoral mollusc assemblages in the vicinity, indicating several tens of meters of water depth. Fossils suggest that sedimentation in this area started about 8 Ma ago.

  16. Variability in form and growth of sediment waves on turbidite channel levees

    Science.gov (United States)

    Normark, W.R.; Piper, D.J.W.; Posamentier, H.; Pirmez, C.; Migeon, S.

    2002-01-01

    Fine-grained sediment waves have been observed in many modern turbidite systems, generally restricted to the overbank depositional element. Sediment waves developed on six submarine fan systems are compared using high-resolution seismic-reflection profiles, sediment core samples (including ODP drilling), multibeam bathymetry, 3D seismic-reflection imaging (including examples of burried features), and direct measurements of turbidity currents that overflow their channels. These submarine fan examples extend over more than three orders of magnitude in physical scale. The presence or absence of sediment waves is not simply a matter of either the size of the turbidite channel-levee systems or the dominant initiation process for the turbidity currents that overflow the channels to form the wave fields. Both sediment-core data and seismic-reflection profiles document the upslope migration of the wave forms, with thicker and coarser beds deposited on the up-current flank of the waves. Some wave fields are orthogonal to channel trend and were initiated by large flows whose direction was controlled by upflow morphology, whereas fields subparallel to channel levees resulted from local spillover. In highly meandering systems, sediment waves may mimic meander planform. Larger sediment waves form on channel-levee systems with thicker overflow of turbidity currents, but available data indicate that sediment waves can be maintaned during conditions of relatively thin overflow. Coarser-grained units in sediment waves are typically laminated and thin-bedded sand as much as several centimetres thick, but sand beds as thick as several tens of centimetres have been documented from both modern and buried systems. Current production of hydrocarbons from sediment-wave deposits suggests that it is important to develop criteria for recognising this overbank element in outcrop exposures and borehole data, where the wavelength of typical waves (several kilometres) generally exceeds outcrop

  17. MORPHOLOGIC VARIATIONS OF THE TRACE FOSSIL RUTICHNUS IN CM-THICK TURBIDITES FROM THE VERGHERETO FORMATION (NORTHERN APENNINES, ITALY

    Directory of Open Access Journals (Sweden)

    PAOLO MONACO

    2011-03-01

    Full Text Available The analysis of 56 specimens of the branched, walled post-depositional trace fossil Rutichnus, sampled from 31 thin-bedded, overbank turbidites from the Verghereto Formation, Romagna Apennines, indicates high morphologic variability of this ichnotaxon in hypichnial preservation. The variability concerns the arrangement of outer and inner walls, number and shape of annulations, distribution of pustules, the (false branching arrangement and the general external shape. Highest variability has been observed mainly in the Rutichnus rutis ichnospecies, clearly less in the R. irregularis ichnospecies that is rare. The Dino-Lite microscope camera analysis of oriented thin sections indicates that endichnial preservation exhibits many structures due to burrowing in soft substrate, destroying  laminae of sand. Consequently Rutichnus probably was produced by a worm or arthropod, inducing strong deformation in turbidite sand during the feeding activity on phytodetritus and organic matter transported by the turbidity flow. 

  18. Small-scale spatial variation in near-surface turbidites around the JFAST site near the Japan Trench

    Science.gov (United States)

    Yoshikawa, Shuro; Kanamatsu, Toshiya; Kasaya, Takafumi

    2016-03-01

    This paper aims to improve our understanding of the depositional processes associated with turbidites related to recent earthquake events. A series of short sediment cores (ca. 20-30 cm long) were recovered from the landward slope of the Japan Trench around JFAST (Japan Trench Fast Drilling Project) site C0019 by a remotely operated vehicle, KAIKO 7000 II, and the sample sites were accurately located using an LBL (long base line) acoustic navigation system. The properties of the cores were analyzed using visual observations, soft X-ray radiographs, smear slides, measurement of anisotropy of magnetic susceptibility, and analysis of radioactive elements (134Cs, 137Cs, and excess 210Pb). For the first time, small-scale (ca. 200-1000 m) spatial variations in recent earthquake-triggered deep-sea turbidites, the formation of which was probably linked to the 2011 Tohoku-oki earthquake, are described. We also examine the submarine landslide that probably generated the sediment unit below the turbidites, which is thought to be an important process in the study area. The spatial distribution and characteristics of the near-surface seismoturbidite obtained immediately after the earthquake, presented here, will enable precise calibration of offshore evidence of recent earthquakes, and thus facilitate the use of the sedimentary archive for paleoseismic interpretations. Furthermore, although sampling for turbidite seismology on steep slopes has not been widely performed previously, our results suggest that the recent event deposits may be continuously tracked from the slope to the basin using a combination of the present sampling method and conventional large-scale investigation techniques.

  19. Comparison of turbidite facies associations in modern passive-margin Mississippi fan with ancient active-margin fans

    Science.gov (United States)

    Shanmugam, G.; Moiola, R. J.; McPherson, J. G.; O'Connell, S.

    1988-07-01

    Our comparison of the modern passive-margin Mississippi fan (DSDP Leg 96) with ancient active-margin fans (e.g. Eocene Hecho Group, Spain) reveals major differences in turbidite facies associations (Mutti and Ricci Lucchi scheme) and in seismic characteristics in the lower fan area. The lower (outer) Mississippi fan is composed of channel (Facies B and F) and non-channel facies (C? and D), whereas ancient fans are characterized by non-channelized, thickening-upward, depositional lobe facies (C and D). An absence of depositional lobes in the lower Mississippi fan is also suggested by a lack of convex-upward (mounded) seismic reflections with bidirectional downlap. Continuous seismic reflections of the lower Mississippi fan may represent "sheet sands", but not those of true depositional lobes with mounded character. Extensive channelization in modern passive-margin fans appears to be a product of the lateral shifting of a major sinuous distributary system, developed as a consequence of low gradients and the transport of sediment with a relatively low sand/mud ratio. In contrast, channels in active-margin fans are short and of low sinuosity as a result of high gradients and the transport of sediment with a relatively high sand/mud ratio. The turbidite facies association scheme, which was developed exclusively from ancient active-margin fans, should be applied to mature passive-margin fans with qualifications because of the differences in spatial distribution of turbidite facies and their associations.

  20. Response of Cenozoic turbidite system to tectonic activity and sea-level change off the Zambezi Delta

    Science.gov (United States)

    Castelino, Jude A.; Reichert, Christian; Jokat, Wilfried

    2017-09-01

    Submarine fans and turbidite systems are important and sensitive features located offshore from river deltas that archive tectonic events, regional climate, sea level variations and erosional process. Very little is known about the sedimentary structure of the 1800 km long and 400 km wide Mozambique Fan, which is fed by the Zambezi and spreads out into the Mozambique Channel. New multichannel seismic profiles in the Mozambique Basin reveal multiple feeder systems of the upper fan that have been active concurrently or consecutively since Late Cretaceous. We identify two buried, ancient turbidite systems off Mozambique in addition to the previously known Zambezi-Channel system and another hypothesized active system. The oldest part of the upper fan, located north of the present-day mouth of the Zambezi, was active from Late Cretaceous to Eocene times. Regional uplift caused an increased sediment flux that continued until Eocene times, allowing the fan to migrate southwards under the influence of bottom currents. Following the mid-Oligocene marine regression, the Beira High Channel-levee complex fed the Mozambique Fan from the southwest until Miocene times, reworking sediments from the shelf and continental slope into the distal abyssal fan. Since the Miocene, sediments have bypassed the shelf and upper fan region through the Zambezi Valley system directly into the Zambezi Channel. The morphology of the turbidite system off Mozambique is strongly linked to onshore tectonic events and the variations in sea level and sediment flux.

  1. Depositional models of sandy debrites and turbidites of Palaeogene reservoir sands in deep-lacustrine environments, South China

    Science.gov (United States)

    Li, Y.; Chen, G.

    2013-12-01

    Two depositional models are proposed for deep-lacustrine petroleum reservior sands (Palaeogene) in the Fushan Sag, Beibuwan Basin, South China. This facies trend is used as a template for predicting the distribution of reservoir facies of the Fushan oilfield. Based on examination of 150m of conventional cores from 13 drilled wells, four depositional facies have been interpreted: (1) fine-grained massive sandstone with floating mudstone clasts and planar clast fabric (sandy debrite); (2) fine-grained sandstone and siltstone showing contorted bedding, sand injection, and ptygmatic folding (sandy slump), (3) fine-grained sandstone with thin layers of normal grading and flute casts (turbidite), and (4) mudstone with faint laminae (suspension fallout). Combined with multiple seismic attributes, two depositional models are characterized by (1) sublacustrine fan: thick turbidite units occur at the bottom of the western sag beneath a series of normal faults slope. (2) Thinner deposition of sandy debrites mainly distribute at the bottom of eastern sag far from sandy slump at the lake margin slope, which interpreted to be controlled by "two-step" flexure slope break. The transfer zone located in the centre area is confirmed to be the primary origin for such differential depositions. In our study area, sandy debrites constitute the producing petroleum reservoirs, but turbidites are non reservoirs. This dramatic understanding will well account for "eastern much more than western" distribution of proven petroleum reserves and be applicable to predicting reservoir distribution.

  2. Differentiating submarine channel-related thin-bedded turbidite facies: Outcrop examples from the Rosario Formation, Mexico

    Science.gov (United States)

    Hansen, Larissa; Callow, Richard; Kane, Ian; Kneller, Ben

    2017-08-01

    Thin-bedded turbidites deposited by sediment gravity flows that spill from submarine channels often contain significant volumes of sand in laterally continuous beds. These can make up over 50% of the channel-belt fill volume, and can thus form commercially important hydrocarbon reservoirs. Thin-bedded turbidites can be deposited in environments that include levees and depositional terraces, which are distinguished on the basis of their external morphology and internal architecture. Levees have a distinctive wedge shaped morphology, thinning away from the channel, and confine both channels (internal levees) and channel-belts (external levees). Terraces are flat-lying features that are elevated above the active channel within a broad channel-belt. Despite the ubiquity of terraces and levees in modern submarine channel systems, the recognition of these environments in outcrop and in the subsurface is challenging. In this outcrop study of the Upper Cretaceous Rosario Formation (Baja California, Mexico), lateral transects based on multiple logged sections of thin-bedded turbidites reveal systematic differences in sandstone layer thicknesses, sandstone proportion, palaeocurrents, sedimentary structures and ichnology between channel-belt and external levee thin-bedded turbidites. Depositional terrace deposits have a larger standard deviation in sandstone layer thicknesses than external levees because they are topographically lower, and experience a wider range of turbidity current sizes overspilling from different parts of the channel-belt. The thickness of sandstone layers within external levees decreases away from the channel-belt while those in depositional terraces are less laterally variable. Depositional terrace environments of the channel-belt are characterized by high bioturbation intensities, and contain distinctive trace fossil assemblages, often dominated by ichnofabrics of the echinoid trace fossil Scolicia. These assemblages contrast with the lower

  3. Paleomagnetic Results On Clastic Turbidite Systems In Compressional Settings: Example From The Eocene Hecho Group (southern Pyrenees, Spain)

    Science.gov (United States)

    Oms, O.; Dinarès-Turell, J.; Remacha, E.

    The Hecho group clastic turbidites were deposited in the southpyrenean foreland basin during the Paleocene and Eocene. These turbidites have provided well-known strati- graphic and facies models, and can be considered as one of the most studied ancient turbidite models of the world. This is because of the quality and preservation of the sedimentary record (basin-wide lateral continuity of rock-bodies, physical correlation linking deep-sea with platform strata, clear interaction with tectonic structures etc.) However, the Hecho group has not been a target for paleomagnetic studies despite the overwhelming sedimentological knowledge (in fact, sediments from such sedimento- logical and tectonic settings have been largely overlooked in the magnetostratigraphic literature). Here we present the results from a 2200 m-thick section mostly located in the Aragón valley north of the Jaca village (Huesca province). Planktic forams and calcareous nannoplankton data place the section in the middle Eocene. The lower and middle part of the section is representative of the pure flysch stage of the basin evo- lution (in the appenninic sense) and is build up by deep clastic depositional systems including carbonate megabreccias. The upper part of the section involves the transi- tion to a molasse stage by the occurrence of channelized turbidites (known as Rapitán system) that further up evolve to prodelta and platform deposits (Larrés slope marls and Sabiñánigo sandstone formations, respectively). The paleomagnetic investigation is based on the study of about 280 samples from 80 sampling sites, including mea- surements of remanence, anisotropy of the magnetic susceptibility (AMS) and rock magnetic experiments. Our data shows that magnetization is carried out mainly by iron sulphides that define a section dominated by reversed polarities although normal polarity zones are found. Considering the biostratigraphic constraints we make a cor- relation to the standard polarity scale

  4. Stratigraphy and reservoir quality of the turbidite deposits, western sag, Bohai bay, China P.R.

    Science.gov (United States)

    Rotimi, Oluwatosin J.; Ako, Bankole D.; Zhenli, Wang

    2014-11-01

    Stratigraphic and subtle reservoirs such as pinchouts, sand lenses and unconformities have been discovered in Bohai basin. These reservoirs occur in sub-basins and sag structures called depressions. A prolific depression is the Liaohe depression that has been filled with rapidly changing mixed alluvial fan deposit of the Cenozoic age. Attempts made at recovering residual hydrocarbon from the subtle reservoir have necessitated the re-evaluation of available data to characterize and model the prolific Shahejie Formation turbidite deposit occurring as pinchouts and sand lenses for hydrocarbon assessment, reservoir quality and possible recovery through enhanced methods. Methods employed covered well logs analysis, clustering analysis for electrofacies and fuzzy logic analysis to predict missing log sections. Stratigraphic and structural analysis was done on SEGY 3D seismic volume after seismic to well tie. Stochastic simulation was done on both discrete and continuous upscaled data. This made it possible to correctly locate and laterally track identified reservoir formation on seismic data. Petrophysical parameters such as porosity and permeability were modeled with result of clustering analysis. Result shows that electrofacies converged on 2 rock classes. The area is characterized by the presence of interbeded sand-shale blanket formations serving as reservoir and seal bodies. The reservoir quality of the formations as seen on the petrophysical analysis done is replicated in simulation volume results. Reservoir rocks have porosity between 0.1 and 0.25, permeability between 1 and 2mD and hydrocarbon saturation as high as 89%. Lithofacies are observed to be laterally inconsistent, sub-parallel to dipping and occurring as porous and permeable continuous beds or pinchouts hosting hydrocarbon. The stochastic stratigraphic model depicts rock units in associations that are synsedimentary. The prevalent configuration gotten from the model gave an insight into exploring and

  5. Hydrodynamic processes, velocity structure and stratification in natural turbidity currents: Results inferred from field data in the Var Turbidite System

    Science.gov (United States)

    Migeon, Sébastien; Mulder, Thierry; Savoye, Bruno; Sage, Françoise

    2012-03-01

    The Var Turbidite System (NW Mediterranean Sea) is fed during the present-day highstand sea level by large earthquake-induced ignitive turbidity currents, low-density turbidity currents resulting from retrogressive failures triggered on the upper continental slope, and hyperpycnal flows related to the Var River floods. Using a large dataset including bathymetric data, side-scan sonar images, seismic-reflection profiles, cores and photographs of the seafloor, this paper attempts to better constrain the hydrodynamic behaviour of debris flows and turbidity currents along the Upper and Middle Valley of the Var Turbidite System. The drastic change of the seafloor morphology between the Upper and the Middle Valley suggests that gravity flows undergo rapid transformation from cohesive to fully turbulent behaviour. This transformation is related to a hydraulic jump caused by an abrupt decrease in slope angle at the transition between the Upper and the Middle Valley and is associated with en masse deposition and elevation of the seafloor. Strong seafloor erosion prevails in the Middle Valley, suggesting that, for a low and constant slope angle, turbulent flows must regain a balance between concentration and flow thickness rapidly after they experience hydraulic jump. The internal stratification and vertical grain-size distribution within turbulent flows are inferred from the distribution of fine- to coarse-grained turbidites found in cores located along the crest of the Var Sedimentary Ridge with a decreasing elevation above the floor of the Middle Valley. The theoretical vertical velocity profile deduced from the vertical grain-size distribution exhibits a general trend and an inflection of the gradient curve different from those of the velocity profiles classically obtained using numerical modelling.

  6. Deformation Rates From Climate Cycles in Marine Synorogenic Turbidites, Jaca Basin, Spanish Pyrenees

    Science.gov (United States)

    Anastasio, D. J.; Kodama, K. P.; Pares, J. M.; Hinnov, L. A.

    2007-12-01

    variability and ecology in intermountain watersheds. Lithologic parameters sensitive to sea level, such as bed thickness and grain size variations in the turbidite section record strong obliquity and eccentricity modulation, whereas, the ARM derived magnetite concentrations record terrestrial watershed sensitive processes such as aridity and windiness operating at precessional time scales.

  7. Heavy mineral sorting and distributions within massive sandstone divisions (Bouma A divisions) of Brushy Canyon Formation turbidites

    Science.gov (United States)

    Motanated, K.; Tice, M. M.

    2009-12-01

    KANNIPA MOTANATED and MICHAEL M. TICE Department of Geology and Geophysics, Texas A&M University, College Station, TX 77843-3115, USA Sediment sorting data are commonly used for interpreting depositional environments, analyzing mechanisms of deposition and transportation, and inferring relative transport distance of sediments. Typically, sorting in sandstones is estimated by point-counting thin sections which is a time consuming procedure and requires cutting sections of rock samples. We demonstrate a new technique for quantifying sediment sorting using element distribution maps obtained by x-ray fluorescence microscopy. We show that hydraulic sorting of Zr- and Ti- bearing grains (probably zircon and rutile, respectively) results in characteristic vertical profiles of Zr and Ti abundances within the Bouma A divisions of turbidites of the Brushy Canyon Formation, Delaware Basin, southern New Mexico. Zr- and Ti- bearing grains decrease in abundance and diameter from bases to tops of A divisions in every sample examined in this study. These results contrast with previous observations which suggest that grading in Brushy Canyon Formation structureless sandstones is absent or rare. The data support turbiditic interpretations of these rocks against traction current interpretations which rely on the lack of textural grading. Grading is reflected in vertical profiles of Ti/Al, Zr/Al and Zr/Ti ratios, which each decrease upward. These compositional variations could potentially be used as geochemical proxies for physical sorting, and might be useful for inferring depositional processes and relative transport distances.

  8. Deep-Sea Turbidites as Guides to Holocene Earthquake History at the Cascadia Subduction Zone—Alternative Views for a Seismic-Hazard Workshop

    Science.gov (United States)

    Atwater, Brian F.; Griggs, Gary B.

    2012-01-01

    This report reviews the geological basis for some recent estimates of earthquake hazards in the Cascadia region between southern British Columbia and northern California. The largest earthquakes to which the region is prone are in the range of magnitude 8-9. The source of these great earthquakes is the fault down which the oceanic Juan de Fuca Plate is being subducted or thrust beneath the North American Plate. Geologic evidence for their occurrence includes sedimentary deposits that have been observed in cores from deep-sea channels and fans. Earthquakes can initiate subaqueous slumps or slides that generate turbidity currents and which produce the sedimentary deposits known as turbidites. The hazard estimates reviewed in this report are derived mainly from deep-sea turbidites that have been interpreted as proxy records of great Cascadia earthquakes. The estimates were first published in 2008. Most of the evidence for them is contained in a monograph now in press. We have reviewed a small part of this evidence, chiefly from Cascadia Channel and its tributaries, all of which head offshore the Pacific coast of Washington State. According to the recent estimates, the Cascadia plate boundary ruptured along its full length in 19 or 20 earthquakes of magnitude 9 in the past 10,000 years; its northern third broke during these giant earthquakes only, and southern segments produced at least 20 additional, lesser earthquakes of Holocene age. The turbidite case for full-length ruptures depends on stratigraphic evidence for simultaneous shaking at the heads of multiple submarine canyons. The simultaneity has been inferred primarily from turbidite counts above a stratigraphic datum, sandy beds likened to strong-motion records, and radiocarbon ages adjusted for turbidity-current erosion. In alternatives proposed here, this turbidite evidence for simultaneous shaking is less sensitive to earthquake size and frequency than previously thought. Turbidites far below a channel

  9. Connectivity estimation between turbiditic channels and overbank deposits from the modelling of an outcrop analogue (Pab Formation, Maastrichitan, Pakistan).

    Science.gov (United States)

    Eschard, R.; Deschamps, R.; Doligez, B.; Lerat, O.

    2012-04-01

    Conceptual models showing the sedimentary architecture of the turbidite depositional systems and their evolution trough time, such as those published by E. Mutti and his school, were first established in the outcrop. At the reservoir scale, the field development of turbidite reservoirs now requires detailed reservoir models finely describing the distribution of the heterogeneity which may influence the reservoir dynamic behaviour during production. Information derived from quantified outcrop models can then be used to better constrain the reservoir models in the subsurface. Outcrops models first focused on the heterogeneity distribution within the channel conduits, emphasizing the diversity of the channel architecture regarding to the complexity of the depositional processes. The facies architecture of turbiditic overbank deposits laterally to the channels are even less understood than within the channels. If the general geometry of levees can be easily seen on seismic, their facies, and the sand/shale ratio close to the channel border, are poorly known as overflow deposits are rarely drilled in the subsurface, and crevasse lobes are below seismic resolution. The conceptual models of the overbank distribution at the reservoir scale must then rely on outcrops models. The questions on which we would like to focus are the followings: 1) What kind of facies model can we expect in the overbank deposits laterally to the channel conduits? 2) Do these facies constitute reservoir bodies with a significant volume? 3) Is there any heterogeneity between the channel conduits and the levees which may reduce their connectivity 4) Can overbank deposits, such as crevasses or spill over lobes, insure connectivity between two channel conduits and homogenise the pressure regime during the reservoir production? The relationship between channels and overbank are well exposed in the Pab mountain range outcrops, in Pakistan. In this paper, we propose to characterize the relationships

  10. Provenance of a large Lower Cretaceous turbidite submarine fan complex on the active Laurasian margin: Central Pontides, northern Turkey

    Science.gov (United States)

    Akdoğan, Remziye; Okay, Aral I.; Sunal, Gürsel; Tari, Gabor; Meinhold, Guido; Kylander-Clark, Andrew R. C.

    2017-02-01

    The Pontides formed the southern active margin of Laurasia during the Mesozoic. They became separated from mainland Laurasia during the Late Cretaceous, with the opening of the Black Sea as an oceanic back-arc basin. During the Early Cretaceous, a large submarine turbidite fan complex developed in the Central Pontides. The turbidites cover an area of 400 km by 90 km with a thickness of more than 2 km. We have investigated the provenance of these turbidites-the Çağlayan Formation-using paleocurrent measurements, U-Pb detrital zircon ages, REE abundances of dated zircons and geochemistry of detrital rutile grains. 1924 paleocurrent measurements from 96 outcrop stations indicate flow direction from northwest to southeast in the eastern part of the Çağlayan Basin and from north-northeast to west-southwest in the western part. 1194 detrital zircon ages from 13 Lower Cretaceous sandstone samples show different patterns in the eastern, central and western parts of the basin. The majority of the U-Pb detrital zircon ages in the eastern part of the basin are Archean and Paleoproterozoic (61% of all zircon ages, 337 grains); rocks of these ages are absent in the Pontides and present in the Ukrainian Shield, which indicates a source north of the Black Sea. In the western part of the basin the majority of the zircons are Carboniferous and Neoproterozoic (68%, 246 grains) implying more local sources within the Pontides. The detrital zircons from the central part show an age spectrum as mixture of zircons from western and eastern parts. Significantly, Jurassic and Early Cretaceous zircons make up less than 2% of the total zircon population, which implies lack of a coeval magmatic arc in the region. This is compatible with the absence of the Lower Cretaceous granites in the Pontides. Thus, although the Çağlayan Basin occupied a fore-arc position above the subduction zone, the arc was missing, probably due to flat subduction, and the basin was largely fed from the Ukrainian

  11. Origin of a thick, redeposited carbonate bed in Eocene turbidites of the Hecho Group, south-central Pyrenees, Spain

    Science.gov (United States)

    Johns, D. R.; Mutti, E.; Rosell, J.; Séguret, M.

    1981-04-01

    Large-scale carbonate beds interbedded in basin-plain turbidites of the Eocene Hecho Group, northern Spain, are interpreted as giant turbidity-current deposits because of their internal organization and lateral extent. One such bed, the Roncal Unit, has been traced down the axis of the basin for 75 km and commonly reaches thicknesses in excess of 100 m. Internally, the Roncal Unit displays an overall upward decrease in grain size, from a basal megabreccia with large slabs of carbonate platform debris to a calcareous mudstone. The Roncal Unit was probably deposited from a highly mobile and competent sediment gravity flow generated by an earthquake shock, which led to the catastrophic collapse and subsequent transport of the upper part of a carbonate platform flanking the basin. *Present addresses: (Johns) Koninklijke/Shell Exploratie en Produktie Laboratorium, Rijswijk, Netherlands; (Mutti) Istituto di Geologia, Universitá di Ferrara, Ferrara, Italy

  12. 3D stratigraphic modeling of the Congo turbidite system since 210 ka: an investigation of factors controlling sedimentation

    Science.gov (United States)

    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

  13. Seismic architecture and lithofacies of turbidites in Lake Mead (Arizona and Nevada, U.S.A.), an analogue for topographically complex basins

    Science.gov (United States)

    Twichell, D.C.; Cross, V.A.; Hanson, A.D.; Buck, B.J.; Zybala, J.G.; Rudin, M.J.

    2005-01-01

    Turbidites, which have accumulated in Lake Mead since completion of the Hoover Dam in 1935, have been mapped using high-resolution seismic and coring techniques. This lake is an exceptional natural laboratory for studying fine-grained turbidite systems in complex topographic settings. The lake comprises four relatively broad basins separated by narrow canyons, and turbidity currents run the full length of the lake. The mean grain size of turbidites is mostly coarse silt, and the sand content decreases from 11-30% in beds in the easternmost basin nearest the source to 3-14% in the central basins to 1-2% in the most distal basin. Regionally, the seismic amplitude mimics the core results and decreases away from the source. The facies and morphology of the sediment surface varies between basins and suggests a regional progression from higher-energy and possibly channelized flows in the easternmost basin to unchannelized flows in the central two basins to unchannelized flows that are ponded by the Hoover Dam in the westernmost basin. At the local scale, turbidites are nearly flat-lying in the central two basins, but here the morphology of the basin walls strongly affects the distribution of facies. One of the two basins is relatively narrow, and in sinuous sections reflection amplitude increases toward the outsides of meanders. Where a narrow canyon debouches into a broad basin, reflection amplitude decreases radially away from the canyon mouth and forms a fan-like deposit. The fine-grained nature of the turbidites in the most distal basin and the fact that reflections drape the underlying pre-impoundment surface suggest ponding here. The progression from ponding in the most distal basin to possibly channelized flows in the most proximal basin shows in plan view a progression similar to the stratigraphic progression documented in several minibasins in the Gulf of Mexico. Copyright ?? 2005, SEPM (Society for Sedimentary Geology).

  14. The classical turbidite outcrop at San Clemente, California revisited: An example of sandy submarine channels with asymmetric facies architecture

    Science.gov (United States)

    Li, Pan; Kneller, Benjamin C.; Hansen, Larissa; Kane, Ian A.

    2016-12-01

    A 1.1-1.2 km long, 3-15 m thick exposure of the late Miocene to Pliocene Capistrano Formation crops out at San Clemente, California, providing a superb example of submarine channel elements with an asymmetric cross-sectional facies distribution. Coarser-grained, thicker bedded and more amalgamated channel axial deposits are partitioned towards one side of channel elements (200-400 m wide), whilst finer-grained and thinner bedded channel margin deposits are partitioned towards the other side. Two end-member types of silty channel-base and intra-channel drapes are recognized, namely, bypass drapes and deposition drapes. There are both draping silty turbidites that show either strong (bypass drapes) or insignificant (deposition drapes) evidence of erosion and/or sediment bypass during deposition. Bypass drapes and deposition drapes are interpreted to result from flow bypass and flow stratification, respectively, and have significantly different implications for reservoir connectivity and down-dip sediment transport. Channel elements are nested to form two channel complexes. Channel complex 1 comprises four channel elements and shows a vertical aggradation dominated stacking pattern, whilst channel complex 2 comprises five channel elements and shows a mixed lateral migration/vertical aggradation stacking pattern. This study also suggests that these exposures represent only a fragment of a larger channel complex set that might bear varying degrees of resemblance to its formative geomorphic channel(s) on the paleo-seafloor. The reinterpretation of this classic outcrop provides valuable insight into other turbidite channel systems at outcrop and in the subsurface, both in a sedimentological and applied context.

  15. Rapid and frequent turbidite accumulation in the bottom of Izu-Ogasawara Trench: Chemical and radiochemical evidence

    Science.gov (United States)

    Nozaki, Yoshiyuki; Ohta, Yoichi

    1993-12-01

    Two sediment cores (pilot gravity and piston) were obtained from the bottom of the Izu-Ogasawara Trench at 9750 m and analyzed for various elements and radioisotopes. The results showed a history of complex and frequent turbidite deposition: In the gravity core, eight layers rich in manganese were observed, of which five are enriched in Cu and Co as well. The other three are also enriched in Mo but no other heavy metals, suggesting the presence of at least two mechanisms of formation. Trapping of iron manganese micronodules can account for the enrichment of Mn, Cu and Co. The other three layers rich in Mn and Mo appear to be formed by a post-depositional diagenetic process of Mn mobilization and redeposition in the sediment column. A strong correlation between Ra-226 and Cu in the gravity core suggests that the Ra-226 was also carried into the bottom of the trench in turbidites in association with Mn micronodules. Little excess of Pb-210 over Ra-226 was found at the top but the excess was significant at mid-depths from 30 to 70 cm, indicating that those sediments were deposited within the last 200 y. In the piston core there is a sharp discontinuity of chemical and radiochemical composition around a depth of 250 cm. Below that depth the sediments appear to be dominated by materials derived from terrestrial sources, as compared with those in the upper layer which are of contemporary marine origin. Ra-226 is deficient relative to Th-230 throughout the sediment column down to about 6 m. This finding is consistent with the finding that the average rate of sediment accumulation is 1-2 orders of magnitude faster than that in the western North Pacific abyssal plain, suggesting the convergence of materials into the bottom of the trench.

  16. Soft-sediment deformations (convolute lamination and load structures) in turbidites as indicators of flow reflections against bounding slopes

    Science.gov (United States)

    Tinterri, Roberto; Muzzi Magalhaes, Pierre; Tagliaferri, Alessio; Cunha, Rogerio S.; Laporta, Michele

    2015-04-01

    Soft-sediment deformations, such as convolute laminations, load structures and water escapes are very rapid deformations that occur in unconsolidated sediments near the depositional surface during or shortly after deposition and before significant diagenesis. These types of deformations develop when primary stratifications are deformed by a system of driving forces, while the sediment is temporarily in a weakened state due to the action of a deformation mechanism know as liquidization. This deformation occurs if the applied stress exceeds the sediment strength, either through an increase in the applied stress or through a temporary reduction in sediment strength. Liquidization mechanisms can be triggered by several agents, such as seismic shaking, rapid sedimentation with high-fallout rates or cyclic-pressure variations associated with storm waves or breaking waves. Consequently, soft-sediment deformations can be produced by different processes and form ubiquitous sedimentary structures characterizing many sedimentary environments. However, even though these types of structures are relatively well-known in terms of geometry and sedimentary characteristics, many doubts arise when the understanding of deformation and trigger mechanisms is attempted. As stressed also by the recent literature, the main problem lies in the fact that the existing approaches for the identification of triggering agents rely on criteria that are not diagnostic or not applicable to outcrop-based studies, because they are not always based on detailed facies analysis related to a paleoenvironmental-context approach. For this reason, this work discusses the significance of particular types of soft-sediment deformations that are very common in turbidite deposits, namely convolute laminations and load structures, especially on the basis of a deep knowledge of the stratigraphic framework and geological setting in which these structures are inserted. More precisely, detailed facies analyses of the

  17. Paleocene Turbidite Deposition in the Central American Seaway (NW Costa Rica): Geochemical Analysis and Provenance of Detrital Spinel and Clinopyroxene

    Science.gov (United States)

    Giblin, A. C.

    2015-12-01

    The Central American Land Bridge is the crucial connection between North and South America, and the Miocene closure of the Panama seaway led to a change in global oceanic circulation patterns. Modern Costa Rica is part of the island arc that formed over the western Caribbean subduction zone, and the Santa Elena peninsula is on the northwest coast of Costa Rica next to the Sandino forearc basin. This study focuses on the origin and provenance of the Paleocene deep-water Rivas and Descartes turbidites that crop out on the northern part of the Santa Elena peninsula in northwestern Costa Rica. Understanding the sedimentary fill of the Sandino Basin that contributed to the closing of the seaway may lead to a better understanding of the Late Cretaceous-Paleogene arcs. Provenance studies of the Santa Elena Peninsula turbidite sandstone bodies constrain the history of the paleogeography and tectonics of the region. Petrographic analyses of rock thin sections constrain source areas; geochemical analysis of individual detrital heavy minerals from rock samples give indications of sediment sources and tectonic setting during deposition. This study is a provenance analysis based on (i) semi-quantitative energy-dispersive spectrometry analysis of heavy minerals, (ii) quantitative wavelength-dispersive spectrometry for major elements of detrital clinopyroxene and spinel grains, (iii) trace element analysis through laser ablation of single detrital clinopyroxene grains, and (iv) comparative analysis of the different potential source rocks to clearly identify the most likely sediment sources. The detrital spinel and clinopyroxene are possibly sourced from: mantle ophiolites, mid-ocean ridge gabbros, or volcanic arc tholeiitic basalts or calc-alkaline andesites. Spinel and clinopyroxne geochemistry suggests a possible peridotitic source, linked to mantle rocks that are now covered by Tertiary volcanics or have completely eroded. The character of the crustal minerals indicates

  18. Determining flow directions in turbidites: An integrated sedimentological and magnetic fabric study of the Miocene Marnoso Arenacea Formation (northern Apennines, Italy)

    Science.gov (United States)

    Felletti, Fabrizio; Dall'Olio, Eleonora; Muttoni, Giovanni

    2016-04-01

    Depositional models of turbidity flows require estimating paleocurrent directions using sedimentological indicators such as flute and ripple marks, but these are not always present in outcrop sections or drill cores. In this study, we apply the anisotropy of magnetic susceptibility (AMS) as an alternative tool to estimate paleocurrent directions in a case-study turbiditic system: the Marnoso Arenacea foredeep turbidites of Miocene age exposed in the northern Apennines of Italy. Different depositional facies have been sampled for AMS and additional rock-magnetic analyses. We observed a good agreement between paleocurrent directions from flute casts at the base of turbidite beds and mean directions of maximum magnetic susceptibility axes in organized facies such as massive and laminated sandstones, even if a relatively small but apparently consistent offset of ~ 15-20° seems to be present. Highly dispersed AMS fabrics were instead observed in disordered facies such as convoluted and undulated sandstones as well as debrites. This strong correlation between hydrodynamic regimes of depositional facies and AMS data represents a novel contribution and confirms the validity of the AMS method to estimate flow directions in the absence of sedimentological indicators. Finally, paleomagnetic analyses from the literature were used to reconstruct the paleogeography of the Marnoso Arenacea basin and make inferences about the origin and direction of transport of the sediments at the basin scale.

  19. When Organic-Rich Turbidites Reach 5000 m: "Cold-Seep Like" Life in the Congo Deep-Sea Fan

    Science.gov (United States)

    Pastor, L.; Toffin, L.; Cathalot, C.; Olu, K.; Brandily, C.; Bessette, S.; Lesongeur, F.; Godfroy, A.; Khripounoff, A.; Decker, C.; Taillefert, M.; Rabouille, C.

    2016-12-01

    The Congo canyon, located on the west coast of Africa, is a unique example of a canyon directly connected to a major river (The Congo River). Turbidites are responsible for a large input of terrestrial organic matter at depths up to 5000 m. These high inputs led to global high organic matter mineralization rates, with very localized hot spots that were visually observed and specifically sampled with a ROV. These hot spots, featuring substantial concentration of reduced compounds, mainly methane and sulfides, were recognizable in surface by the presence of reduced sediment patches, bacterial mats, and/or vesicomyid bivalves that host bacterial endosymbionts able to process H2S. In this paper we present geochemical sediment profiles of sulfate, methane, sulfide and dissolved iron together with phylogenetic diversity of 16S rRNA communities. This will give a first understanding of biogeochemical processes occurring in this peculiar ecosystem, mainly sulfate reduction, methanogenesis and subsequent anaerobic oxidation of methane with bacterial and archaeal assemblages similar to cold seeps environments. Iron also seems to play a major role in this system and iron/sulfur interactions as a sink for H2S can probably compete with H2S consumption by chemosynthetic bivalves, estimated at one site by vesicomyds gills incubations in a sulfide-rich solution.

  20. Crime scene investigation involving a large turbidite - a 1h-teaching unit in Limnogeology/Sedimentology

    Science.gov (United States)

    Gilli, Adrian; Kremer, Katrina

    2017-04-01

    In 1996, a dead corpse (named „Brienzi") was found at the banks of the picturesque Lake Brienz in the Bernese Alps/Switzerland. What is the origin of this corpse and which chain of events lead to this crime scene? This is the starting position for a 1h exercise/game for undergraduate students in Earth Sciences/Geosciences.The students are provided with a wealth of evidences like statements from people potentially involved in the case, age data on the human corpse and monitoring data from the lake and its surroundings. The students are guided through the game step by step. After solving a task, the students get a feedback and can check if they were correct with their interpretation. Interestingly for earth science students, a lacustrine mass moment plays an important role in these investigations, but more should not be given at this point. In this exercise, we can also check if the teached content of the previous lessons have been acquired correctly by the students, as it deals with diverse limnogeological and sedimentological aspects. The game is strongly based on a study of Girardclos et al. (2007) and uses their argumentation for the occurrence of a large mass movement in Lake Brienz in 1996. A copy of the game is available by the author upon request. Reference: Girardclos, S., Schmidt, O.T., Sturm, M., Ariztegui, D., Pugin, A. and Anselmetti, F.S., 2007, The 1996 AD delta collapse and large turbidite in Lake Brienz. Marine Geology, 241, pp.137-154. doi:10.1016/j.margeo.2007.03.011

  1. Drone photogrammetry for geological research: field digital stratigraphic logs for turbiditic reservoir analog studies in Calabria, Southern Italy.

    Science.gov (United States)

    Guillois, Maxime; Brocheray, Sandra; Paron, Paolo

    2017-04-01

    Drone technology combined with new algorithms like Structure from Motion (SfM) has revived and expanded the uses of photogrammetry bringing new flexibility and the capacity to carry on close range photogrammetry to inaccessible areas. This characteristics are particularly appealing in field geology offering the option to reconstruct continuous digital outcrop models of vertical or difficult to reach outcrops. In this light we present the results of a digital outcrop modelling of a Miocene turbiditic system (mainly sandstone) in Calabria (Southern Italy) generated through field data collected by means of a light-weight commercial drone, a detailed geological field survey and cloud point photogrammetric analyses comparing different software for this purpose (Agisoft Photoscan, Drone deploy, Arc3D). The geological model has been used as an input for preliminary reservoir modelling. We generated digital geological sections (stratigraphic logs) of 1,200 m of sections using expert digital image and terrain model interprepation from the DTM generated with drone data, with the goal to reconstruct the real thickness of each layer. We then compared the results with previously created detailed field geological cross sections. The comparison between drone-derived sections and field-survey sections shows a global accuracy of the thickness ranging between 1% to 10%. Although this new methodology still has to be validated in other morpho-lithological context it already demonstrating its usefulness for preliminary geological outcrop investigation and modelling in remote areas. We also compared the different softwares used and we made recommendations for future deployment. This research has been made possible thanks to a collaboration between UNESCO-IHE, The Netherlands, and UniLaSalle Beauvais, France.

  2. Tectonic control on turbiditic sedimentation: The Late Cretaceous-Eocene successions in the Sinop-Boyabat Basin of north-central Turkey

    Energy Technology Data Exchange (ETDEWEB)

    Janbu, Nils Erik

    2004-07-01

    The aim of this study: Tectonics is widely recognized by geologists as the single most important factor controlling the development, filling and deformation of sedimentary basins. In general terms, the role of tectonics seems rather ''obvious'' to most geologists, because we know reasonably well as what tectonics ''can do'' as the agent of structural deformation. Therefore, the role of tectonics is often invoked as a kind of ballpark variable - as the obvious cause of ''subsidence'' or ''uplift'' - and seems to some authors even too obvious to mention. Relatively little attempt has been in sedimentological and stratigraphic studies to recognize as to what effects exactly the tectonic activity had on sedimentation in a particular basin. The principal aim of the present study has been to improve our understanding of how tectonic activity can affect deep-water turbiditic sedimentation in a particular basin, including its ''external'' influences (basin geometry, basin-margin configuration, sediment source/supply and relative sea-level change) and ''internal'' effects (basin-floor subsidence, seafloor deformation). Foreland basins are some of the most active tectonically, and the Sinop- Boyabat Basin is a fascinating case of a rift converted into a foreland basin and increasingly deformed. Summary of papers: The main part of the field study, concerned with the sedimentology and facies analysis of the turbiditic succession, is summarized in Papers 1-3, which put special emphasis on the physical character and morphodynamic evolution of the depositional systems and on the tectonic control on their development. Paper 4 focuses on the frequency distribution of bed thickness data collected by detailed logging of various turbiditic assemblages: siliciclastic deposits of nonchannelized currents (lobe and overbank facies); siliciclastic deposits of poorly

  3. Tectonic control on turbiditic sedimentation: The Late Cretaceous-Eocene successions in the Sinop-Boyabat Basin of north-central Turkey

    Energy Technology Data Exchange (ETDEWEB)

    Janbu, Nils Erik

    2004-07-01

    The aim of this study: Tectonics is widely recognized by geologists as the single most important factor controlling the development, filling and deformation of sedimentary basins. In general terms, the role of tectonics seems rather ''obvious'' to most geologists, because we know reasonably well as what tectonics ''can do'' as the agent of structural deformation. Therefore, the role of tectonics is often invoked as a kind of ballpark variable - as the obvious cause of ''subsidence'' or ''uplift'' - and seems to some authors even too obvious to mention. Relatively little attempt has been in sedimentological and stratigraphic studies to recognize as to what effects exactly the tectonic activity had on sedimentation in a particular basin. The principal aim of the present study has been to improve our understanding of how tectonic activity can affect deep-water turbiditic sedimentation in a particular basin, including its ''external'' influences (basin geometry, basin-margin configuration, sediment source/supply and relative sea-level change) and ''internal'' effects (basin-floor subsidence, seafloor deformation). Foreland basins are some of the most active tectonically, and the Sinop- Boyabat Basin is a fascinating case of a rift converted into a foreland basin and increasingly deformed. Summary of papers: The main part of the field study, concerned with the sedimentology and facies analysis of the turbiditic succession, is summarized in Papers 1-3, which put special emphasis on the physical character and morphodynamic evolution of the depositional systems and on the tectonic control on their development. Paper 4 focuses on the frequency distribution of bed thickness data collected by detailed logging of various turbiditic assemblages: siliciclastic deposits of nonchannelized currents (lobe and overbank facies); siliciclastic deposits of poorly

  4. Dynamics of the transfer of terrestrial organic matter in the late Quaternary turbiditic system of the Ogooué River (Gabon)

    Science.gov (United States)

    Mignard, Salomé; Mulder, Thierry; Martinez, Philippe; Garlan, Thierry

    2016-04-01

    In many cases (Hedges et al., 1995, Xing et al., 2011) the supply of terrestrial organic matter (OM) in the oceanic environment is confined to the continental and upper slope of continental margins. However, some recent studies (Huc et al., 2001, Baudin et al., 2010, Biscara et al., 2011, Stetten et al., 2015) demonstrated that significant amounts of continental OM can be transported and deposited in deep sea sediments. This transfer is more efficient in turbiditic systems which are linked to important river deltas. In such systems, the terrigenous influx are important and the downslope sediment-laden currents can indeed transport and rapidly bury important quantities of TOM transferred from the river mouth and the shelf to the abyssal plain. The turbiditic system associated with the Ogooué River offshore Gabon has been selected to study more precisely the modalities of transfer of continental OM from the shelf to the deep offshore. The works focuses on the concentration of OM in both hemipelagites and turbidites as well as the different parameters influencing the spatial distribution and concentration. For this study 10 cores located along the system from the continental shelf to the distal lobes have been selected. The quantity of OM in the sediments as well as its origin (continental vs marine) have been measured using bulk geochemical analyses (% OC, δ13Corg). The stratigraphy of the cores was determined using a combination of planktonic foraminiferal assemblages, δ18O on benthic foraminifers and 14C dates on planktonic foraminifers, and calcium carbonate content calibrated with XRF measurements. The studied cores contain various amounts of organic carbon ranging from 0.7wt% to more than 9wt%. The highest contents are found in turbidite beds where woody detritus and well preserved fragmentary leaf debris are concentrated. In the hemipelagic facies, organic matter is composed of a mixture of marine and land derived organic matter associated with clay

  5. Distal turbidite fan/lobe succession of the Late Oligocene Zuberec Fm. - architecture and hierarchy (Central Western Carpathians, Orava-Podhale basin)

    Science.gov (United States)

    Starek, Dušan; Fuksi, Tomáš

    2017-08-01

    A part of the Upper Oligocene sand-rich turbidite systems of the Central Carpathian Basin is represented by the Zuberec Formation. Sand/mud-mixed deposits of this formation are well exposed in the northern part of the basin, allowing us to interpret the turbidite succession as terminal lobe deposits of a submarine fan. This interpretation is based on the discrimination of three facies associations that are comparable to different components of distributive lobe deposits in deep-water fan systems. They correspond to the lobe off-axis, lobe fringe and lobe distal fringe depositional subenvironments, respectively. The inferences about the depositional paleoenvironment based on sedimentological observations are verified by statistical analyses. The bed-thickness frequency distributions and vertical organization of the facies associations show cyclic trends at different hierarchical levels that enable us to reconstruct architectural elements of a turbidite fan. First, small-scale trends correspond with shift in the lobe element centroid between successive elements. Differences in the distribution and frequency of sandstone bed thicknesses as well as differences in the shape of bed-thickness frequency distributions between individual facies associations reflect a gradual fining and thinning in a down-dip direction. Second, meso-scale trends are identified within lobes and they generally correspond to the significant periodicity identified by the time series analysis of the bed thicknesses. The meso-scale trends demonstrate shifts in the position of the lobe centroid within the lobe system. Both types of trends have a character of a compensational stacking pattern and could be linked to autogenic processes. Third, a largescale trend documented by generally thickening-upward stacking pattern of beds, accompanied by a general increase of the sandstones/mudstones ratio and by a gradual change of percentage of individual facies, could be comparable to lobe-system scale. This

  6. Summary of November 2010 meeting to evaluate turbidite data for constraining the recurrence parameters of great Cascadia earthquakes for the update of national seismic hazard maps

    Science.gov (United States)

    Frankel, Arthur D.

    2011-01-01

    This report summarizes a meeting of geologists, marine sedimentologists, geophysicists, and seismologists that was held on November 18–19, 2010 at Oregon State University in Corvallis, Oregon. The overall goal of the meeting was to evaluate observations of turbidite deposits to provide constraints on the recurrence time and rupture extent of great Cascadia subduction zone (CSZ) earthquakes for the next update of the U.S. national seismic hazard maps (NSHM). The meeting was convened at Oregon State University because this is the major center for collecting and evaluating turbidite evidence of great Cascadia earthquakes by Chris Goldfinger and his colleagues. We especially wanted the participants to see some of the numerous deep sea cores this group has collected that contain the turbidite deposits. Great earthquakes on the CSZ pose a major tsunami, ground-shaking, and ground-failure hazard to the Pacific Northwest. Figure 1 shows a map of the Pacific Northwest with a model for the rupture zone of a moment magnitude Mw 9.0 earthquake on the CSZ and the ground shaking intensity (in ShakeMap format) expected from such an earthquake, based on empirical ground-motion prediction equations. The damaging effects of such an earthquake would occur over a wide swath of the Pacific Northwest and an accompanying tsunami would likely cause devastation along the Pacifc Northwest coast and possibly cause damage and loss of life in other areas of the Pacific. A magnitude 8 earthquake on the CSZ would cause damaging ground shaking and ground failure over a substantial area and could also generate a destructive tsunami. The recent tragic occurrence of the 2011 Mw 9.0 Tohoku-Oki, Japan, earthquake highlights the importance of having accurate estimates of the recurrence times and magnitudes of great earthquakes on subduction zones. For the U.S. national seismic hazard maps, estimating the hazard from the Cascadia subduction zone has been based on coastal paleoseismic evidence of great

  7. Arroyo el Mimbral, Mexico, K/T unit: Origin as debris flow/turbidite, not a tsunami deposit

    Science.gov (United States)

    Bohor, Bruce F.; Betterton, William J.

    1993-01-01

    Coarse, spherule-bearing, elastic units have been discovered at 10 marine sites that span the K/T boundary in northeastern Mexico. We examined one of the best exposed sites in Arroyo el Mimbral, northwest of Tampico. The Mimbral outcrop displays a layered elastic unit up to 3 m thick enclosed by marly limestones of the Mendez (Latest Maastrichian) and Velasco (Earliest Danian) Formations. At its thickest point, this channelized elastic unit is comprised of 3 subunits: (1) a basal, poorly-sorted, ungraded calcareous spherule bed 1 m thick containing relict impact glass and shocked mineral grains, (2) a massive set of laminated calcite-cemented sandstones up to 2 m thick with plant debris at its base, (3) capped by a thin (up to 20 cm) set of rippled sandstone layers separated by silty mudstone drapes containing a small (921 pg/g) iridium anomaly. This tripartite elastic unit is conformably overlain by marls of the Velasco Formation. We also visited the La Lajilla site east of Ciudad Victoria; its stratigraphy is similar to Mimbral's, but its elastic beds are thinner and less extensive laterally. The Mimbral elastic unit has been interpreted previously as being deposited by a megawave or tsunami produced by an asteroid impact on nearby Yucatan (Chicxulub crater). However, a presumed 400-m paleodepth of water at the Mimbral site, channeling of the spherule subunit into the underlying Mendez Formation marls, and the overtopping of the basal, spherule-bearing subunit by the laminated sandstone subunit, all suggest a combined debris flow/turbidite origin for this elastic unit similar to that proposed for Upper Pleistocene sand/silt beds occurring elsewhere in the Gulf of Mexico. In this latter model, the sediment source region for the elastic unit is the lower continental shelf and slope escarpment. For the K/T unit at Mimbral, we propose that thick ejecta blanket deposits composed mostly of spherules were rapidly loaded onto the lower shelf and slope from an impact

  8. Proto-Pacific-margin source for the Ordovician turbidite submarine fan, Lachlan Orogen, southeast Australia: Geochemical constraints

    Science.gov (United States)

    Offler, R.; Fergusson, C. L.

    2016-04-01

    The Early Palaeozoic proto-Pacific Pacific margin of Gondwana was characterised by a huge turbidite submarine fan with abundant clastic detritus derived from unknown sources within Gondwana. These deposits are widespread in the Lachlan Orogen of southeast Australia and include the Ordovician Adaminaby Group. Here we show that the mudstones and sandstones of the Adaminaby Group have chemical compositions that indicate the detritus in them was derived from a felsic, continental source similar in composition to Post Archean Australian Shales (PAAS). Chondrite normalised REE patterns showing LREE enrichment, flat PAAS normalised patterns and elemental ratios La/Sc, Cr/Th, Cr/V, Th/Sc and Th/U, have been used to support this interpretation. The dominance of quartz, and to a lesser degree plagioclase and biotite in the sandstones, suggests that the source was mainly granodioritic to tonalitic in composition. Th/Yb and Ta/Yb ratios indicate that the source was probably calc-alkaline, continental and shoshonitic. In addition, the presence of detrital muscovite, low-grade metamorphic and felsic volcanic clasts, demonstrates that a low-grade metamorphic terrane and volcanic arc contributed to the detritus observed in the samples. The presence of well-rounded zircons and tourmalines, very high Zr contents, high Zr/Sc and higher Cr/V ratios in some samples particularly in the Shoalhaven River area, indicate that some of the detritus was recycled. SiO2 versus (Al2O3 + K2O + Na2O) plots suggest the source areas experienced conditions varying from humid/semi-humid to semi-arid. Textural features and weathering trends of samples from all locations follow a curved pathway on Al2O3 - (CaO* + Na2O) - K2O (ACNK) diagrams, and indicate that the clays formed from weathering had been K-metasomatised prior to penetrative deformation. Chemical indices of alteration (CIA) reveal that even the freshest sandstones are altered and others are moderately to strongly altered. Discrimination

  9. Distal turbidite fan/lobe succession of the Late Oligocene Zuberec Fm. – architecture and hierarchy (Central Western Carpathians, Orava–Podhale basin

    Directory of Open Access Journals (Sweden)

    Starek Dušan

    2017-08-01

    Full Text Available A part of the Upper Oligocene sand-rich turbidite systems of the Central Carpathian Basin is represented by the Zuberec Formation. Sand/mud-mixed deposits of this formation are well exposed in the northern part of the basin, allowing us to interpret the turbidite succession as terminal lobe deposits of a submarine fan. This interpretation is based on the discrimination of three facies associations that are comparable to different components of distributive lobe deposits in deep-water fan systems. They correspond to the lobe off-axis, lobe fringe and lobe distal fringe depositional subenvironments, respectively. The inferences about the depositional paleoenvironment based on sedimentological observations are verified by statistical analyses. The bed-thickness frequency distributions and vertical organization of the facies associations show cyclic trends at different hierarchical levels that enable us to reconstruct architectural elements of a turbidite fan. First, small-scale trends correspond with shift in the lobe element centroid between successive elements. Differences in the distribution and frequency of sandstone bed thicknesses as well as differences in the shape of bed-thickness frequency distributions between individual facies associations reflect a gradual fining and thinning in a down-dip direction. Second, meso-scale trends are identified within lobes and they generally correspond to the significant periodicity identified by the time series analysis of the bed thicknesses. The meso-scale trends demonstrate shifts in the position of the lobe centroid within the lobe system. Both types of trends have a character of a compensational stacking pattern and could be linked to autogenic processes. Third, a largescale trend documented by generally thickening-upward stacking pattern of beds, accompanied by a general increase of the sandstones/mudstones ratio and by a gradual change of percentage of individual facies, could be comparable to lobe

  10. Deep Cenezoic Sediments in Front of the Barbados Ridge Complex, Odp Site 672: Hemipelagites, Turbidites, and Possible Contourites in Western Central Atlantic Ocean Sédiments cénozoïques au front du complexe de la Barbade, site ODP 672 : hémipélagites, turbidites, et possibles contourites dans l'Atlantique central occidental

    Directory of Open Access Journals (Sweden)

    Mascle A.

    2006-11-01

    Full Text Available The cenozoic sediments cover of western central Atlantic oceanic floor was cored at about 5 000 m depth, close to the deformation front of the Barbados Accretionary Prism. Good preservation of sedimentary structures and high recovery rate allowed the recognition and study of hemipelagic calcareous or siliceous clays and muds, with or without interbedded airfall volcanic ash beds, and with or without interbedded coarser deposits coming from lateral inputs. The latters are either calcareous fine-grained turbidites coming from local shallower oceanic areas, or terrigenous and calcareous (more hypothetical contourites (reworking turbidites related to bottom currents running along the South-America margin. Fluid-escape veinstructures, related to dewatering process - upward, vertical to almost horizontal advection - were identified, especially in relation with the beginning of offscraping stress in early Miocene incipient décollementhorizon. Twenty-four color print photos of splitted cores are presented; the macroscopic features they show are commented and discussed. La couverture sédimentaire cénozoïque du plancher océanique de l'Atlantique Central occidental a été carottée à environ 5000 m de profondeur, à proximité du front de déformation du prisme d'accrétion de la Barbade. Une bonne préservation des structures sédimentaires et un taux de récupération élevé ont permis la reconnaissance et l'étude d'argilites et shales hémipélagiques, calcaires ou siliceuses, localement intercalées de lits de cendres volcaniques, et auxquelles s'ajoutent des niveaux plus grossiers attribués à des apports latéraux. Ces derniers consistent, soit en turbidites calcareuses à grain fin provenant de hauts-fonds océaniques proches, soit en (plus hypothétiques contourites calcareuses et terrigènes (remaniant des turbidites attribuées à l'activité de courants profonds longeant la marge sud-américaine. Des veinesd'échappement de fluides

  11. Geochemical evidence of multistage retrogressive failure during the 160,000ka Icod landslide from turbidite facies analysis: multidisciplinary investigative approaches using destructive and non-destructive methodologies

    Science.gov (United States)

    Hunt, James; Wynn, Russell; Masson, Doug; Croudace, Ian

    2010-05-01

    The study of modern deep-sea systems through targeted piston coring has enabled detailed investigations into the process mechanics of turbidity currents. In complex systems such as the Moroccan Turbidite System the derivation of provenance is of vital importance, since flows from different sources in this system have been found to behave differently. Early provenance studies in the Madeira Abyssal Plain found that bulk sand-fraction geochemical analysis through ICP-AES could enable successful attribution of provenance to specific turbidites alongside electron microprobe analysis (de Lange, Jarvis & Kuijpers, 1987; Pearce & Jarvis, 1992). These sources including the Moroccan siliclastic shelf, Tenerife, Las Palma, El Hierro and Madeira. ICP-AES, MC-ICP-MS and XRF have been utilised here, however these present destructive methodologies, using 0.1-5g of material >63µm. Deep-sea piston cores are also expensive to collect, and often there is not enough material to remove for analysis without compromising the core. Furthermore, routine sampling, preparation and analysis using the destructive methods stated above are undertaken at considerable cost and analytical time. The successful use of non-destructive instruments to yield quantitative geochemical has become paramount at the NOC. This presentation serves to show the successful application of the TM-1000 tabletop SEM EDS analyser, ITRAX micro-XRF analyser and the GEOTEK XYZ logger, in coincidence with traditional destructive methods. These instruments can only supply semi-quantitative data, unless correct calibration can be achieved, and will be shown here. The 160,000ka Icod landslide from Tenerife generated a 150km3 debris avalanche with a runout of 105km and a >180km3 turbidity, which will form the case study for application of these instruments. The vertically stacked subunit facies of the Icod turbidite has been attributed to generation from a multistage retrogressive failure (Wynn & Masson, 2003). Here there

  12. CFD simulation on the generation of turbidites in deepwater areas:a case study of turbidity current processes in Qiongdongnan Basin, northern South China Sea

    Institute of Scientific and Technical Information of China (English)

    JIANG Tao; ZHANG Yingzhao; TANG Sulin; ZHANG Daojun; ZUO Qianmei; LIN Weiren; WANG Yahui; SUN Hui; WANG Bo

    2014-01-01

    Turbidity currents represent a major agent for sediment transport in lakes, seas and oceans. In particu-lar, they formulate the most significant clastic accumulations in the deep sea, which become many of the world’s most important hydrocarbon reservoirs. Several boreholes in the Qiongdongnan Basin, the north-western South China Sea, have recently revealed turbidity current deposits as significant hydrocarbon res-ervoirs. However, there are some arguments for the potential provenances. To solve this problem, it is es-sential to delineate their sedimentary processes as well as to evaluate their qualities as reservoir. Numerical simulations have been developed rapidly over the last several years, offering insights into turbidity current behaviors, as geologically significant turbidity currents are difficult to directly investigate due to their large scale and often destructive nature. Combined with the interpretation of the turbidity system based on high-resolution 3D seismic data, the paleotophography is acquired via a back-stripping seismic profile integrated with a borehole, i.e., Well A, in the western Qiongdongnan Basin; then a numerical model is built on the basis of this back-stripped profile. After defining the various turbidity current initial boundary conditions, includ-ing grain size, velocity and sediment concentration, the structures and behaviors of turbidity currents are investigated via numerical simulation software ANSYS FLUENT. Finally, the simulated turbidity deposits are compared with the interpreted sedimentary bodies based on 3D seismic data and the potential provenances of the revealed turbidites by Well A are discussed in details. The simulation results indicate that a sedimen-tary body develops far away from its source with an average grain size of 0.1 mm, i.e., sand-size sediment. Taking into account the location and orientation of the simulated seismic line, the consistence between normal forward simulation results and the revealed cores

  13. Submarine slides, slumps and turbidites in relation to various tectonic and sedimentary processes in the Çinarcik Basin of the eastern Marmara Sea (Turkey)

    Science.gov (United States)

    Ergin, Mustafa; Sakitas, Alper; Sarikavak, Kerim; Keskin, Seref

    2013-04-01

    The main purpose of this study was to determine and understand the impacts of the climatic changes, active tectonism, slope instability and sediment mass movements in the eastern Marmara Sea (Turkey) during the Holocene. Of these, sea level changes, earth quakes, slides, slumps and turbidites were considered to be the major causes to shape the seafloor in the region. With this in mind and within a framework of a larger Project (TÜBİTAK-YDABAG 101Y071), after the major earthquake of 17 August 1999 in Kocaeli-Turkey, both sediment samples and seismic reflection profiles were obtained during the August 2000 Cruise of the Research Vessel "MTA "SİSMİK 1" at water depths between 58 and 1249 meters in the Çınarcık Basin of the eastern Marmara Sea (NW Turkey). Offshore studies covered shelf, slope and basin-floor subenvironments. Onboard, airgun and multichannel seismic reflection system was used along 7 tracklines aligned to N-S and E-W directions. At 15 sites gravity cores were deployed and from 53 to 367 cm thick core sediments were obtained. Grain size analysis, visual core descriptions, and conventional radicarbon datings were also made. To interpret seismic profiles, well-known seismic facies analysis and stratigraphic methods were applied. Fine-grained and grayish-green colored siliciclastic mud was the dominant sediment type (also called "homogenite") deposited on the floor. The coarser-grained intervals and laminations would likely suggest effects of not only turbidites from active tectonism but they can also be related to the wind-driven offshore storm deposits and river floods after heavy rain-falls. Active normal faults on the shelves, fault scarps along the slopes and negative flower structure of syntectonic sedimentation in the deep basin floor observed on the seismic profiles all must indicate the consequences of westerly extension of the North Anatolian Fault Zone in the Marmara Sea. Seismic profiles displayed sediment structures of underwater

  14. Influence of explosive volcanic events on the activation versus de-activation of a modern turbidite system: the example of the Dohrn canyon-fan in the continental slope of the Campania volcanic district (Naples Bay, Italy - Western Mediterranean)

    Science.gov (United States)

    Roca, M.; Budillon, F.; Pappone, G.; Insinga, D.

    2015-12-01

    The interplay between volcanic activity, volcano-clastic yield and activation/deactivation of a turbidite system can be evaluated along the continental margin of Campania region (Tyrrhenian Sea - Italy), an active volcanic area, where three wide canyon-fans occur at short distances one to another. Actually, the Dohrn, Magnaghi and Cuma canyons cut the continental slope and shelf off Ischia and Procida volcanic islands and off the Campania Plain where Phlegraean Field and Mt. Vesuvius active vents are located. This research, partly supported by the Italian Flagship Project Ritmare, is based on single-channel, high-resolution seismic profiles (Sparker-One 16 kJ, 0.5 s twtt), swath-bathymetry and litho- and tephra-stratigraphy of gravity cores. We focused on the stratigraphic constraint of paleo-thalweg features and channel/levees deposits in seismics, debris flow, turbidites and hemipelagites in cores, to learn more on the activation/deactivation stages of the canyon Dohrn, in the frame of relative eustatic sea level variations over the Middle Pleistocene-Holocene time span.Preliminary outcomes suggest that even major volcanic events occurred in the last 300 ky, such as ignimbrite eruptions or large fallouts, have caused the infilling of the canyon head and the cover of pre-existing seabed morphology. As a consequence, the temporary deactivation of the turbidite system has occurred, despite the volcano-clastic overload in the coastal environment. Phases of renewed activities of the thalweg are observed to be in step with falling stages of sea level, which have driven the re-incision of canyon valleys through continuous volcano-clastic debris and turbidites down-flows. Since Holocene, the quiescence of the Dohrn Canyon has been documented, despite the intense volcano-tectonic activity in the area.

  15. Turbidite record of frequency and source of large volume (>100 km3) Canary Island landslides in the last 1.5 Ma: Implications for landslide triggers and geohazards

    Science.gov (United States)

    Hunt, J. E.; Wynn, R. B.; Talling, P. J.; Masson, D. G.

    2013-07-01

    During the last two decades, numerous studies have focused on resolving the landslide histories of the Canary Islands. Issues surrounding the preservation and dating of onshore and proximal submarine landslide deposits precludes accurate determination of event ages. However, submarine landslides often disaggregate and generate sediment gravity flows. Volcaniclastic turbidites sampled from Madeira Abyssal Plain piston cores represent a record of eight large-volume failures from the Western Canary Islands in the last 1.5 Ma. During this time, there is a mean recurrence rate of 200 ka, while the islands of El Hierro and Tenerife have individual landslide recurrences of 500 ka and 330 ka, respectively. Deposits from the 15 ka El Golfo landslide from El Hierro and 165 ka Icod landslide from Tenerife are examined. This study also identifies potential deposits associated with the Orotava (535 ka), Güímar (850 ka), and Rogues de García landslides (1.2 Ma) from Tenerife, El Julan (540 ka), and El Tiñor (1.05 Ma) landslides from El Hierro, and the Cumbre Nueva landslide (485 ka) from La Palma. Seven of eight landslides occurred during major deglaciations or subsequent interglacial periods, which represent 55% of the time. However, all of the studied landslides occur during or at the end of periods of protracted island volcanism, which generally represent 60% of the island histories. Although climate may precondition failures, it is suggested that volcanism presents a more viable preconditioning and trigger mechanism for Canary Island landslides.

  16. Stress orientation and fracturing during three-dimensional buckling: Numerical simulation and application to chocolate-tablet structures in folded turbidites, SW Portugal

    Science.gov (United States)

    Reber, J. E.; Schmalholz, S. M.; Burg, J.-P.

    2010-10-01

    Two orthogonal sets of veins, both orthogonal to bedding, form chocolate tablet structures on the limbs of folded quartzwackes of Carboniferous turbidites in SW Portugal. Structural observations suggest that (1) mode 1 fractures transverse to the fold axes formed while fold amplitudes were small and limbs were under layer-subparallel compression and (2) mode 1 fractures parallel to the fold axes formed while fold amplitudes were large and limbs were brought to be under layer-subparallel tension. We performed two- and three-dimensional numerical simulations investigating the evolution of stress orientations during viscous folding to test whether and how these two successive sets of fractures were related to folding. We employed ellipses and ellipsoids for the visualization and quantification of the local stress field. The numerical simulations show a change in the orientation of the local σ1 direction by almost 90° with respect to the bedding plane in the fold limbs. The coeval σ3 direction rotates from parallel to the fold axis at low fold amplitudes to orthogonal to the fold axis at high fold amplitudes. The stress orientation changes faster in multilayers than in single-layers. The numerical simulations are consistent with observation and provide a mechanical interpretation for the formation of the chocolate tablet structures through consecutive sets of fractures on rotating limbs of folded competent layers.

  17. Paleothermal structure of the Point San Luis slab of central California: Effects of Late Cretaceous underplating, out-of-sequence thrusting, and late Cenozoic dextral offset

    Science.gov (United States)

    Underwood, Michael B.; Laughland, Matthew M.

    2001-02-01

    Late Cretaceous shale and sandstone turbidites of the Point San Luis "slab" are isoclinally folded, locally sheared, and faulted, but their severity of stratal disruption is relatively mild when compared to adjacent polymictic mélange of the Franciscan Complex. We tested the interpretation of a trench-slope basin origin for these strata by documenting their paleothermal structure, including contacts between turbidites and mélange. Values of mean random vitrinite reflectance (Rm) from turbidites are 0.9-1.7% estimates of maximum paleotemperature are 135°-200°C. Mélange matrix samples yield Rm values of 1.1-2.5%, with an average of 1.5%, and peak temperatures between 160° and 240°C. The turbidite-over-mélange contact is locally "cooler over warmer" and was folded after peak heating. The relatively high paleotemperatures cast doubt on a shallow slope basin model (i.e., 1-2 km burial depth). We suggest, instead, that thermal maturation of the Point San Luis slab occurred much deeper in an accretionary prism (10-15 km), where offscraped trench wedge deposits were faulted against underplated mélange. The paleothermal structure was offset and tilted after peak heating by two out-of-sequence faults. Late Oligocene to Pliocene strata rest unconformably above the Franciscan, and there is a significant gap in thermal maturity across this unconformity, with no evidence to show that Franciscan rocks were reset thermally following the main episode of uplift and erosion. Three-dimensional orientations of isoreflectance surfaces on opposite sides of the San Gregorio-San Simeon-Hosgri fault system also can be used to test interpretations of strike-slip neotectonics. The failure to match these geometries among suspected piercing points at Point San Luis, Cambria, and Point Sur favors a suggestion that differential, post thermal peak, dextral offset of Franciscan basement has not exceeded 10-15 km.

  18. Do submarine landslides and turbidites provide a faithful record of large magnitude earthquakes in the Western Mediterranean?

    Science.gov (United States)

    Clare, Michael

    2016-04-01

    Large earthquakes and associated tsunamis pose a potential risk to coastal communities. Earthquakes may trigger submarine landslides that mix with surrounding water to produce turbidity currents. Recent studies offshore Algeria have shown that earthquake-triggered turbidity currents can break important communication cables. If large earthquakes reliably trigger landslides and turbidity currents, then their deposits can be used as a long-term record to understand temporal trends in earthquake activity. It is important to understand in which settings this approach can be applied. We provide some suggestions for future Mediterranean palaeoseismic studies, based on learnings from three sites. Two long piston cores from the Balearic Abyssal Plain provide long-term (sensitive to earthquake-triggered slope failures and is less suitable for future palaeoseismology investigations. Landslide events identified from contourite drift and mound sequences in the Tyrrhenian Sea indicate a regular temporal spacing. No landslides are identified over the last 10,000 years, however, and the inferred recurrence between events is in the order of tens to hundreds of thousands of years. The preconditioning agents and triggers for failures are interpreted to be related to oversteepening of depositional mounds, current-related erosion and geotechnical properties of contourite sediments, rather than earthquake effects. Major hiatuses (up to 2 Myr) result in local incompleteness of the depositional record. Therefore this setting is also unlikely to yield useful palaeoseismological records. This is not intended as a pessimistic tale, however, but instead aims to provide guidance for the future. Efforts should focus on sites that ideally feature: sediments that can be dated accurately from proximal to distal sites; near-constant sediment accumulation rates through time, that provide high enough sensitivities to failure; limited modification by bottom-currents; and, known historical earthquake

  19. Automatic sequences

    CERN Document Server

    Haeseler, Friedrich

    2003-01-01

    Automatic sequences are sequences which are produced by a finite automaton. Although they are not random they may look as being random. They are complicated, in the sense of not being not ultimately periodic, they may look rather complicated, in the sense that it may not be easy to name the rule by which the sequence is generated, however there exists a rule which generates the sequence. The concept automatic sequences has special applications in algebra, number theory, finite automata and formal languages, combinatorics on words. The text deals with different aspects of automatic sequences, in particular:· a general introduction to automatic sequences· the basic (combinatorial) properties of automatic sequences· the algebraic approach to automatic sequences· geometric objects related to automatic sequences.

  20. Provenance of Conglomerates within a Late Cretaceous Turbidite Channel System on the North American Margin: the Rosario Formation, Baja California, Mexico

    Science.gov (United States)

    Dos Santos, Thisiane; Kneller, Benjamin; Morton, Andrew; Armelenti, Garibaldi; Pantopoulos, George; De Ros, Luiz Fernando

    2017-04-01

    The Rosario Formation forms part of the Peninsular Ranges forearc basin complex, which crops out discontinuously along the Pacific coast of the Baja California Peninsula, Mexico. This study concerns the upper, deep marine part of the Rosario Formation , which includes several slope channel systems, one of these, the San Fernando channel systems consists of five channel complex sets (CCS1 to CCS5), each characterized by three filling stages. Stage I consists of predominantly clast­ and matrix-supported conglomerates, with subordinate medium to coarse grained sandstones. Stage II consists of units of clast-supported conglomerates with subordinate medium to coarse-grained sandstones, separated by mainly thinly-bedded turbidites (intercalation of thin beds of fine-grained sandstones and mudstones). Stage III consists mainly of hemipelagic mudstones. The main objective of this research is to determine source area and to compare the coarse fraction and finer fraction (fragments <2 cm) from conglomerates of each channel set, combining provenance methodology such as heavy minerals, clast counting, geochemistry, bulk petrography and U/Pb in detrital zircons by LA-ICPMS and SHRIMP. The heavy minerals assembly identified were Ca amphibole, epidote, clinozoisite, titanite, garnet, tourmaline, apatite, rutile and zircon, among them amphiboles are by far the most abundant detrital mineral. Clast counting and petrographic characterization showed that the pebble fraction of the conglomerates is constituted at least 18 different, and the majority being composed by pyroclastic, porphyritic volcanic and sandstone rocks. Bulk quantification indicates that the main provenance tectonic mode of the fine fraction of the conglomerates can be interpreted as dissected magmatic arc, with subordinate uplifted basement and recycled orogenic contributions. The preliminary conclusion is that the sedimentary supply to the Rosario Formation was mostly derived from volcanic and plutonic rocks of

  1. An ice-contact rhythmite (turbidite) succession deposited during the November 1996 catastrophic outburst flood (jökulhlaup), Skeiðarárjökull, Iceland

    Science.gov (United States)

    Russell, Andrew J.; Knudsen, Óskar

    1999-08-01

    This paper presents new evidence of coarse-grained deposition from a turbulent suspension within a low-energy `slack-water' location during a recent well-documented, volcanically related, high-magnitude glacier outburst flood or jökulhlaup, Skeiðarárjökull, Iceland. This study uses established spatial and temporal constraints on processes observed during the November 1996 jökulhlaup to interpret resultant flood sediments. Coarse-grained sediments were deposited within flood slack-water conditions from suspension load by repeated turbulent flow pulses with durations of seconds-minutes. Depositional processes are thought to be analogous to turbidity currents. A minimum thickness of 15 m of rhythmites record suspended sediment dynamics at a conduit mouth during the late rising and early falling stages of the jökulhlaup. The morphology and sedimentology of deposits in a large ice-walled chamber are consistent with previous models proposed for bar deposition during cataclysmic floods. Flood flows within subglacial conduits and ice-walled open channels were sufficiently powerful to carry material up to boulder size in suspension. Macro-turbulent flows carried huge quantities of suspended sediment to high levels within the main outlet channel. High-frequency, short-duration flow pulses entering a complex ice-walled channel geometry generated highly unsteady and non-uniform flows capable of both erosional and depositional work. This study lends support to the deposition of multiple rhythmites per flood under main flow slack-water conditions. Identification of high-magnitude jökulhlaups in the ice-marginal sedimentary record will depend on the identification and correct interpretation of feeder channel and slack-water turbidite sediments. The results described here may also have application to rhythmic deposits formed by large turbulent flows in other environmental settings.

  2. Summary of November 2010 meeting to evaluate turbidite data for constraining the recurrence parameters of great Cascadia earthquakes for the update of national seismic hazard maps

    Science.gov (United States)

    Frankel, Arthur D.

    2011-01-01

    This report summarizes a meeting of geologists, marine sedimentologists, geophysicists, and seismologists that was held on November 18–19, 2010 at Oregon State University in Corvallis, Oregon. The overall goal of the meeting was to evaluate observations of turbidite deposits to provide constraints on the recurrence time and rupture extent of great Cascadia subduction zone (CSZ) earthquakes for the next update of the U.S. national seismic hazard maps (NSHM). The meeting was convened at Oregon State University because this is the major center for collecting and evaluating turbidite evidence of great Cascadia earthquakes by Chris Goldfinger and his colleagues. We especially wanted the participants to see some of the numerous deep sea cores this group has collected that contain the turbidite deposits. Great earthquakes on the CSZ pose a major tsunami, ground-shaking, and ground-failure hazard to the Pacific Northwest. Figure 1 shows a map of the Pacific Northwest with a model for the rupture zone of a moment magnitude Mw 9.0 earthquake on the CSZ and the ground shaking intensity (in ShakeMap format) expected from such an earthquake, based on empirical ground-motion prediction equations. The damaging effects of such an earthquake would occur over a wide swath of the Pacific Northwest and an accompanying tsunami would likely cause devastation along the Pacifc Northwest coast and possibly cause damage and loss of life in other areas of the Pacific. A magnitude 8 earthquake on the CSZ would cause damaging ground shaking and ground failure over a substantial area and could also generate a destructive tsunami. The recent tragic occurrence of the 2011 Mw 9.0 Tohoku-Oki, Japan, earthquake highlights the importance of having accurate estimates of the recurrence times and magnitudes of great earthquakes on subduction zones. For the U.S. national seismic hazard maps, estimating the hazard from the Cascadia subduction zone has been based on coastal paleoseismic evidence of great

  3. Influence de la luminosité nocturne et de la turbidité sur le comportement vertical de migration de la civelle d'anguille (Anguilla anguilla L. dans l'estuaire de l'Adour

    Directory of Open Access Journals (Sweden)

    DE CASAMAJOR M. N.

    1999-07-01

    Compte tenu des observations effectuées, le schéma migratoire vertical de l'espèce peut être modélisé de la manière suivante : l'interaction entre la luminosité nocturne et la turbidité influence les déplacements de civelles dans la colonne d'eau en relation avec leur comportement lucifuge. Plus la lumière nocturne qui pénètre dans la colonne d'eau est importante et plus les civelles migrent en profondeur.

  4. The CIRCEE-HR survey in the Calabrian arc and offshore E Sicily (Ionian Sea and Southern Italy): investigating active faults, recent deformation and the deep marine paleoseismic record (turbidites)

    Science.gov (United States)

    Gutscher, M.; Babonneau, N.; Cattaneo, A.; Gallais, F.; Graindorge, D.; San Pedro, L.

    2013-12-01

    (CIRCEE-HR - Calabrian arc Ionian sea Research and Catastrophic historical EarthquakE s in southern italy - a High Resolution seismic survey) We report on a recent marine geophysical and geological survey conducted onboard the R/V Le Suroit from 2-24 October in the Ionian Sea, offshore Eastern Sicily. The primary aim of the CIRCEE-HR cruise proposal was to conduct a neo-tectonic study of the Calabrian subduction zone offshore Southern Italy, a region struck repeatedly by the most destructive earthquakes in European history. The CIRCEE-HR survey targeted the region struck by the 1693 Catania earthquake (60,000 killed) and the 1908 Messina earthquakes, which produced intensity X-XI shaking and tsunamis. The 1908 (normal faulting mechanism) earthquake triggered a turbidite flow that ruptured submarine cables. The source of some strong historical earthquakes (1169, 1542, 1693) remains unknown. Several crustal scale structures have been proposed as being seismogenic: the Malta escarpment, a lithospheric tear fault (STEP), the subduction fault plane and other related faults. The main objectives of the cruise were therefore to seek evidence of active faults associated with these structures, and to characterize the degree of activity of the Calabria accretionary wedge (sedimentary deformation, dewatering processes) in order to better assess its seismogenic potential. Another major objective is to try to determine the typical recurrence interval for large earthquakes in the region (by coring and dating of turbidites triggered by great earthquakes). The Augias mega-turbidite dated either 3.5 ka (Cita et al., 1996) or 365 AD (Polonia et al., 2013) covers the entire floor of the Ionian abyssal plain with a thickness of 10-15m representing a volume of > 100km3. This layer serves as a stratigraphic marker to identify recent deformation in the abyssal domain. The methods applied were 72-channel high-resolution seismic profiles and sub-bottom profiling (chirp) (with 1200km of

  5. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies...

  6. Stabilization of garnet in metamorphosed altered turbidites near the St. Eugene lead-zinc deposit, southeastern British Columbia: Equilibrium and kinetic controls

    Science.gov (United States)

    Pattison, David R. M.; Seitz, JennaLee D.

    2012-03-01

    The St. Eugene lead-zinc deposit, near Moyie, southeastern British Columbia, is a Mesoproterozoic vein deposit hosted by metaturbidites of the 1.5-1.4 Ga Belt-Purcell Supergroup. The regional metamorphic grade of the rocks is biotite zone, with the age of metamorphism being Mesoproterozoic (ca. 1.35 Ga). The vein system is enveloped by a metamorphosed alteration zone of increasing intensity as the vein is approached. Thin argillaceous tops of turbidite beds away from the vein are garnet-free, whereas those in the inner alteration zone are garnet-bearing. Compared to rocks away from the vein, those near the vein are enriched in Fe, Mn, Pb and Zn, with proportional reduction in other compositional parameters. Thermodynamic modeling of three rocks across the alteration gradient predicts increasing stabilization of garnet with increasing degree of alteration. Predicted and observed modes of garnet in the samples are in close agreement. In the most altered rock, the garnet-in line is displaced down-temperature by ~ 100 °C relative to the least altered rock. Approximately 2/3 of the garnet stabilization is accounted for by increase in Mn content and the rest by increase in Fe/(Fe + Mg). Kinetic factors played a role in the development of the mineral assemblages, including metastable persistence of zoisite, and disequilibrium (overstepped) initial growth of garnet. Estimates of peak pressure-temperature conditions from mineral assemblage constraints and from compositional isopleths are complicated by the kinetic effects but yield similar results: 490-510 °C and 3.6-4.0 kbar. The pressure-temperature estimates imply an average linear geothermal gradient of ~ 35 °C/km, broadly consistent with burial metamorphism in the Belt-Purcell extensional basin. However, the estimated pressure, equivalent to a depth of 13-15 km, is greater than the estimated ~ 8 km (~ 2.2 kbar) of stratigraphic overburden at the time of metamorphism. The results of this study support the idea that

  7. 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...

  8. Sequence stratigraphy and depositional systems in the Paleogene, Liaodong Bay

    Institute of Scientific and Technical Information of China (English)

    Ji Hancheng

    2008-01-01

    Based on drilling and seismic data,the Paleogene developed in Liaodong Bay can be divided into five third-order sequences bounded by six sequence boundaries.Through analyzing depositional systems in each sequence in detail,the Es-3 time was defined as fast rifting.During the deposition of the Es-3 member,the lake basin was continuous along the N-S direction but compartmentalized along the E-W direction by several N-S trending faults.Deposition was dominated by steep slope fans and fan deltas.The time of Es-2 and Es-1 was stable settling.The lake basin expanded substantially.The fan delta system and braided fluvial system were developed.Carbonate and clastic deposits were formed on the Liaoxi (west Liaohe) Rise.The time of Ed-3 time was again fast rifting.During this time,shale was deposited.In the time of Es-2,tectonic movement weakened.The basin was higher in the west and north,and lower in the east and south.A series of delta depositionai systems were developed and smallscale slumping turbidite fans were present in semi-deep lake to deep lake.In the time of Ed-1,tectonic movement stopped.Flood plain deposition occurred.Finally the paper presents the characteristics of evolution and distribution of depositional systems both vertically and horizontally.

  9. Dna Sequencing

    Science.gov (United States)

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  10. 鄂尔多斯盆地长7浊积岩特征及成藏条件分析%ANALYSES ON THE CHARACTERISTICS AND RESERVOIR FORMING CONDITIONS OF CHANG 7 GROUP TURBIDITE IN ORDOS BASIN

    Institute of Scientific and Technical Information of China (English)

    时保宏; 张艳; 张雷; 杨亚娟

    2013-01-01

    利用岩心、测井等资料对鄂尔多斯盆地长7浊积岩特征及成藏条件的分析结果表明,长7油层组沉积层理、沉积构造及砂岩粒度等反映晚三叠世延长组长7沉积时在深湖—半深湖相发育浊积岩.长7浊积岩的电性响应特征表现为自然伽马曲线具有明显的齿化现象,在地震反射剖面上则表现为不稳定沉积、相带变化大等特点.浊积岩储集体的物性条件相对较差,孔隙度平均为8.5%,渗透率平均为0.12×10-3μm2,属超低孔、低渗储层,但由于其紧邻优质烃源岩,成藏条件优越,可大面积成藏.%With the help of the data of cores and well loggings, the characteristics of the turbidite and the conditions of the reservoir formation are analyzed for the above group of Ordos Basin. The analyzed results show that the sedimentary beddings, structures, sandstone particles and so on of the reservoir group reflect the deep and semi-deep lake facies developed environments of Late Triassic Yanchang Formation. The response characteristics of electrical property of Chang 7 Group turbidite display the obvious toothed phenomenon of GR ( gamma ray) curve, and moreover show the features of the unstable sedimentation and enormous facies changes on the seismic reflection profiles. The physical conditions of the turbidite accumulating body are relatively poorer, whose average porosity and permeability are respectively 8. 5% and 0. 12 × 10-3μm2 , belong to ultra-low porosity and low permeability reservoir. However, for the body is close to the regions with high-quality source rocks and favorable hydrocarbon enriched conditions, so it can form reservoirs on a large scale.

  11. The coupling of dynamics and permeability in the hydrocarbon accumulation period controls the oil-bearing potential of low permeability reservoirs: a case study of the low permeability turbidite reservoirs in the middle part of the third member of Shahejie Formation in Dongying Sag

    DEFF Research Database (Denmark)

    Yang, Tian; Cao, Ying-Chang; Wang, Yan-Zhong

    2016-01-01

    The relationships between permeability and dynamics in hydrocarbon accumulation determine oilbearing potential (the potential oil charge) of low permeability reservoirs. The evolution of porosity and permeability of low permeability turbidite reservoirs of the middle part of the third member of t...

  12. Feasibility of Optimizing Recovery and Reserves from a Mature and Geological Complex Multiple Turbidite Offshore Calif. Reservoir through the Drilling and Completion of a Trilateral Horizontal Well, Class III

    Energy Technology Data Exchange (ETDEWEB)

    Pacific Operators Offshore, Inc.

    2001-04-04

    The intent of this project was to increase production and extend the economic life of this mature field through the application of advanced reservoir characterization and drilling technology, demonstrating the efficacy of these technologies to other small operators of aging fields. Two study periods were proposed; the first to include data assimilation and reservoir characterization and the second to drill the demonstration well. The initial study period showed that a single tri-lateral well would not be economically efficient in redevelopment of Carpinteria's multiple deep water turbidite sand reservoirs, and the study was amended to include the drilling of a series of horizontal redrills from existing surplus well bores on Pacific Operators' Platform Hogan.

  13. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Nucleotide Sequence Nucleotide sequence of full length cDNA (trimmed sequence) kome_ine_full_seq...uence_db.fasta.zip kome_ine_full_sequence_db.zip kome_ine_full_sequence_db ...

  14. Paleogene sequence on the Alaska Peninsula

    Energy Technology Data Exchange (ETDEWEB)

    Detterman, R.L.

    1985-04-01

    Paleogene strata are exposed nearly the entire length of the Alaska Peninsula. They include continental and marine volcaniclastic rocks and a thick volcanic sequence. The strata are divided into the Tolstoi, Stepovak, Meshik, and Belkofski (in part) Formations in the southern part of the peninsula, and into the nonmarine clastic West Foreland Formation and the Hemlock Conglomerate in the northern part. The Tolstoi Formation (Paleocene and Eocene), 670-1380 m thick, consists mainly of continental quartz- and chert-rich sandstone and conglomerate, siltstone, and coal. Volcanic clasts and tuffaceous detritus increase in abundance upward. Neritic strata are present as interbeds in the type area. The formation overlies, with a major unconformity, strata ranging in age from Late Jurassic to Late Cretaceous. Partly coeval strata at the north end of the peninsula (West Foreland Formation) are mainly volcanic sandstone and conglomerate. The Stepovak Formation, 1800-2000 m thick, represents two contrasting depositional environments - a lower dark siltstone and sandstone turbidite, about 975 m thick, and a shallow neritic sandstone and siltstone, rich in volcanic material, about 1000 m thick. Locally, the upper part is deltaic sandstone, siltstone, and coal. An abundant metafauna of Eocene and Oligocene age is found in the neritic deposits. A thick coeval volcanic unit, the Meshik Formation, is present in the central part of the peninsula. Andesitic to basaltic lava, breccia, tuff, and lahars, as much as 1500 m thick, have been K-Ar dated at 27-38 m.y. Similar rocks with interbedded sediment at the end of the peninsula are included with the Belkofski Formation.

  15. Geometry of the proximal part of the modern turbidite depositional system of the Carapebus Formation, Campos Basin: a model for reservoir heterogeneities; Geometria da porcao proximal do sistema deposicional turbiditico moderno da Formacao Carapebus, Bacia de Campos; modelo para heterogeneidades de reservatorio

    Energy Technology Data Exchange (ETDEWEB)

    Machado, Luis Claudio Ribeiro; Kowsmann, Renato Oscar; Almeida Junior, Waldemar de; Murakami, Celso Yoshihito; Schreiner, Simone; Miller, Dennis James; Piauilino, Pedro Orlando Vasconcelos [PETROBRAS, Rio de Janeiro, RJ (Brazil). Exploracao e Producao. Unidade de Servico Submarino]. E-mail: machadolc@petrobras.com.br

    2004-11-01

    The deep-water marine sedimentary environment of the Cenozoic of the Campos Basin is examined at the modern sea floor, where it can be better understood. This environment is responsible for the genesis of the turbidite systems of the Carapebus Formation, the reservoirs that hold more than 90% of Brazil's petroleum reserves. The study was developed with the records of regional side-scan sonar, swath bathymetry, sub-bottom profiler data, standard multichannel 3D seismic surveys and piston cores covering almost the entire basin. After leaving the Almirante Camara Canyon, the turbiditic flows erode the muddy debris apron surrounding the continental slope and begin to deposit thick layers of clean sand into a big trough in water depths of 1800 m to 3000 m. The trough is 3.5 km wide, 150 m deep, 150 km long, and is formed by a chain of salt withdrawal mini-basins. In some places the sea floor is flat enough to develop today a depositional lobe, in all aspects analogous to the best, geologically ancient petroleum reservoirs in the basin. Aspects of the system: 1) the arcosean sands are brought by the river, cross the shelf, the incised valley, the canyon, and deposit as turbidites - they do not originate from a collapse of the continental slope; 2) a wide muddy debris apron surrounds the continental slope (slope apron), and represents a huge volume of sediment in the Campos Basin ; 3) the turbidites do not develop a submarine fan, but are deposited in an elongated trough formed by salt tectonics; 4) the turbidite beds, both in the lobe or in the trough, are not deposited during a single episode, but in multiple events over significant geologic time in which small channels which brought the turbidites avulse and meander along the entire depositional area, building a single amalgamated bed; 5) classic channel-levees are not present because this system comprises a sandy braid plain and the levees are as sandy as the channel; 6) a hierarchical depositional model for bulb

  16. Sequence stratigraphy of Taciba and Rio Bonito formations in Mafra, SC area, eastern Parana Basin, Brazil; Estratigrafia de sequencias das formacoes Taciba e Rio Bonito (Membro Triunfo) na regiao de Mafra/SC, leste da Bacia do Parana

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2005-05-01

    The Taciba and Rio Bonito ('lower' Triunfo Mbr) formations are divided into six depositional sequences based on cores, gamma-ray and electrical logs from shallow drillings from northern Santa Catarina State, Brazil. Each sequence is formed by two systems tracts, a lower one, sandy (low stand) and an upper one, shaly (high stand). The Taciba Formation has three sequences, S{sub 0} to S{sub 2}; sequence S{sub 0} has a thick turbidite sandstone at the base (Rio Segredo Member) that pinches out towards the eastern margin and even disappears in the Mafra outcrop area. Sequence S{sub 1} varies from a thin fluvial-estuarine system to a thick turbidite sandstone of a channelled fan system; S{sub 1} upper shaly system tract is marine in well PP-11, and it is glacially influenced in well PP-10. Sequence S{sub 2} is a thick sandstone body of shallow marine origin, but restricted to one well (PP-11); its upper shaly tract is dominated by massive siltstones intercalated with thin, distal tempestites. The 'lower' Triunfo Member (or 'Taciba- Triunfo transition') begins with the arrival of deltaic clastics of sequence S{sub 3} lower tract, coarsening-up from medial- to proximal delta front sandstones. Sequence S{sub 4} is quite similar to S{sub 3}, both showing sandstone pro gradation from north to south, as opposed to the southwest-sourced transgressive diamictites. Sequence S{sub 5} consists of fluvial deposits at well PP-12, and two transgressive cycles from wells PP-11 to PP-9, each one of them composed of fluvial-estuarine to marine systems. Well PP-10 is an exception, where the lower cycle presents de glaciation to marine deposits. (author)

  17. Mesozoic and late tertiary submarine fan sequences and their tectonic significance, Sumba, Indonesia

    Science.gov (United States)

    Von Der Borch, C. C.; Grady, A. E.; Hardjoprawiro, S.; Prasetyo, H.; Hadiwisastra, S.

    1983-12-01

    The Indonesian island of Sumba occupies a critical zone which separates a "normal" subduction complex (Java Trench System) from a continent-island arc collision zone (Banda Arc). Sumba is considered by some authors to be a microcontinental fragment, although in this context its pre-fragmentation origin is uncertain. Detailed studies of the stratigraphy of Sumba, however, throw light on the origin and subsequent geological history of the island and surrounding areas. On available evidence, the oldest outcropping rocks are of Cretaceous age and locally contain a tropical Tethyan marine fauna. They comprise dark-coloured, sometimes carbonaceous and often volcanogenic mudstones, sandstones, gravels and diamictites, pervasively intruded by andesitic and dacitic dykes and locally intruded by granodiorite plutons. These sediments are siliclastic and appear to have had a continental provenance. The Cretaceous rocks in many areas compromise part of a major submarine fan complex which, at least in south-central Sumba, prograded towards the southwest and south. Shallow marine and non-marine Paleogene sediments and volcanic agglomerates lie unconformably above the uplifted, tilted and eroded Cretaceous strata. These are overlain in turn by the widely outcropping Miocene Sumba Formation, an oceanic sequence with island-arc affinities. Accessible outcrops of the Sumba Formation comprise platform carbonates with abundant reef developments in west Sumba, and a major submarine fan—pelagic chalk complex in east Sumba. The fan complex, which extends beneath the southern Savu Sea north of Sumba, is dominated by large-scale slumps, olistostromes and thin- and thick-bedded turbidites. Turbidite sands and gravels invariably are volcaniclastic, containing components derived from a typical inner (volcanic) arc complex. Paleocurrent indicators are difficult to find in the Sumba Formation, thus it is uncertain at this stage whether the volcaniclastic turbidites were derived from the

  18. Tectonic settings of Paleozoic turbidites in the Beishan orogen and its implications for regional accretionary tectonics%北山造山带古生代浊积岩构造环境探讨及其大地构造意义

    Institute of Scientific and Technical Information of China (English)

    郭谦谦; 肖文交; 侯泉林; 韩春明; 曲军锋; 田忠华; 宋东方

    2013-01-01

    北山造山带是研究中亚造山带增生造山的关键地区之一,浊积岩是增生造山带的重要组成部分.北山古生代浊积岩主要出露于营毛沱、柳园和黑山口地区.营毛沱浊积岩发育于下奥陶统,古水流方向由南向北,内部砂岩具中高等风化程度的长英质源区,构造背景为被动陆缘.早二叠世柳园浊积岩内部砂岩具低到中等风化程度的中基性源区,构造背景为大洋岛弧.早二叠世黑山口浊积岩中的砂岩源区具中等风化程度,环境相对柳园砂岩较为稳定,和长英质源区的沉积岩具相似性,构造环境可能为活动陆缘弧.对北山古生代浊积岩的解剖揭示北山古生代经历了复杂的俯冲增生过程.早古生代花牛山—火石山一带发育向北的俯冲,火石山南部被动陆缘形成营毛沱浊积岩,之后的俯冲带局部后撤形成泥盆纪墩墩山岛弧.柳园地区晚古生代洋壳向花牛山和石板山岛弧带俯冲分别形成了柳园和黑山口浊积岩.本研究支持北山增生时间持续到早二叠世的观点,对认识天山、索伦缝合带的衔接对比研究具有重要的意义.%The Beishan orogen is one of the key parts to study the accretionary orogenesis of the Altaids, and turbidites are an important composition of the accretionary orogenic belt. The Paleozoic turbidites in the Beishan are mainly distributed in the Yingmaotuo, Liuyuan and Heishankou areas. The turbidites in the Yingmaotuo area is Early Ordovician in age and were derived from felsic sources by medium-high weathering degree, indicating a passive continental margin tectonic setting. The turbidites in the Liuyuan area is Early Permian in age, and were derived from intermediate-basic sources by low-medium weathering degree, indicating an oceanic arc tectonic setting. The Heishankou turbidites are a little younger than the Liuyuan turbidites, and were derived from felsic sources by medium weathering degree, indicating a

  19. Late Triassic - Early Jurassic successions of the Atuel depocenter: sequence stratigraphy and tectonic controls

    Directory of Open Access Journals (Sweden)

    Silvia Lanés

    2008-12-01

    Full Text Available Biostratigraphic correlations of the Late Triassic - Early Jurassic successions of the Atuel depocenter allowed determining the accommodation changes and the possible tectonic controls on sedimentation. The Rhaetian - late Early Sinemurian deposits contain facies of slope-type fan deltas, braided fluvial systems and low sinuosity rivers with alternate bars deposited during a synrift phase. The late Early Sinemurian - Toarcian series host facies of intermediate (Gilbert to shelf type fan deltas, braided and low sinuosity fluvial systems, wave-dominated estuaries, transgressive storm-dominated and turbidite-influenced marine shelves which record the sag phase. According to different criteria two stratigraphic schemes are proposed, the first one considering tectosedimentary units (TSU and the second one using "Exxon-like" sequences. In the first scheme the synrift TSU matches the actual Precuyo Mesosequence and the sag TSU is partly equivalent to the Cuyo Mesosequence, mainly keeping the current mesosequence scheme for the Neuquén basin but assigning the fandeltaic deposits to the Precuyo Mesosequence. The second sequence scheme considers the whole Late Triassic - Early Jurassic succession as a part of the Cuyo Mesosequence, where the synrift deposits composes the detached lowstand system tract (LST and most of the sag deposits makes the transgressive system tract (TST. The basal sequence boundary does not crop out, the flooding surface at the TST base and the maximum flooding surface at the TST top are respectively marked by the lowest estuarine levels and by black shales with suboxic-compatible bivalves (Bositra sp..

  20. Classifying Genomic Sequences by Sequence Feature Analysis

    Institute of Scientific and Technical Information of China (English)

    Zhi-Hua Liu; Dian Jiao; Xiao Sun

    2005-01-01

    Traditional sequence analysis depends on sequence alignment. In this study, we analyzed various functional regions of the human genome based on sequence features, including word frequency, dinucleotide relative abundance, and base-base correlation. We analyzed the human chromosome 22 and classified the upstream,exon, intron, downstream, and intergenic regions by principal component analysis and discriminant analysis of these features. The results show that we could classify the functional regions of genome based on sequence feature and discriminant analysis.

  1. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Amino Acid Sequence Amino Acid sequence of full length cDNA (Longest ORF) kome_ine_full_seq...uence_amino_db.fasta.zip kome_ine_full_sequence_amino_db.zip kome_ine_full_sequence_amino_db ...

  2. 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.

  3. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  4. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence.

  5. Coordinate cytokine regulatory sequences

    Science.gov (United States)

    Frazer, Kelly A.; Rubin, Edward M.; Loots, Gabriela G.

    2005-05-10

    The present invention provides CNS sequences that regulate the cytokine gene expression, expression cassettes and vectors comprising or lacking the CNS sequences, host cells and non-human transgenic animals comprising the CNS sequences or lacking the CNS sequences. The present invention also provides methods for identifying compounds that modulate the functions of CNS sequences as well as methods for diagnosing defects in the CNS sequences of patients.

  6. Description of Cretaceous Sedimentary Sequence of the Second and Third Member of the Qingshankou Formation Recovered by CCSD-SK-Is Borehole in Songliao Basin: Lithostratigraphy, Sedimentary Facies and Cyclic Stratigraphy

    Science.gov (United States)

    Wang, Pujun; Gao, Youfeng; Cheng, Rihui; Wang, Guodong; Wu, Heyong; Wan, Xiaoqiao; Yang, Gansheng; Wang, Zhongxing

    The second and third member of the Qingshankou Formation recovered by CCSD-SK-Is borehole (China Cretaceous Continental Scientific Drilling-SongkeI-the south borehole) is 415.61 m long and 100% of cores recovery. The age of the member corresponds approximately to the Coniacian. The sequence and process of lithology-lithofacies and cyclic stratigraphy were revealed by a detailed core description. 12 rock types and 2 kinds of sedimentary subfacies including semi-deep lake and shallow lake were recognized from the drilling core of the second and third member of the Qingshankou Formation. 10 sedimentary microfacies are present, including dolomite, marl, limestone, oil shale, semi-deep lake turbidite, volcanic ash, seismite, semi-deep lake mudstone, shallow lake mudstone, and shallow lake turbidite microfacies. The second and third member of the Qingshankou Formation represents 422 meter-scale cycles (sixth-order cycle), 130 fifth-order cycles, 21 fourth-order cycles, and one third-order cycles. The special lithologies, such as mudstone, seismite, dolomite, volcanic ash, and so on are important to researches on source rocks and lacustrine event sediments.

  7. Late Paleozoic tectonics of the Solonker Zone in the Wuliji area, Inner Mongolia, China: Insights from stratigraphic sequence, chronology, and sandstone geochemistry

    Science.gov (United States)

    Shi, Guanzhong; Song, Guangzeng; Wang, Hua; Huang, Chuanyan; Zhang, Lidong; Tang, Jianrong

    2016-09-01

    The geology in the Wuliji area (including the Enger Us and Quagan Qulu areas) is important for understanding the Late Paleozoic tectonics of the Solonker Zone. Ultramafic/mafic rocks in the Enger Us area, previously interpreted as an ophiolitic suture, are actually lava flows and sills in a Permian turbiditic sequence and a small body of fault breccia containing serpentinite. Subduction zone features, such as accretionary complexes, magmatic arc volcanics or LP/HP metamorphism are absent. Early Permian N-MORB mafic rocks and Late Permian radiolarian cherts accompanied by turbidites and tuffeous rocks indicate a deep water setting. In the Quagan Qulu area, outcrops of the Late Carboniferous to Permian Amushan Formation are composed of volcano-sedimenary rocks and guyot-like reef limestone along with a Late Permian volcano-sedimentary unit. A dacite lava in the Late Permian volcano-sedimentary unit yields a zircon U-Pb age of 254 Ma. The gabbros in the Quagan Qulu area are intruded into the Amushan Formation and caused contact metamorphism of country rocks. Sandstones in the Upper Member of the Amushan Formation contain detrital clasts of volcanic fragments and mineral clasts of crystalline basement rocks (i.e. biotite, muscovite and garnet). Geochemical analysis of volcaniclastic sandstones shows a magmatic affinity to both continental island arc (CIA) and active continental margin (ACM) tectonic settings. A Late Permian incipient rift setting is suggested by analyzing the lithostratigraphic sequence and related magmatism in the Wuliji area. The volcano-sedimentary rocks in the Wuliji area experienced a nearly N-S shortening that was probably related to the Early Mesozoic nearly N-S compression well developed in other areas close to the Wuliji area.

  8. Glass chemistry in volcaniclastic sediments of ODP Leg 107, Site 650, sedimentary sequence: provenance and chronological implications

    Science.gov (United States)

    Calanchi, Natale; Gasparotto, Giorgio; Romagnoli, Claudia

    1994-03-01

    A detailed chemical investigation of volcanic glass fragments from volcaniclastic strata (6 tephras, 1 volcanic debris flow, 12 volcanic turbidites) of ODP Leg 107, Site 650, sedimentary sequence, leads to a varied pattern in terms of both provenance and age constraints. The six analyzed tephra strata indicate a provenance from at least three different volcanic provinces: Aeolian, Campanian, and Sicilian Channel (Pantelleria Island). The older tephra strata (021, 018, 012) have a large amount of "orogenic" rhyodacite/rhyolite deposits that may be attributed to the Aeolian province, although no subaerial coeval volcanic activity of similar composition has so far been documented in the Aeolian Arc. Tephra 007 is related to the Pantelleria Island activity and, particularly, to an ignimbrite episode dated circa 130 ka. Tephra strata 005 and 003, have a clear Campanian provenance, and are correlated with analogous tephra layers, observed in the Tyrrhenian and Ionian seas, dated circa 107 and 60 ka respectively. In the oldest portion of the sequence (from 1.3 to 0.13 Ma), the volcaniclastic sediments were only derived from the Aeolian domain whereas in the latest 130 ka, the Campanian influx becomes much more predominant. Therefore, a general K-enrichment trend is observed in the temporal sequence of all the analyzed samples (almost 700 point analyses) which may be related both to a variation in the source area and to the specific Pleistocene magmatic evolution of the peri-Tyrrhenian volcanic provinces.

  9. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  10. Contamination of sequence databases with adaptor sequences

    Energy Technology Data Exchange (ETDEWEB)

    Yoshikawa, Takeo; Sanders, A.R.; Detera-Wadleigh, S.D. [National Institute of Mental Health, Bethesda, MD (United States)

    1997-02-01

    Because of the exponential increase in the amount of DNA sequences being added to the public databases on a daily basis, it has become imperative to identify sources of contamination rapidly. Previously, contaminations of sequence databases have been reported to alert the scientific community to the problem. These contaminations can be divided into two categories. The first category comprises host sequences that have been difficult for submitters to manage or control. Examples include anomalous sequences derived from Escherichia coli, which are inserted into the chromosomes (and plasmids) of the bacterial hosts. Insertion sequences are highly mobile and are capable of transposing themselves into plasmids during cloning manipulation. Another example of the first category is the infection with yeast genomic DNA or with bacterial DNA of some commercially available cDNA libraries from Clontech. The second category of database contamination is due to the inadvertent inclusion of nonhost sequences. This category includes incorporation of cloning-vector sequences and multicloning sites in the database submission. M13-derived artifacts have been common, since M13-based vectors have been widely used for subcloning DNA fragments. Recognizing this problem, the National Center for Biotechnology Information (NCBI) started to screen, in April 1994, all sequences directly submitted to GenBank, against a set of vector data retrieved from GenBank by use of key-word searches, such as {open_quotes}vector.{close_quotes} In this report, we present evidence for another sequence artifact that is widespread but that, to our knowledge, has not yet been reported. 11 refs., 1 tab.

  11. Upper cretaceous to paleocene depositional sequences and sandstone petrography of southwestern Patagonia (Argentina and Chile)

    Science.gov (United States)

    Macellari, C. E.; Barrio, C. A.; Manassero, M. J.

    Upper Cretaceous to Paleocene strata exposed along the Andean margin of Patagonia south of 50°S were deposited in a foreland basin and comprise a complex transition from continental to marine facies. Three unconformity-bounded sequences are observed within the sedimentary succession studied. Sequence 1 (upper Campanian) displays a rapid north-to-south transition from upper delta plain mudstones (Cerro Fortaleza Formation) through lower delta plain and subaqueous delta plain sandstones (La Anita Formation) to delta-slope and basinal turbidites (Alta Vista and Tres Pasos Formations). Sequence 2 (Maastrichtian-Paleocene) was initiated with braided river sediments (La Irene Formation), deposited over a Type II unconformity ( sensu Vail et al., 1984). These rocks are overlain by meandering fluvial sandstones and mudstones (Chorrillo Formation) that interfinger to the south with fossiliferous shallow marine sandstones (upper Cerro Cazador Formation). Sequence 3 (Paleocene) is composed of shallow marine conglomerates and crossbedded sandstones (Calafate and Cerro Dorotea Formations). These rocks are separated by an angular unconformity from subjacent units. Sandstone petrographic analysis indicates the presence of two main petrofacies within the rocks studied. A quartz-rich petrofacies, present to the north of the basin during late Campanian to early Maastrichtian time, was derived from continental crustal block and recycled orogen sources that were possibly exposed to the northwest of the basin. The second petrofacies (volcanic-rich petrofacies) was restricted to the south of the basin during the late Campanian to early Maastrichtian, but covered the entire area during the late Maastrichtian and Paleocene. These sediments were derived from a dissected magmatic arc located to the west of the study area. The presence of abundant tuffaceous intercalations, as well as fresh andesitic fragments, indicates contemporaneous volcanism near the Cretaceous/Tertiary boundary. The

  12. Automated DNA Sequencing System

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, G.A.; Ekkebus, C.P.; Hauser, L.J.; Kress, R.L.; Mural, R.J.

    1999-04-25

    Oak Ridge National Laboratory (ORNL) is developing a core DNA sequencing facility to support biological research endeavors at ORNL and to conduct basic sequencing automation research. This facility is novel because its development is based on existing standard biology laboratory equipment; thus, the development process is of interest to the many small laboratories trying to use automation to control costs and increase throughput. Before automation, biology Laboratory personnel purified DNA, completed cycle sequencing, and prepared 96-well sample plates with commercially available hardware designed specifically for each step in the process. Following purification and thermal cycling, an automated sequencing machine was used for the sequencing. A technician handled all movement of the 96-well sample plates between machines. To automate the process, ORNL is adding a CRS Robotics A- 465 arm, ABI 377 sequencing machine, automated centrifuge, automated refrigerator, and possibly an automated SpeedVac. The entire system will be integrated with one central controller that will direct each machine and the robot. The goal of this system is to completely automate the sequencing procedure from bacterial cell samples through ready-to-be-sequenced DNA and ultimately to completed sequence. The system will be flexible and will accommodate different chemistries than existing automated sequencing lines. The system will be expanded in the future to include colony picking and/or actual sequencing. This discrete event, DNA sequencing system will demonstrate that smaller sequencing labs can achieve cost-effective the laboratory grow.

  13. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  14. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  15. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  16. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  17. sequenceMiner algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  18. Stratigraphy and tectono-sedimentary evolution of the Upper Cretaceous Tertiary sequence in the southern part of the Malatya Basin, East Anatolia, Turkey

    Science.gov (United States)

    Önal, Mehmet; Kaya, Meral

    2007-03-01

    The Malatya Basin is situated on the southern Taurus-Anatolian Platform. The southern part of the basin contains a sedimentary sequence which can be divided into four main units, each separated by an unconformity. From base to top, these are: (1) Permo-Carboniferous; (2) Upper Cretaceous-Lower Paleocene, (3) Middle-Upper Eocene and (4) Upper Miocene. The Upper Cretaceous-Tertiary sedimentary sequence resting on basement rocks is up to 700 m thick. The Permo-Carboniferous basement consist of dolomites and recrystallized limestones. The Upper Cretaceous-Lower Paleocene transgressive-regressive sequence shows a transition from terrestrial environments, via lagoonal to shallow-marine limestones to deep marine turbiditic sediments, followed upwards by shallow marine cherty limestones. The marine sediments contain planktic and benthic foraminifers indicating an upper Campanian, Maastrichtian and Danian age. The Middle-Upper Eocene is a transgressive-regressive sequence represented by terrestrial and lagoonal clastics, shallow-marine limestones and deep marine turbidites. The planktic and benthic foraminifers in the marine sediments indicate a Middle-Upper Eocene age. The upper Miocene sequence consists of a reddish-brown conglomerate-sandstone-mudstone alternation of alluvial and fluvial facies. During Late Cretaceous-Early Paleocene times, the Gündüzbey Group was deposited in the southern part of a fore-arc basin, simultaneously with volcanics belonging to the Yüksekova Group. During Middle-Late Eocene times, the Yeşilyurt Group was deposited in the northern part of the Maden Basin and the Helete volcanic arc. The Middle-Upper Eocene Malatya Basin was formed due to block faulting at the beginning of the Middle Eocene time. During the Late Paleocene-Early Eocene, and at the end of the Eocene, the study areas became continental due to the southward advance of nappe structures. The rock sequences in the southern part of the Malatya Basin may be divided into four

  19. Enhanced virome sequencing using targeted sequence capture.

    Science.gov (United States)

    Wylie, Todd N; Wylie, Kristine M; Herter, Brandi N; Storch, Gregory A

    2015-12-01

    Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ∼1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications.

  20. DNA sequences encoding erythropoietin

    Energy Technology Data Exchange (ETDEWEB)

    Lin, F.K.

    1987-10-27

    A purified and isolated DNA sequence is described consisting essentially of a DNA sequence encoding a polypeptide having an amino acid sequence sufficiently duplicative of that of erythropoietin to allow possession of the biological property of causing bone marrow cells to increase production of reticulocytes and red blood cells, and to increase hemoglobin synthesis or iron uptake.

  1. Sequence development of a latest Devonian-Tournaisian distally-steepened mixed carbonate-siliciclastic ramp, Canning Basin, Australia

    Science.gov (United States)

    Seyedmehdi, Zahra; George, Annette D.; Tucker, Maurice E.

    2016-03-01

    The sequence development and evolution of latest Devonian-earliest Carboniferous Fairfield Group in the Canning Basin have been established through integration of detailed sedimentological analysis of core, petrophysical data, existing biostratigraphic data and new seismic interpretations. The Fairfield Group on the Lennard Shelf was deposited on a mixed carbonate-siliciclastic distally-steepened ramp with a broad inner ramp, narrow mid ramp and steepened outer ramp. The majority of facies associations (FA1-FA8) were formed in intertidal-shallow subtidal conditions in proximal to distal inner ramp including siliciclastic tidal flats (FA1), carbonate intertidal flats (FA2), tidal flats and channels (FA3), lagoons (FA4-FA5), and shallow subtidal (FA6), backshoal (FA7) and fore-shoal areas (FA8). Bioclastic muddy sandstone (FA9) and bioclastic mudstone (FA10) are the dominant mid-ramp facies. Recognition of turbiditic facies of middle to lower slope of the outer ramp (FA11-FA13) led to the identification of a distally-steepened ramp. Antecedent topography exerted a significant control on platform morphology and the development of the widespread inner-ramp facies on the Lennard Shelf. A sequence-stratigraphic analysis reveals that the Fairfield Group ramp deposits consists of four third-order sequences (S1-S4) that were largely deposited during sea-level highstands (HST) characterized by progradational trends and dominant shallow subtidal inner-ramp facies associations. Transgressive systems tracts (TST) are well developed in S1 and S3 and have a retrogradational facies pattern with dominant deep subtidal mid-outer ramp facies associations. Lowstand systems tracts, characterized by lowstand wedges and turbiditic facies, are identified in the lower parts of S2 and S3. Coarse and fine-grained siliciclastic facies are mixed with carbonate facies as a result of coeval deposition on the inner and mid ramp, and reciprocal deposition on the outer ramp. A temporal variation in

  2. Low autocorrelation binary sequences

    Science.gov (United States)

    Packebusch, Tom; Mertens, Stephan

    2016-04-01

    Binary sequences with minimal autocorrelations have applications in communication engineering, mathematics and computer science. In statistical physics they appear as groundstates of the Bernasconi model. Finding these sequences is a notoriously hard problem, that so far can be solved only by exhaustive search. We review recent algorithms and present a new algorithm that finds optimal sequences of length N in time O(N {1.73}N). We computed all optimal sequences for N≤slant 66 and all optimal skewsymmetric sequences for N≤slant 119.

  3. Repdigits in -Lucas Sequences

    Indian Academy of Sciences (India)

    Jhon J J Bravo; Florian Luca

    2014-05-01

    For an integer ≥ 2, let $(L_n^{(k)})_n$ be the -Lucas sequence which starts with $0,\\ldots,0,2,1$ ( terms) and each term afterwards is the sum of the preceding terms. In 2000, Luca (Port. Math. 57(2) 2000 243-254) proved that 11 is the largest number with only one distinct digit (the so-called repdigit) in the sequence $(L_n^{(2)})_n$. In this paper, we address a similar problem in the family of -Lucas sequences. We also show that the -Lucas sequences have similar properties to those of -Fibonacci sequences and occur in formulae simultaneously with the latter.

  4. On Maximal Green Sequences

    CERN Document Server

    Brüstle, Thomas; Pérotin, Matthieu

    2012-01-01

    Maximal green sequences are particular sequences of quiver mutations which were introduced by Keller in the context of quantum dilogarithm identities and independently by Cecotti-Cordova-Vafa in the context of supersymmetric gauge theory. Our aim is to initiate a systematic study of these sequences from a combinatorial point of view. Interpreting maximal green sequences as paths in various natural posets arising in representation theory, we prove the finiteness of the number of maximal green sequences for cluster finite quivers, affine quivers and acyclic quivers with at most three vertices. We also give results concerning the possible numbers and lengths of these maximal green sequences. Finally we describe an algorithm for computing maximal green sequences for arbitrary valued quivers which we used to obtain numerous explicit examples that we present.

  5. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    the feasibility of predicting the fetal KEL1 phenotype using next-generation sequencing (NGS) technology. STUDY DESIGN AND METHODS: The KEL1/2 single-nucleotide polymorphism was polymerase chain reaction (PCR) amplified with one adjoining base, and the PCR product was sequenced using a genome analyzer (GAIIx......, Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...

  6. Séquences biosédimentaires et environnement morphostructural sur l'escarpement de Malte (Campagne Escarmed 3 Biosedimentary Sequences and Morphostructural Environment on the Malta Escarpment (Escarmed 3 Campaign

    Directory of Open Access Journals (Sweden)

    Bizon G.

    2006-11-01

    Full Text Available La confrontation de données biostratigraphiques, sédimentologiques, minéralogiques, géochimiques et géotechniques obtenues sur quelques carottes de l'escarpement de Malte a amené à la définition d'une séquence biosédimentaire d'origine climatique sur le glacis. L'altération (érosion, hiatus de cette séquence, voire sa destructuration (turbidite, débris-flow sur la bordure et au pied de la falaise inférieure traduisent l'instabilité de cette marge, jusqu'au Pléistocène supérieur. Dans ce contexte morphostructural particulier, les facteurs dynamique et hydrologique sont également considérés. Les résultats biostratigraphiques (courbe climatique, subdivisions des carottes en différents intervalles, essais de corrélation s'appuient sur des données statistiques concernant les foraminifères planctoniques (comptage et sur la répartition des principaux foraminifères benthiques. A comparison of biostratigraphic, sedimentological, mineralogical, geochemical and geotechnical data obtained from several core samples from the Malta escarpment has resulted in the definition of a biosedimentary sequence of climatic origin on the continental rise. The weathering of this sequence (erosion, gap or even its destructuring (turbidite, debris flow on the edge and at the foot of the lower cliff reveal the instability of this margin up to the Upper Pleistocene. In this specific morphostructural context, the dynamic and hydrological factors are also considered. The biostratigraphic findings (climatic curve, subdivision of the core samples into different intervals, correlation tests are based on statistical data concerning the planktonic foraminifers (counting and on the distribution of the leading benthic foraminifers.

  7. Hardware bitstream sequence recognizer

    OpenAIRE

    Karpin, Oleksandr; Sokil, Volodymyr

    2009-01-01

    This paper describes how to implement in hardware a bistream sequence recognizer using the PSoC Pseudo Random Sequence Generator (PRS) User Module. The PRS can be used in digital communication systems with the serial data interface for automatic preamble detection and extraction, control words selection, etc.

  8. Cosmetology: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a cosmetology vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  9. DNA sequencing by CE.

    Science.gov (United States)

    Karger, Barry L; Guttman, András

    2009-06-01

    Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA-sequencing methods have evolved from the labor-intensive slab gel electrophoresis, through automated multiCE systems using fluorophore labeling with multispectral imaging, to the "next-generation" technologies of cyclic-array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes were only possible with the advent of modern sequencing technologies that were a result of step-by-step advances with a contribution of academics, medical personnel and instrument companies. While next-generation sequencing is moving ahead at breakneck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of CE in DNA sequencing based in part of several of our articles in this journal.

  10. Sequencing the maize genome.

    Science.gov (United States)

    Martienssen, Robert A; Rabinowicz, Pablo D; O'Shaughnessy, Andrew; McCombie, W Richard

    2004-04-01

    Sequencing of complex genomes can be accomplished by enriching shotgun libraries for genes. In maize, gene-enrichment by copy-number normalization (high C(0)t) and methylation filtration (MF) have been used to generate up to two-fold coverage of the gene-space with less than 1 million sequencing reads. Simulations using sequenced bacterial artificial chromosome (BAC) clones predict that 5x coverage of gene-rich regions, accompanied by less than 1x coverage of subclones from BAC contigs, will generate high-quality mapped sequence that meets the needs of geneticists while accommodating unusually high levels of structural polymorphism. By sequencing several inbred strains, we propose a strategy for capturing this polymorphism to investigate hybrid vigor or heterosis.

  11. RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

    OpenAIRE

    Shibata, Kazuhiro; Itoh, Masayoshi; Aizawa, Katsunori; Nagaoka, Sumiharu; Sasaki, Nobuya; Carninci, Piero; Konno, Hideaki; AKIYAMA, Junichi; Nishi, Katsuo; Kitsunai, Tokuji; Tashiro, Hideo; Itoh, Mari; Sumi, Noriko; Ishii, Yoshiyuki; Nakamura, Shin

    2000-01-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto seque...

  12. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  13. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  14. Formation of source and reservoir rocks in a sequence stratigraphic framework Jameson Land East Greenland

    Energy Technology Data Exchange (ETDEWEB)

    Piasecki, S.; Dam, G.; Hansen, C.F.; Koppelhus, E.B.; Stemmerik, L.; Surlyk, F.

    1996-12-31

    Sedimentological, biostratigraphical and sequence stratigraphical analyses of East Greenland sedimentary successions with significant source and reservoir qualities have resulted in a major increase in the understanding of their depositional conditions, distribution and geometry`s. A biostratigraphical scheme of the Jurassic succession based on spores, pollen and dinoflaggelate cyst has been constructed for correlation and dating of the very detailed sequence stratigraphical units across the North Atlantic Ocean. Middle and Upper Jurassic dinoflaggelate stratigraphy is closely correlated to Boreal ammonite stratigraphy and deviations from the NW-European standard dinocyst stratigraphy have been recorded. The Upper Permian Folvik Creek Group was deposited in a marine, carbonate-dominated depositional system under arid climatic conditions. The organic-rich shales of the Ravnefjeld Formation represents highstand systems tracts. Reservoir rocks were formed by secondary dissolution of carbonates which were exposed during low relativ sea-level and as sandy turbidites deposited in lowstand systems tract. The uppermost Triassic - lowermost Jurassic Kap Stewart Group was deposited in a large rift lake. Organic-rich shales were deposited distally during lake level highstand. Deltaic reservoir sandstones were deposited in lowstand systems tracts as a respond to forced regressin induced by rapid variations in relative lake-level. The overlying marine Jurassic deposits include several sandstone units with reservoir potential representing both lowstand and high stand systems tracts. The organic rich mudstones were only developed as potential source rocks for oil when the deposition was combined with high marine organic production and basinal anoxic conditions e.g. during deposition of the Middle Jurassic Sortehat Formation and the Upper Jurassic Hareelv Formations. Several of the largestloilfields in the North Sea and on the Norwegian shelf have close analogues in the Jurassic

  15. Formation of source and reservoir rocks in a sequence stratigraphic framework Jameson Land East Greenland

    Energy Technology Data Exchange (ETDEWEB)

    Piasecki, S.; Dam, G.; Hansen, C.F.; Koppelhus, E.B.; Stemmerik, L.; Surlyk, F.

    1996-12-31

    Sedimentological, biostratigraphical and sequence stratigraphical analyses of East Greenland sedimentary successions with significant source and reservoir qualities have resulted in a major increase in the understanding of their depositional conditions, distribution and geometry`s. A biostratigraphical scheme of the Jurassic succession based on spores, pollen and dinoflaggelate cyst has been constructed for correlation and dating of the very detailed sequence stratigraphical units across the North Atlantic Ocean. Middle and Upper Jurassic dinoflaggelate stratigraphy is closely correlated to Boreal ammonite stratigraphy and deviations from the NW-European standard dinocyst stratigraphy have been recorded. The Upper Permian Folvik Creek Group was deposited in a marine, carbonate-dominated depositional system under arid climatic conditions. The organic-rich shales of the Ravnefjeld Formation represents highstand systems tracts. Reservoir rocks were formed by secondary dissolution of carbonates which were exposed during low relativ sea-level and as sandy turbidites deposited in lowstand systems tract. The uppermost Triassic - lowermost Jurassic Kap Stewart Group was deposited in a large rift lake. Organic-rich shales were deposited distally during lake level highstand. Deltaic reservoir sandstones were deposited in lowstand systems tracts as a respond to forced regressin induced by rapid variations in relative lake-level. The overlying marine Jurassic deposits include several sandstone units with reservoir potential representing both lowstand and high stand systems tracts. The organic rich mudstones were only developed as potential source rocks for oil when the deposition was combined with high marine organic production and basinal anoxic conditions e.g. during deposition of the Middle Jurassic Sortehat Formation and the Upper Jurassic Hareelv Formations. Several of the largest oilfields in the North Sea and on the Norwegian shelf have close analogues in the Jurassic

  16. Appalachian Blue Ridge cover sequence ranges at least into the Ordovician

    Science.gov (United States)

    Tull, James F.; Ausich, William I.; Groszos, Mark S.; Thompson, Troy W.

    1993-03-01

    The first direct evidence that stratified rocks of the central core of the southern Appalachian Blue Ridge range in age into the Paleozoic comes from a pelmatozoan echinoderm column discovered within a unit directly above the Murphy Marble in North Carolina. Before this discovery most geologists had considered all stratified rocks of the Blue Ridge east of the frontal imbricate thrust blocks to be Late Proterozoic or Early Cambrian(?). The echinoderm fragment is in a lower amphibolite facies interbedded mica schist-impure marble zone that lies directly above the Murphy Marble. Rocks above the Murphy Marble are dominantly turbiditic metaclastic rocks with minor carbonate and metavolcanic rocks, interpreted as having formed within a successor basin unconformably above upper Precambrian rift facies and lower Paleozoic drift facies rocks of the Laurentian passive margin. An upper bound for the age of the successor basin in the Murphy belt has not been established; similar sequences in the Talladega belt to the southwest, and possibly the Foothills belt to the west, range at least into the Devonian. Most Appalachian tectonic models assert that during the Taconic orogeny a Middle Ordovician synorogenic clastic wedge, now located in the easternmost Tennessee foreland salient, was derived by erosion from the metamorphosed pre-Ordovician Blue Ridge basement and cover sequence to the east, which was uplifted as part of an advancing Taconic crystalline thrust wedge. The presence of Ordovician or younger rocks described here, which were deposited east of the proposed Taconic orogenic front, suggests the need to modify models for Taconic clastic wedge formation in the southern Appalachians. The results presented here also suggest that peak metamorphism in the region was post-Ordovician, and thus was probably not contemporaneous with the Taconic orogeny, as previously thought.

  17. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  18. Scope and Sequence.

    Science.gov (United States)

    Callison, Daniel

    2002-01-01

    Discusses scope and sequence plans for curriculum coordination in elementary and secondary education related to school libraries. Highlights include library skills; levels of learning objectives; technology skills; media literacy skills; and information inquiry skills across disciplines by grade level. (LRW)

  19. Evolution of DNA sequencing

    National Research Council Canada - National Science Library

    Tipu, Hamid Nawaz; Shabbir, Ambreen

    2015-01-01

    Sanger and coworkers introduced DNA sequencing in 1970s for the first time. It principally relied on termination of growing nucleotide chain when a dideoxythymidine triphosphate (ddTTP) was inserted...

  20. Pierre Robin sequence

    Science.gov (United States)

    Pierre Robin syndrome; Pierre Robin complex; Pierre Robin anomaly ... The exact causes of Pierre Robin sequence are unknown. It may be part of many genetic syndromes. The lower jaw develops slowly before birth, but may grow ...

  1. In Favor of Sequencing?

    NARCIS (Netherlands)

    van der Borgh, G.J.C.

    2014-01-01

    This short article is a contribution to an online discussion about political sequencing and stability. It argues that despite all the risks of democratization in fragile states,a more gradual approach should be preferred.

  2. Gomphid DNA sequence data

    Data.gov (United States)

    U.S. Environmental Protection Agency — DNA sequence data for several genetic loci. This dataset is not publicly accessible because: It's already publicly available on GenBank. It can be accessed through...

  3. Text Mining: (Asynchronous Sequences

    Directory of Open Access Journals (Sweden)

    Sheema Khan

    2014-12-01

    Full Text Available In this paper we tried to correlate text sequences those provides common topics for semantic clues. We propose a two step method for asynchronous text mining. Step one check for the common topics in the sequences and isolates these with their timestamps. Step two takes the topic and tries to give the timestamp of the text document. After multiple repetitions of step two, we could give optimum result.

  4. Malaria Genome Sequencing Project

    Science.gov (United States)

    2004-01-01

    million cases and up to 2.7 million A whole chromosome shotgun sequencing strategy was used to deaths from malaria each year. The mortality levels are...deaths from malaria each year. The mortality levels are greatest in determine the genome sequence of P. falciparum clone 3D7. This sub-Saharan Africa...aminolevulinic acid dehydratase. Cura . Genet. 40, 391-398 (2002). 15. Lasonder, E. et al Analysis of the Plasmodium falciparum proteome by high-accuracy mass

  5. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene......This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis...

  6. Genome sequencing conference II

    Energy Technology Data Exchange (ETDEWEB)

    1990-01-01

    Genome Sequencing Conference 2 was held September 30 to October 30, 1990. 26 speaker abstracts and 33 poster presentations were included in the program report. New and improved methods for DNA sequencing and genetic mapping were presented. Many of the papers were concerned with accuracy and speed of acquisition of data with computers and automation playing an increasing role. Individual papers have been processed separately for inclusion on the database.

  7. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  8. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed Affan

    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.

  9. Controlled processing during sequencing.

    Science.gov (United States)

    Thothathiri, Malathi; Rattinger, Michelle

    2015-01-01

    Longstanding evidence has identified a role for the frontal cortex in sequencing within both linguistic and non-linguistic domains. More recently, neuropsychological studies have suggested a specific role for the left premotor-prefrontal junction (BA 44/6) in selection between competing alternatives during sequencing. In this study, we used neuroimaging with healthy adults to confirm and extend knowledge about the neural correlates of sequencing. Participants reproduced visually presented sequences of syllables and words using manual button presses. Items in the sequence were presented either consecutively or concurrently. Concurrent presentation is known to trigger the planning of multiple responses, which might compete with one another. Therefore, we hypothesized that regions involved in controlled processing would show greater recruitment during the concurrent than the consecutive condition. Whole-brain analysis showed concurrent > consecutive activation in sensory, motor and somatosensory cortices and notably also in rostral-dorsal anterior cingulate cortex. Region of interest analyses showed increased activation within left BA 44/6 and correlation between this region's activation and behavioral response times. Functional connectivity analysis revealed increased connectivity between left BA 44/6 and the posterior lobe of the cerebellum during the concurrent than the consecutive condition. These results corroborate recent evidence and demonstrate the involvement of BA 44/6 and other control regions when ordering co-activated representations.

  10. Controlled processing during sequencing

    Directory of Open Access Journals (Sweden)

    Malathi eThothathiri

    2015-10-01

    Full Text Available Longstanding evidence has identified a role for the frontal cortex in sequencing within both linguistic and non-linguistic domains. More recently, neuropsychological studies have suggested a specific role for the left premotor-prefrontal junction (BA 44/6 in selection between competing alternatives during sequencing. In this study, we used neuroimaging with healthy adults to confirm and extend knowledge about the neural correlates of sequencing. Participants reproduced visually presented sequences of syllables and words using manual button presses. Items in the sequence were presented either consecutively or concurrently. Concurrent presentation is known to trigger the planning of multiple responses, which might compete with one another. Therefore, we hypothesized that regions involved in controlled processing would show greater recruitment during the concurrent than the consecutive condition. Whole-brain analysis showed concurrent > consecutive activation in sensory, motor and somatosensory cortices and notably also in rostral-dorsal anterior cingulate cortex (ACC. Region of interest analyses showed increased activation within left BA 44/6 and correlation between this region’s activation and behavioral response times. Functional connectivity analysis revealed increased connectivity between left BA 44/6 and the posterior lobe of the cerebellum during the concurrent than the consecutive condition. These results corroborate recent evidence and demonstrate the involvement of BA 44/6 and other control regions when ordering co-activated representations.

  11. Program Synthesizes UML Sequence Diagrams

    Science.gov (United States)

    Barry, Matthew R.; Osborne, Richard N.

    2006-01-01

    A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.

  12. Sequencing BPS Spectra

    CERN Document Server

    Gukov, Sergei; Saberi, Ingmar; Stosic, Marko; Sulkowski, Piotr

    2015-01-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincar\\'e polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (refined) modular $S$-matrix. This leads to the identifi...

  13. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    information obtained allows well for statistical analysis of the data. This general approach can be integrated into current laboratory practice and has numerous applications. Besides DNA-based predictions of blood group phenotypes, platelet phenotypes, or sickle cell anemia, and the determination of zygosity......, Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...

  14. Sedimentology and Sequence Stratigraphy of the Lower Cretaceous Fortress Mountain and Torok Formations Exposed Along the Siksikpuk River, North-Central Alaska

    Science.gov (United States)

    Houseknecht, David W.; Schenk, Christopher J.; Wartes, Marwan A.

    2007-01-01

    An exposure of the Lower Cretaceous Fortress Mountain and Torok Formations along the Siksikpuk River in north-central Alaska provides a rare opportunity to observe the stratigraphic contact between these two formations and to interpret the depositional facies and sequence stratigraphy of the exposed strata. The Fortress Mountain Formation at the base of the measured section includes braided-fluvial and coastal-plain facies deposited in a lowstand-systems tract, and an overlying succession of mostly shallow marine facies deposited in the basal part of a transgressive-systems tract. The overlying Torok Formation includes a thick, upward-deepening succession of marine-shelf to marine-slope facies deposited in the upper part of the transgressive-systems tract. The upper part of the section includes marine-slope and incised-slope-channel turbidite deposits of the Torok Formation, interpreted as a highstand-systems tract. Consideration of the balance between accommodation and sediment flux inferred from the sequence-stratigraphic analysis suggests that both tectonics and eustasy may have influenced deposition of the lowstand-systems and transgressive-systems tracts. In contrast, the highstand-systems tract may have been primarily influenced by progradation of a regional sediment-dispersal system and by subsidence induced by sediment loading.

  15. Family Sequencing and Cooperation

    NARCIS (Netherlands)

    Grundel, S.; Ciftci, B.B.; Borm, P.E.M.; Hamers, H.J.M.

    2012-01-01

    To analyze the allocation problem of the maximal cost savings of the whole group of jobs, we define and analyze a so-called corresponding cooperative family sequencing game which explicitly takes into account the maximal cost savings for any coalition of jobs. Using nonstandard techniques we prove t

  16. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak Syst

  17. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak

  18. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene...

  19. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

  20. Rapid-Sequence Intubation

    Directory of Open Access Journals (Sweden)

    Evangelina Dávila Cabo de Villa

    2015-09-01

    Full Text Available In medical practice there are several situations that require immediate intervention of the airway in some patients, in order to ensure proper entrance and exit of gases into and out of the lungs and prevent aspiration. Rapid-sequence intubation has been considered as the administration of a hypnotic agent and a neuromuscular relaxant consecutively (virtually simultaneously to facilitate orotracheal intubation in critically ill patients and minimize the risk of aspiration. This paper aims to collect elements that promote a successful medical management according to the situation presented, since there is no single way of proceeding in case of rapid-sequence intubation. The elements to consider include: knowing the anatomy of the upper respiratory tract, having a group of drugs to choose from, receiving adequate training and having an alternative plan for the difficulties that may arise.

  1. Sequence Classification: 885394 [

    Lifescience Database Archive (English)

    Full Text Available 703); The expression pattern of this gene is described in PMID:12000842; possible frameshift detected when compared...Non-TMB TMH Non-TMB Non-TMB Non-TMB Non-TMB >gi|23619146|ref|NP_705108.1| Slight di...fference exist when compared to the published sequence of EBL-1 from Dd2 strain of P. falciparum (PMID:10613

  2. Sequencing of aromatase inhibitors

    OpenAIRE

    2005-01-01

    Since the development of the third-generation aromatase inhibitors (AIs), anastrozole, letrozole and exemestane, these agents have been the subject of intensive research to determine their optimal use in advanced breast cancer. Not only have they replaced progestins in second-line therapy and challenged the role of tamoxifen in first-line, but there is also evidence for a lack of cross-resistance between the steroidal and nonsteroidal AIs, meaning that they may be used in sequence to obtain p...

  3. Properties of Semijoin Sequences

    Institute of Scientific and Technical Information of China (English)

    BengC.Ooi; B.Srinivasan

    1989-01-01

    The problem of finding optimum semijoin sequ4ence of an arbitrary query under linear cost function for the transmission cost is NP.hard.Hence heuristic algorithms with desirable properties are explored.In this paper four properties of semijoin programs for distributed query processing are identified,The use of these properties in constructing semijoin sequence is justified.An existing algorithm is modified incorporating these properties.Empirical comparison with existing algorithms shows the superiority of the proposed algorithm.

  4. Learning Sequence Neighbourhood Metrics

    CERN Document Server

    Bayer, Justin; van der Smagt, Patrick

    2011-01-01

    Recurrent neural networks (RNNs) in combination with a pooling operator and the neighbourhood components analysis (NCA) objective function are able to detect the characterizing dynamics of sequences and embed them into a fixed-length vector space of arbitrary dimensionality. Subsequently, the resulting features are meaningful and can be used for visualization or nearest neighbour classification in linear time. This kind of metric learning for sequential data enables the use of algorithms tailored towards fixed length vector spaces such as R^n.

  5. Sequencing BPS spectra

    Science.gov (United States)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-03-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d {N}=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  6. Image sequence analysis

    CERN Document Server

    1981-01-01

    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  7. The Galaxy End Sequence

    Science.gov (United States)

    Eales, Stephen; de Vis, Pieter; Smith, Matthew W. L.; Appah, Kiran; Ciesla, Laure; Duffield, Chris; Schofield, Simon

    2017-03-01

    A common assumption is that galaxies fall in two distinct regions of a plot of specific star formation rate (SSFR) versus galaxy stellar mass: a star-forming galaxy main sequence (GMS) and a separate region of 'passive' or 'red and dead galaxies'. Starting from a volume-limited sample of nearby galaxies designed to contain most of the stellar mass in this volume, and thus representing the end-point of ≃12 billion years of galaxy evolution, we investigate the distribution of galaxies in this diagram today. We show that galaxies follow a strongly curved extended GMS with a steep negative slope at high galaxy stellar masses. There is a gradual change in the morphologies of the galaxies along this distribution, but there is no clear break between early-type and late-type galaxies. Examining the other evidence that there are two distinct populations, we argue that the 'red sequence' is the result of the colours of galaxies changing very little below a critical value of the SSFR, rather than implying a distinct population of galaxies. Herschel observations, which show at least half of early-type galaxies contain a cool interstellar medium, also imply continuity between early-type and late-type galaxies. This picture of a unitary population of galaxies requires more gradual evolutionary processes than the rapid quenching process needed to explain two distinct populations. We challenge theorists to predict quantitatively the properties of this 'Galaxy End Sequence'.

  8. Sequencing BPS spectra

    Energy Technology Data Exchange (ETDEWEB)

    Gukov, Sergei [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Max-Planck-Institut für Mathematik,Vivatsgasse 7, D-53111 Bonn (Germany); Nawata, Satoshi [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Centre for Quantum Geometry of Moduli Spaces, University of Aarhus,Nordre Ringgade 1, DK-8000 (Denmark); Saberi, Ingmar [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Stošić, Marko [CAMGSD, Departamento de Matemática, Instituto Superior Técnico,Av. Rovisco Pais, 1049-001 Lisbon (Portugal); Mathematical Institute SANU,Knez Mihajlova 36, 11000 Belgrade (Serbia); Sułkowski, Piotr [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland)

    2016-03-02

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  9. Information Theory of DNA Sequencing

    CERN Document Server

    Motahari, Abolfazl; Tse, David

    2012-01-01

    DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are assembled to reconstruct the original sequence. By drawing an analogy between the DNA sequencing problem and the classic communication problem, we define an information theoretic notion of sequencing capacity. This is the maximum number of DNA base pairs that can be resolved reliably per read, and provides a fundamental limit to the performance that can be achieved by any assembly algorithm. We compute the sequencing capacity explicitly for a simple statistical model of the DNA sequence and the read process. Using this framework, we also study the impact of noise in the read process on the sequencing capacity.

  10. A vision for ubiquitous sequencing.

    Science.gov (United States)

    Erlich, Yaniv

    2015-10-01

    Genomics has recently celebrated reaching the $1000 genome milestone, making affordable DNA sequencing a reality. With this goal successfully completed, the next goal of the sequencing revolution can be sequencing sensors--miniaturized sequencing devices that are manufactured for real-time applications and deployed in large quantities at low costs. The first part of this manuscript envisions applications that will benefit from moving the sequencers to the samples in a range of domains. In the second part, the manuscript outlines the critical barriers that need to be addressed in order to reach the goal of ubiquitous sequencing sensors.

  11. Psychoacoustic Properties of Fibonacci Sequences

    Directory of Open Access Journals (Sweden)

    J. Sokoll

    2008-01-01

    Full Text Available 1202, Fibonacci set up one of the most interesting sequences in number theory. This sequence can be represented by so-called Fibonacci Numbers, and by a binary sequence of zeros and ones. If such a binary Fibonacci Sequence is played back as an audio file, a very dissonant sound results. This is caused by the “almost-periodic”, “self-similar” property of the binary sequence. The ratio of zeros and ones converges to the golden ratio, as do the primary and secondary spectral components intheir frequencies and amplitudes. These Fibonacci Sequences will be characterized using listening tests and psychoacoustic analyses. 

  12. Sedimentology and sequence stratigraphy of the Cretaceous Nanushuk, Seabee, and Tuluvak formations exposed on Umiat Mountain, north-central Alaska

    Science.gov (United States)

    Houseknecht, David W.; Schenk, Christopher J.

    2005-01-01

    Upper Cretaceous strata of the upper part of the Nanushuk Formation, the Seabee Formation, and the lower part of the Tuluvak Formation are exposed along the Colville River on the east flank of Umiat Mountain in north-central Alaska. The Ninuluk sandstone, which is the uppermost unit of the Nanushuk Formation, displays a vertical succession of facies indicative of deposition in an upward-deepening estuarine through shoreface setting. A marine-flooding surface lies between the Ninuluk sandstone and organic-rich shale of the basal part of the Seabee Formation. The Ninuluk sandstone and the lower part of the Seabee Formation are interpreted as components of a transgressive-systems tract. The lowest, well-exposed strata in the Seabee Formation are a succession of shoreface sandstone beds in the middle of the formation. Integration of outcrop information and the Umiat No. 11 well log suggests that this sandstone succession rests on a sequence boundary and is capped by a marine-flooding surface. The sandstone succession is interpreted as a lowstand-systems tract. The upper part of the Seabee Formation includes a thick interval of organic-rich shale deposited in a dysaerobic offshore environment, and the gradational Seabee-Tuluvak contact is a coarsening-upward shale-to-sandstone succession deposited in a prodelta/delta-front environment. The observation that the upper part of the Seabee Formation correlates with seismic clinoforms suggests that dysaerobic conditions extended well up onto the prodelta slope during intervals of transgression and highstand. Correlation of the Umiat Mountain outcrop section with well logs and seismic data suggests that sequence boundaries and lowstand shoreface deposits may be common in the Seabee Formation and that wave action may have been important in transporting sand to the paleoshelf margin. These conclusions may contribute to an enhanced understanding of sand distribution in prospective lowstand turbidite deposits in the subsurface of

  13. The Sediment Sequence in the Southern Gulf of California — Distribution, Thickness, Sedimentlogical and Rock Magnetic Properties

    Science.gov (United States)

    Fucugauchi, J. U.; Perez-Cruz, L.

    2008-05-01

    The Gulf of California is a young tectonic ocean basin formed by sea-floor spreading and transform faulting along the Pacific-North America plate boundary. The Gulf of California is an elongated narrow basin oriented almost N- S, and bordered by the Baja California peninsula and mainland Mexico. To the north, it limits with the basins and transform fault of the San Andreas, and in the south with the East Pacific Rise and transform faults of the Rivera and Cocos plates. Here we focus on the sediment sequence in the southern sector at the mouth of the Gulf and the margin and central basins, which constitute a rich archive of the Gulf tectonic opening, plate boundary reorganizations and the paleoclimatic and paleoenvironmental evolution. Marine magnetic anomalies can be traced to approximately 3.6 Ma ago in the area of the mouth of the Gulf. There are relatively few studies of magnetic mineralogy, rock magnetism, magnetostratigraphy and paleomagnetism in these marine sediments. Here we present initial results of a study on the distribution and relative thickness of the sediment sequences in the mouth of the Gulf from geophysical surveys. Relative distribution and thicknes of sediments correlate with the bathymetry and location with respect to spreading center, transform faults and margins of the peninsula and mainland Mexico. Main sediment sources are silicic rocks from the Comondu Formation in the Baja California peninsula and the intrusive and volcanic rocks in Jalisco and Nayarit, including the Puerto Vallarta batholith. Pluvial terrigenous, fine-grained eolian and biogenic sediments are present in the sediment cores with less frequent turbiditic and tephra deposits. Core analyses of rock magnetic properties and mineralogy at few locations are summarized and discussed in terms of sediment sources, transport and deposition processes, diagenesis, paleoceanographic and paleoclimatic evolution during the Late Quaternary.

  14. Nd isotopic compositions of the Tethyan Himalayan Sequence in southeastern Tibet

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The Himalayan orogen consists of three major lithologic units that are separated by two major north-dipping faults: the Lesser Himalayan Sequence (LHS) below the Main Central Thrust (MCT), the Greater Himalayan Crystalline Complex (GHC) above the MCT, and the Tethyan Himalayan Sequence (THS) juxtaposed by the South Tibet Detachment fault (STD) over the GHC. Due to widespread meta-morphism and intense deformation, differentiating the above three lithologic units is often difficult. This problem has been overcome by the use of Sm-Nd isotopic analysis. The previous studies suggested that the LHS can be clearly distinguished from the GHC and THS by their Nd isotope compositions. However, the lack of detailed and systematic Sm-Nd isotopic studies of the THS across the Himalaya in general has made differentiation of this unit from the nearby GHC impossible, as the two appear to share overlapping Nd compositions and model ages. To address this problem, we systematically sam-pled and analyzed Nd isotopes of the THS in southeastern Tibet directly north of Bhutan. Our study identifies two distinctive fields in a εNd -TDM plot. The first is defined by the εNd(210 Ma) values of -3.45 to -7.34 and TDM values of 1.15 to 1.29 Ga from a Late Triassic turbidite sequence, which are broadly similar to those obtained from the Lhasa block. The second field is derived from the Early Cretaceous meta-sedimentary rocks with εNd(130 Ma) values from -15.24 to -16.61 and TDM values from 1.63 to 2.00 Ga; these values are similar to those obtained from the Greater Himalayan Crystalline Complex in Bhutan directly south of our sampling traverse, which has εNd(130 Ma) values of -10.89 to -16.32 and Nd model ages (TDM) of 1.73 to 2.20 Ga. From the above observations, we suggest that the Late Triassic strata of the southeast Tibetan THS were derived from the Lhasa block in the north, while the Early Cretaceous strata of the THS were derived from a source similar to the High Himalayan Crystalline

  15. Infinite sequences and series

    CERN Document Server

    Knopp, Konrad

    1956-01-01

    One of the finest expositors in the field of modern mathematics, Dr. Konrad Knopp here concentrates on a topic that is of particular interest to 20th-century mathematicians and students. He develops the theory of infinite sequences and series from its beginnings to a point where the reader will be in a position to investigate more advanced stages on his own. The foundations of the theory are therefore presented with special care, while the developmental aspects are limited by the scope and purpose of the book. All definitions are clearly stated; all theorems are proved with enough detail to ma

  16. Next-Generation Sequencing Platforms

    Science.gov (United States)

    Mardis, Elaine R.

    2013-06-01

    Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

  17. Spaces of Ideal Convergent Sequences

    Directory of Open Access Journals (Sweden)

    M. Mursaleen

    2014-01-01

    Full Text Available In the present paper, we introduce some sequence spaces using ideal convergence and Musielak-Orlicz function ℳ=Mk. We also examine some topological properties of the resulting sequence spaces.

  18. Sequence Handling by Sequence Analysis Toolbox v1.0

    DEFF Research Database (Denmark)

    Ingrell, Christian Ravnsborg; Matthiesen, Rune; Jensen, Ole Nørregaard

    2006-01-01

    The fact that mass spectrometry have become a high-throughput method calls for bioinformatic tools for automated sequence handling and prediction. For efficient use of bioinformatic tools, it is important that these tools are integrated or interfaced with each other. The purpose of sequence...... analysis toolbox v1.0 was to have a general purpose sequence analyzing tool that can import sequences obtained by high-throughput sequencing methods. The program includes algorithms for calculation or prediction of isoelectric point, hydropathicity index, transmembrane segments, and glycosylphosphatidyl...

  19. The Galaxy End Sequence

    CERN Document Server

    Eales, Stephen; Smith, Matthew; Appah, Kiran; Ciesla, Laure; Duffield, Chris; Schofield, Simon

    2016-01-01

    A common assumption is that galaxies fall in two distinct regions on a plot of specific star-formation rate (SSFR) versus galaxy stellar mass: a star-forming Galaxy Main Sequence (GMS) and a separate region of `passive' or `red and dead galaxies'. Starting from a volume-limited sample of nearby galaxies designed to contain most of the stellar mass in this volume, and thus being a fair representation of the Universe at the end of 12 billion years of galaxy evolution, we investigate the distribution of galaxies in this diagram today. We show that galaxies follow a strongly curved extended GMS with a steep negative slope at high galaxy stellar masses. There is a gradual change in the morphologies of the galaxies along this distribution, but there is no clear break between early-type and late-type galaxies. Examining the other evidence that there are two distinct populations, we argue that the `red sequence' is the result of the colours of galaxies changing very little below a critical value of the SSFR, rather t...

  20. Rapid Polymer Sequencer

    Science.gov (United States)

    Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)

    2013-01-01

    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  1. Novel sequences propel familiar folds.

    Science.gov (United States)

    Jawad, Zahra; Paoli, Massimo

    2002-04-01

    Recent structure determinations have made new additions to a set of strikingly different sequences that give rise to the same topology. Proteins with a beta propeller fold are characterized by extreme sequence diversity despite the similarity in their three-dimensional structures. Several fold predictions, based in part on sequence repeats thought to match modular beta sheets, have been proved correct.

  2. Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

    DEFF Research Database (Denmark)

    Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon

    2012-01-01

    Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS...... the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56...... MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types...

  3. RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

    Science.gov (United States)

    Shibata, Kazuhiro; Itoh, Masayoshi; Aizawa, Katsunori; Nagaoka, Sumiharu; Sasaki, Nobuya; Carninci, Piero; Konno, Hideaki; Akiyama, Junichi; Nishi, Katsuo; Kitsunai, Tokuji; Tashiro, Hideo; Itoh, Mari; Sumi, Noriko; Ishii, Yoshiyuki; Nakamura, Shin; Hazama, Makoto; Nishine, Tsutomu; Harada, Akira; Yamamoto, Rintaro; Matsumoto, Hiroyuki; Sakaguchi, Sumito; Ikegami, Takashi; Kashiwagi, Katsuya; Fujiwake, Syuji; Inoue, Kouji; Togawa, Yoshiyuki; Izawa, Masaki; Ohara, Eiji; Watahiki, Masanori; Yoneda, Yuko; Ishikawa, Tomokazu; Ozawa, Kaori; Tanaka, Takumi; Matsuura, Shuji; Kawai, Jun; Okazaki, Yasushi; Muramatsu, Masami; Inoue, Yorinao; Kira, Akira; Hayashizaki, Yoshihide

    2000-01-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3′ end and 5′ end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can

  4. RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer.

    Science.gov (United States)

    Shibata, K; Itoh, M; Aizawa, K; Nagaoka, S; Sasaki, N; Carninci, P; Konno, H; Akiyama, J; Nishi, K; Kitsunai, T; Tashiro, H; Itoh, M; Sumi, N; Ishii, Y; Nakamura, S; Hazama, M; Nishine, T; Harada, A; Yamamoto, R; Matsumoto, H; Sakaguchi, S; Ikegami, T; Kashiwagi, K; Fujiwake, S; Inoue, K; Togawa, Y

    2000-11-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3' end and 5' end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can be

  5. Musical Sequences in Comics

    Directory of Open Access Journals (Sweden)

    Kieron Michael Brown

    2013-11-01

    Full Text Available Critical attention paid to the media of music and comics has historically focused on parallels between the temporal rhythm and pacing of music and the implied rhythm and temporality of comics (Eisner 2008, Godek 2007. Recent attention has begun to focus on both comics’ potential to represent the character of music (Whitted 2011 and the effects of musical images and themes on comics’ narratology (Peters 2013.    I suggest that analyses of comics that combine the traditional interplay of image and word with the use of elements of musical notation are able to shed further light on each of these areas, via the connotations and conventions of symbols pulled exclusively from the realms of music, and their integration with the other elements of the page in sequence.

  6. Solid phase sequencing of biopolymers

    Energy Technology Data Exchange (ETDEWEB)

    Cantor, Charles (Del Mar, CA); Koster, Hubert (La Jolla, CA)

    2010-09-28

    This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include DNA or RNA in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

  7. Seismic inversion for incoming sedimentary sequence in the Nankai Trough margin off Kumano Basin, southwest Japan

    Science.gov (United States)

    Naito, K.; Park, J.

    2012-12-01

    The Nankai Trough off southwest Japan is one of the best subduction-zone to study megathrust earthquake mechanism. Huge earthquakes have been repeated in the cycle of 100-150 years in the area, and in these days the next emergence of the earthquake becomes one of the most serious issue in Japan. Therefore, detailed descriptions of geological structure are urgently needed there. IODP (Integrated Ocean Drilling Program) have investigated this area in the NanTroSEIZE science plan. Seismic reflection, core sampling and borehole logging surveys have been executed during the NanTroSEIZE expeditions. Core-log-seismic data integration (CLSI) is useful for understanding the Nankai seismogenic zone. We use the seismic inversion method to do the CLSI. The seismic inversion (acoustic impedance inversion, A.I. inversion) is a method to estimate rock physical properties using seismic reflection and logging data. Acoustic impedance volume is inverted for seismic data with density and P-wave velocity of several boreholes with the technique. We use high-resolution 3D multi-channel seismic (MCS) reflection data obtained during KR06-02 cruise in 2006, and measured core sample properties by IODP Expeditions 322 and 333. P-wave velocities missing for some core sample are interpolated by the relationship between acoustic impedance and P-wave velocity. We used Hampson-Russell software for the seismic inversion. 3D porosity model is derived from the 3D acoustic impedance model to figure out rock physical properties of the incoming sedimentary sequence in the Nankai Trough off Kumano Basin. The result of our inversion analysis clearly shows heterogeneity of sediments; relatively high porosity sediments on the shallow layer of Kashinosaki Knoll, and distribution of many physical anomaly bands on volcanic and turbidite sediment layers around the 3D MCS survey area. In this talk, we will show 3D MCS, acoustic impedance, and porosity data for the incoming sedimentary sequence and discuss its

  8. Tephrostratigraphy during 3000 years recorded in the sedimentary sequence of Beppu Bay, central Kyushu, Japan

    Science.gov (United States)

    Takemura, K.; Yamada, K.; Kuwae, M.; Yamamoto, M.; Danhara, T.

    2012-12-01

    The tephrostratigraphy around Beppu Bay, central Japan, is investigated using a 9m-long sedimentary core (KT09-3) collected in 2009 with a piston corer. Beppu Bay is located to the east of active volcanic region in Kyushu Island in southwest Japan. Eruptive history of their active volcanoes and widespread tephra records may be preserved in the sedimentary sequence in bay environment. A method to determine the down-hole content of volcanic glass was used in this study. This method consists of four steps: (1) continuous measurement of magnetic susceptibility with lithological observation of sediments, (2) systematic separation of the volcanic glass particles from samples taken at close intervals, and the determination of relative concentration; (3) mineral assemblages counted in the size of 63-125 micro meter fraction; (4) precise measurement of the refractive indices of the separated glass particles. A refractive index measuring system (RIMS) based on the thermal immersion method permitted quick and accurate measurement of the refractive index of a large number of samples. Core (KT09-3) is one of fourteen piston and gravity cores which were retrieved at the center of the basin. Correlation of cores was conducted using sand and silt seams related by events such as turbidite or flood or volcanic ash air fall, and the age-depth model was created by wiggle-matching of forty-two AMS radiocarbon dates from bivalve mollusk shells and excess Pb-210 and Cs-137 concentrations (Kuwae et al., 2012). The sedimentation rates were 230-300 cm/ky. Core is composed of massive diatomaceous clays with 18 event sediments of coarse fractions. Two distinct volcanic ash horizons and several cryptically deposited horizons are found within the sequence. Upper distinct volcanic ash of 509.2 cm depth is composed of many volcanic glasses and heavy minerals of Opx and Cpx with GHb and BHb. Most of volcanic glasses have characteristic high refractive index of about 1.559. This tephra is

  9. Solid phase sequencing of biopolymers

    Science.gov (United States)

    Cantor, Charles R.; Hubert, Koster

    2014-06-24

    This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Probes may be affixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

  10. Graphene nanodevices for DNA sequencing

    Science.gov (United States)

    Heerema, Stephanie J.; Dekker, Cees

    2016-02-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technology. In recent years, a wide range of creative ideas for graphene sequencers have been theoretically proposed and the first experimental demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technology.

  11. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  12. Nonlinear analysis of biological sequences

    Energy Technology Data Exchange (ETDEWEB)

    Torney, D.C.; Bruno, W.; Detours, V. [and others

    1998-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The main objectives of this project involved deriving new capabilities for analyzing biological sequences. The authors focused on tabulating the statistical properties exhibited by Human coding DNA sequences and on techniques of inferring the phylogenetic relationships among protein sequences related by descent.

  13. Biosensors for DNA sequence detection

    Science.gov (United States)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  14. Blazar Sequence in Fermi Era

    Indian Academy of Sciences (India)

    Liang Chen

    2014-09-01

    In this paper, we review the latest research results on the topic of blazar sequence. It seems that the blazar sequence is phenomenally ruled out, while the theoretical blazar sequence still holds. We point out that black hole mass is a dominated parameter accounting for high-power-high-synchrotron-peaked and low-power-low-sychrotron-peaked blazars. Because most blazars have similar size of emission region, theoretical blazar sequence implies that the break of Spectral Energy Distribution (SED) is a cooling break in nature.

  15. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  16. Assembly sequencing with toleranced parts

    Energy Technology Data Exchange (ETDEWEB)

    Latombe, J.C. [Stanford Univ., CA (United States). Robotics Lab.; Wilson, R.H. [Sandia National Labs., Albuquerque, NM (United States). Intelligent Systems and Robotics Center

    1995-02-21

    The goal of assembly sequencing is to plan a feasible series of operations to construct a product from its individual parts. Previous research has thoroughly investigated assembly sequencing under the assumption that parts have nominal geometry. This paper considers the case where parts have toleranced geometry. Its main contribution is an efficient procedure that decides if a product admits an assembly sequence with infinite translations that is feasible for all possible instances of the components within the specified tolerances. If the product admits one such sequence, the procedure can also generate it. For the cases where there exists no such assembly sequence, another procedure is proposed which generates assembly sequences that are feasible only for some values of the toleranced dimensions. If this procedure produces no such sequence, then no instance of the product is assemblable. Finally, this paper analyzes the relation between assembly and disassembly sequences in the presence of toleranced parts. This work assumes a simple, but non-trivial tolerance language that falls short of capturing all imperfections of a manufacturing process. Hence, it is only one step toward assembly sequencing with toleranced parts.

  17. SNMR pulse sequence phase cycling

    Science.gov (United States)

    Walsh, David O; Grunewald, Elliot D

    2013-11-12

    Technologies applicable to SNMR pulse sequence phase cycling are disclosed, including SNMR acquisition apparatus and methods, SNMR processing apparatus and methods, and combinations thereof. SNMR acquisition may include transmitting two or more SNMR pulse sequences and applying a phase shift to a pulse in at least one of the pulse sequences, according to any of a variety cycling techniques. SNMR processing may include combining SNMR from a plurality of pulse sequences comprising pulses of different phases, so that desired signals are preserved and indesired signals are canceled.

  18. The ontology of biological sequences

    Directory of Open Access Journals (Sweden)

    Kelso Janet

    2009-11-01

    Full Text Available Abstract Background Biological sequences play a major role in molecular and computational biology. They are studied as information-bearing entities that make up DNA, RNA or proteins. The Sequence Ontology, which is part of the OBO Foundry, contains descriptions and definitions of sequences and their properties. Yet the most basic question about sequences remains unanswered: what kind of entity is a biological sequence? An answer to this question benefits formal ontologies that use the notion of biological sequences and analyses in computational biology alike. Results We provide both an ontological analysis of biological sequences and a formal representation that can be used in knowledge-based applications and other ontologies. We distinguish three distinct kinds of entities that can be referred to as "biological sequence": chains of molecules, syntactic representations such as those in biological databases, and the abstract information-bearing entities. For use in knowledge-based applications and inclusion in biomedical ontologies, we implemented the developed axiom system for use in automated theorem proving. Conclusion Axioms are necessary to achieve the main goal of ontologies: to formally specify the meaning of terms used within a domain. The axiom system for the ontology of biological sequences is the first elaborate axiom system for an OBO Foundry ontology and can serve as starting point for the development of more formal ontologies and ultimately of knowledge-based applications.

  19. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  20. Sequence Algebra, Sequence Decision Diagrams and Dynamic Fault Trees

    Energy Technology Data Exchange (ETDEWEB)

    Rauzy, Antoine B., E-mail: Antoine.Rauzy@lix.polytechnique.f [LIX-CNRS, Computer Science, Ecole Polytechnique, 91128 Palaiseau Cedex (France)

    2011-07-15

    A large attention has been focused on the Dynamic Fault Trees in the past few years. By adding new gates to static (regular) Fault Trees, Dynamic Fault Trees aim to take into account dependencies among events. Merle et al. proposed recently an algebraic framework to give a formal interpretation to these gates. In this article, we extend Merle et al.'s work by adopting a slightly different perspective. We introduce Sequence Algebras that can be seen as Algebras of Basic Events, representing failures of non-repairable components. We show how to interpret Dynamic Fault Trees within this framework. Finally, we propose a new data structure to encode sets of sequences of Basic Events: Sequence Decision Diagrams. Sequence Decision Diagrams are very much inspired from Minato's Zero-Suppressed Binary Decision Diagrams. We show that all operations of Sequence Algebras can be performed on this data structure.

  1. Three-Distance Sequences with Three Symbols

    OpenAIRE

    SAKAMOTO, Kuniko

    2003-01-01

    We will show that every $3$ dimensional cutting sequence is a three-distance sequence, and there are uncountable many periodic or aperiodic three-distance sequences (with $3$-symbols) which are not $3$ dimensional cutting sequences.

  2. NSIT: novel sequence identification tool.

    Directory of Open Access Journals (Sweden)

    Benjarath Pupacdi

    Full Text Available Novel sequences are DNA sequences present in an individual's genome but absent in the human reference assembly. They are predicted to be biologically important, both individual and population specific, and consistent with the known human migration paths. Recent works have shown that an average person harbors 2-5 Mb of such sequences and estimated that the human pan-genome contains as high as 19-40 Mb of novel sequences. To identify them in a de novo genome assembly, some existing sequence aligners have been used but no computational method has been specifically proposed for this task. In this work, we developed NSIT (Novel Sequence Identification Tool, a software that can accurately and efficiently identify novel sequences in an individual's de novo whole genome assembly. We identified and characterized 1.1 Mb, 1.2 Mb, and 1.0 Mb of novel sequences in NA18507 (African, YH (Asian, and NA12878 (European de novo genome assemblies, respectively. Our results show very high concordance with the previous work using the respective reference assembly. In addition, our results using the latest human reference assembly suggest that the amount of novel sequences per individual may not be as high as previously reported. We additionally developed a graphical viewer for comparisons of novel sequence contents. The viewer also helped in identifying sequence contamination; we found 130 kb of Epstein-Barr virus sequence in the previously published NA18507 novel sequences as well as 287 kb of zebrafish repeats in NA12878 de novo assembly. NSIT requires [Formula: see text]2GB of RAM and 1.5-2 hrs on a commodity desktop. The program is applicable to input assemblies with varying contig/scaffold sizes, ranging from 100 bp to as high as 50 Mb. It works in both 32-bit and 64-bit systems and outperforms, by large margins, other fast sequence aligners previously applied to this task. To our knowledge, NSIT is the first software designed specifically for novel sequence

  3. PERIODIC COMPLEMENTARY BINARY SEQUENCE PAIRS

    Institute of Scientific and Technical Information of China (English)

    XuChengqian; ZhaoXiaoqun

    2002-01-01

    A new set of binary sequences-Periodic Complementary Binary Sequence Pair (PCSP)is proposed .A new class of block design-Difference Family Pair (DFP)is also proposed .The relationship between PCSP and DFP,the properties and exising conditions of PCSP and the recursive constructions for PCSP are given.

  4. PERIODIC COMPLEMENTARY BINARY SEQUENCE PAIRS

    Institute of Scientific and Technical Information of China (English)

    Xu Chengqian; Zhao Xiaoqun

    2002-01-01

    A new set of binary sequences-Periodic Complementary Binary Sequence Pair (PCSP) is proposed. A new class of block design-Difference Family Pair (DFP) is also proposed.The relationship between PCSP and DFP, the properties and existing conditions of PCSP and the recursive constructions for PCSP are given.

  5. DNA Sequencing Sensors: An Overview

    Directory of Open Access Journals (Sweden)

    Jose Antonio Garrido-Cardenas

    2017-03-01

    Full Text Available The first sequencing of a complete genome was published forty years ago by the double Nobel Prize in Chemistry winner Frederick Sanger. That corresponded to the small sized genome of a bacteriophage, but since then there have been many complex organisms whose DNA have been sequenced. This was possible thanks to continuous advances in the fields of biochemistry and molecular genetics, but also in other areas such as nanotechnology and computing. Nowadays, sequencing sensors based on genetic material have little to do with those used by Sanger. The emergence of mass sequencing sensors, or new generation sequencing (NGS meant a quantitative leap both in the volume of genetic material that was able to be sequenced in each trial, as well as in the time per run and its cost. One can envisage that incoming technologies, already known as fourth generation sequencing, will continue to cheapen the trials by increasing DNA reading lengths in each run. All of this would be impossible without sensors and detection systems becoming smaller and more precise. This article provides a comprehensive overview on sensors for DNA sequencing developed within the last 40 years.

  6. Gambling strategies for random sequences

    OpenAIRE

    George Davie

    2010-01-01

    There is a general consensus that it is not possible to gamble successfully against a random se-quence. This consensus is based on results from probability theory that all gambling systems arein some sense futile and the idea that at any stage of the sequence, the next outcome is entirelyunpredictable.

  7. Sequence conserved for subcellular localization

    Science.gov (United States)

    Nair, Rajesh; Rost, Burkhard

    2002-01-01

    The more proteins diverged in sequence, the more difficult it becomes for bioinformatics to infer similarities of protein function and structure from sequence. The precise thresholds used in automated genome annotations depend on the particular aspect of protein function transferred by homology. Here, we presented the first large-scale analysis of the relation between sequence similarity and identity in subcellular localization. Three results stood out: (1) The subcellular compartment is generally more conserved than what might have been expected given that short sequence motifs like nuclear localization signals can alter the native compartment; (2) the sequence conservation of localization is similar between different compartments; and (3) it is similar to the conservation of structure and enzymatic activity. In particular, we found the transition between the regions of conserved and nonconserved localization to be very sharp, although the thresholds for conservation were less well defined than for structure and enzymatic activity. We found that a simple measure for sequence similarity accounting for pairwise sequence identity and alignment length, the HSSP distance, distinguished accurately between protein pairs of identical and different localizations. In fact, BLAST expectation values outperformed the HSSP distance only for alignments in the subtwilight zone. We succeeded in slightly improving the accuracy of inferring localization through homology by fine tuning the thresholds. Finally, we applied our results to the entire SWISS-PROT database and five entirely sequenced eukaryotes. PMID:12441382

  8. Bayesian analysis of binary sequences

    Science.gov (United States)

    Torney, David C.

    2005-03-01

    This manuscript details Bayesian methodology for "learning by example", with binary n-sequences encoding the objects under consideration. Priors prove influential; conformable priors are described. Laplace approximation of Bayes integrals yields posterior likelihoods for all n-sequences. This involves the optimization of a definite function over a convex domain--efficiently effectuated by the sequential application of the quadratic program.

  9. Chameleon sequences in neurodegenerative diseases

    Energy Technology Data Exchange (ETDEWEB)

    Bahramali, Golnaz [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Goliaei, Bahram, E-mail: goliaei@ut.ac.ir [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Minuchehr, Zarrin, E-mail: minuchehr@nigeb.ac.ir [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of); Salari, Ali [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of)

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  10. Rapid Diagnostics of Onboard Sequences

    Science.gov (United States)

    Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

    2012-01-01

    Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command

  11. Spatiotemporal correlations of aftershock sequences

    CERN Document Server

    Peixoto, Tiago P; Davidsen, Jörn

    2010-01-01

    Aftershock sequences are of particular interest in seismic research since they may condition seismic activity in a given region over long time spans. While they are typically identified with periods of enhanced seismic activity after a large earthquake as characterized by the Omori law, our knowledge of the spatiotemporal correlations between events in an aftershock sequence is limited. Here, we study the spatiotemporal correlations of two aftershock sequences form California (Parkfield and Hector Mine) using the recently introduced concept of "recurrent" events. We find that both sequences have very similar properties and that most of them are captured by the space-time epidemic-type aftershock sequence (ETAS) model if one takes into account catalog incompleteness. However, the stochastic model does not capture the spatiotemporal correlations leading to the observed structure of seismicity on small spatial scales.

  12. Quantum Exchangeable Sequences of Algebras

    CERN Document Server

    Curran, Stephen

    2008-01-01

    We extend the notion of quantum exchangeability, introduced by K\\"ostler and Speicher in arXiv:0807.0677, to sequences (\\rho_1,\\rho_2,...c) of homomorphisms from an algebra C into a noncommutative probability space (A,\\phi), and prove a free de Finetti theorem: an infinite quantum exchangeable sequence (\\rho_1,\\rho_2,...c) is freely independent and identically distributed with respect to a conditional expectation. As a corollary we obtain a free analogue of the Hewitt Savage zero-one law. As in the classical case, the theorem fails for finite sequences. We give a characterization of finite quantum exchangeable sequences, which can be viewed as a noncommutative analogue of sampling without replacement. We then give an approximation to how far a finite quantum exchangeable sequence is from being freely independent with amalgamation.

  13. Ossification sequence heterochrony among amphibians.

    Science.gov (United States)

    Harrington, Sean M; Harrison, Luke B; Sheil, Christopher A

    2013-01-01

    Heterochrony is an important mechanism in the evolution of amphibians. Although studies have centered on the relationship between size and shape and the rates of development, ossification sequence heterochrony also may have been important. Rigorous, phylogenetic methods for assessing sequence heterochrony are relatively new, and a comprehensive study of the relative timing of ossification of skeletal elements has not been used to identify instances of sequence heterochrony across Amphibia. In this study, a new version of the program Parsimov-based genetic inference (PGi) was used to identify shifts in ossification sequences across all extant orders of amphibians, for all major structural units of the skeleton. PGi identified a number of heterochronic sequence shifts in all analyses, the most interesting of which seem to be tied to differences in metamorphic patterns among major clades. Early ossification of the vomer, premaxilla, and dentary is retained by Apateon caducus and members of Gymnophiona and Urodela, which lack the strongly biphasic development seen in anurans. In contrast, bones associated with the jaws and face were identified as shifting late in the ancestor of Anura. The bones that do not shift late, and thereby occupy the earliest positions in the anuran cranial sequence, are those in regions of the skull that undergo the least restructuring throughout anuran metamorphosis. Additionally, within Anura, bones of the hind limb and pelvic girdle were also identified as shifting early in the sequence of ossification, which may be a result of functional constraints imposed by the drastic metamorphosis of most anurans.

  14. A Criterion for Regular Sequences

    Indian Academy of Sciences (India)

    D P Patil; U Storch; J Stückrad

    2004-05-01

    Let be a commutative noetherian ring and $f_1,\\ldots,f_r \\in R$. In this article we give (cf. the Theorem in $\\mathcal{x}$2) a criterion for $f_1,\\ldots,f_r$ to be regular sequence for a finitely generated module over which strengthens and generalises a result in [2]. As an immediate consequence we deduce that if $V(g_1,\\ldots,g_r) \\subseteq V(f_1,\\ldots,f_r)$ in Spec and if $f_1,\\ldots,f_r$ is a regular sequence in , then $g_1,\\ldots,g_r$ is also a regular sequence in .

  15. Weak disorder in Fibonacci sequences

    Energy Technology Data Exchange (ETDEWEB)

    Ben-Naim, E [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Krapivsky, P L [Department of Physics and Center for Molecular Cybernetics, Boston University, Boston, MA 02215 (United States)

    2006-05-19

    We study how weak disorder affects the growth of the Fibonacci series. We introduce a family of stochastic sequences that grow by the normal Fibonacci recursion with probability 1 - {epsilon}, but follow a different recursion rule with a small probability {epsilon}. We focus on the weak disorder limit and obtain the Lyapunov exponent that characterizes the typical growth of the sequence elements, using perturbation theory. The limiting distribution for the ratio of consecutive sequence elements is obtained as well. A number of variations to the basic Fibonacci recursion including shift, doubling and copying are considered. (letter to the editor)

  16. Sedimentology, Petrography and Microfacies of the Paleogene Carbonate Sequence - Yaxcopoil-1 Borehole (Chicxulub, Yucatan)

    Science.gov (United States)

    Escobar-Sanchez, E.; Fucugauchi, J. U.

    2013-05-01

    the elevation. In the last meters of Unit 2 (778-772 m), a series of thin layers of marl and calcareous shale interbedded with wackestone are interpreted as a transgressive event. In the first few meters of Unit 3 provides greater energy currents causing variations in the grain size. Petrographic observations show that planktonic and benthic facies are arranged as intermittent flows in parts of the unit, which points to flow currents. Predominance of coarse-grained facies rich in carbonates possibly indicates a prograding event into deep areas. In the sequence several possible changes in sea level are recorded, especially from Unit 5 to 8 Unit, where a possible limit between the Paleocene and Eocene is located between Unit 6 and Unit 7, at about 660 m. Biostratigraphy was obtained by zones corresponding to P4 and P5. In Unit 8 contains the first record of turbidite or storm deposits outer shelf environments that could be related to platform progradation. The Paleocene-Eocene thermal maximum represents a period of global warming and sea level rise. The sedimentological and micropaleontological changes may be correlated with the faunal turnover in the Gulf of Mexico, providing a complementary tool for biostratigraphic inferences.

  17. Integrating sequence stratigraphy and rock-physics to interpret seismic amplitudes and predict reservoir quality

    Science.gov (United States)

    Dutta, Tanima

    This dissertation focuses on the link between seismic amplitudes and reservoir properties. Prediction of reservoir properties, such as sorting, sand/shale ratio, and cement-volume from seismic amplitudes improves by integrating knowledge from multiple disciplines. The key contribution of this dissertation is to improve the prediction of reservoir properties by integrating sequence stratigraphy and rock physics. Sequence stratigraphy has been successfully used for qualitative interpretation of seismic amplitudes to predict reservoir properties. Rock physics modeling allows quantitative interpretation of seismic amplitudes. However, often there is uncertainty about selecting geologically appropriate rock physics model and its input parameters, away from the wells. In the present dissertation, we exploit the predictive power of sequence stratigraphy to extract the spatial trends of sedimentological parameters that control seismic amplitudes. These spatial trends of sedimentological parameters can serve as valuable constraints in rock physics modeling, especially away from the wells. Consequently, rock physics modeling, integrated with the trends from sequence stratigraphy, become useful for interpreting observed seismic amplitudes away from the wells in terms of underlying sedimentological parameters. We illustrate this methodology using a comprehensive dataset from channelized turbidite systems, deposited in minibasin settings in the offshore Equatorial Guinea, West Africa. First, we present a practical recipe for using closed-form expressions of effective medium models to predict seismic velocities in unconsolidated sandstones. We use an effective medium model that combines perfectly rough and smooth grains (the extended Walton model), and use that model to derive coordination number, porosity, and pressure relations for P and S wave velocities from experimental data. Our recipe provides reasonable fits to other experimental and borehole data, and specifically

  18. Calculations of turbidite deposits and tsunamis from submarine landslides

    Energy Technology Data Exchange (ETDEWEB)

    Gisler, Galen R [Los Alamos National Laboratory; Weaver, Robert P [Los Alamos National Laboratory; Gittings, Michael L [Los Alamos National Laboratory

    2009-01-01

    Great underwater landslides like Storegga off the Norwegian coast leave massive deposits on the seafloor and must produce enormous tsunamis. Such events have occurred on continental slopes worldwide, and continue to do so. Triggers for such slides include earthquakes, gas hydrate releases, and underwater volcanos. We have petformed a numerical study of such landslides using the multi-material compressible hydrocode Sage in order to understand the relationship between the rheology of the slide material, the configuration of the resulting deposits on the seafloor, and the tsunami that is produced. Instabilities in the fluid-fluid mixing between slide material and seawater produce vortices and swirls with sizes that depend on the rheology of the slide material. These dynamical features of the flow may be preserved as ridges when the sliding material finally stops. Thus studying the configuration of the ridges in prehistoric slides may give us measures of the circumstances under which the slide was initiated. As part of this study, we have also done a convergence test showing that the slide velocity is sensitive to the resolution adopted in the simulation, but that extrapolation to infinite resolution is possible, and can yield good velocities. We will present two-dimensional simulations of schematic underwater slides for our study of rheology, and a three-dimensional simulation in bathymetric conditions that resemble the pre-Storegga Norwegian margin.

  19. ISIS Individualized Support In Sequencing

    NARCIS (Netherlands)

    Drachsler, Hendrik; Hummel, Hans

    2007-01-01

    Drachsler, H., & Hummel, H. G. K. (2007). ISIS Individualized Support In Sequencing. Presentation given during the PIP meeting on March 22, 2007. Open University of the Netherlands: Heerlen, The Netherlands.

  20. Molecular beacon sequence design algorithm.

    Science.gov (United States)

    Monroe, W Todd; Haselton, Frederick R

    2003-01-01

    A method based on Web-based tools is presented to design optimally functioning molecular beacons. Molecular beacons, fluorogenic hybridization probes, are a powerful tool for the rapid and specific detection of a particular nucleic acid sequence. However, their synthesis costs can be considerable. Since molecular beacon performance is based on its sequence, it is imperative to rationally design an optimal sequence before synthesis. The algorithm presented here uses simple Microsoft Excel formulas and macros to rank candidate sequences. This analysis is carried out using mfold structural predictions along with other free Web-based tools. For smaller laboratories where molecular beacons are not the focus of research, the public domain algorithm described here may be usefully employed to aid in molecular beacon design.

  1. Classification of Base Sequences (+1,

    Directory of Open Access Journals (Sweden)

    Dragomir Ž. Ðoković

    2010-01-01

    Full Text Available Base sequences BS(+1, are quadruples of {±1}-sequences (;;;, with A and B of length +1 and C and D of length n, such that the sum of their nonperiodic autocor-relation functions is a -function. The base sequence conjecture, asserting that BS(+1, exist for all n, is stronger than the famous Hadamard matrix conjecture. We introduce a new definition of equivalence for base sequences BS(+1, and construct a canonical form. By using this canonical form, we have enumerated the equivalence classes of BS(+1, for ≤30. As the number of equivalence classes grows rapidly (but not monotonically with n, the tables in the paper cover only the cases ≤13.

  2. DNA Sequencing Using capillary Electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Barry Karger

    2011-05-09

    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other

  3. Pythagorean Triples from Harmonic Sequences.

    Science.gov (United States)

    DiDomenico, Angelo S.; Tanner, Randy J.

    2001-01-01

    Shows how all primitive Pythagorean triples can be generated from harmonic sequences. Use inductive and deductive reasoning to explore how Pythagorean triples are connected with another area of mathematics. (KHR)

  4. Overview of Sequence Data Formats.

    Science.gov (United States)

    Zhang, Hongen

    2016-01-01

    Next-generation sequencing experiment can generate billions of short reads for each sample and processing of the raw reads will add more information. Various file formats have been introduced/developed in order to store and manipulate this information. This chapter presents an overview of the file formats including FASTQ, FASTA, SAM/BAM, GFF/GTF, BED, and VCF that are commonly used in analysis of next-generation sequencing data.

  5. Structural Complexity of DNA Sequence

    Directory of Open Access Journals (Sweden)

    Cheng-Yuan Liou

    2013-01-01

    Full Text Available In modern bioinformatics, finding an efficient way to allocate sequence fragments with biological functions is an important issue. This paper presents a structural approach based on context-free grammars extracted from original DNA or protein sequences. This approach is radically different from all those statistical methods. Furthermore, this approach is compared with a topological entropy-based method for consistency and difference of the complexity results.

  6. Nanogrid rolling circle DNA sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Church, George M.; Porreca, Gregory J.; Shendure, Jay; Rosenbaum, Abraham Meir

    2017-04-18

    The present invention relates to methods for sequencing a polynucleotide immobilized on an array having a plurality of specific regions each having a defined diameter size, including synthesizing a concatemer of a polynucleotide by rolling circle amplification, wherein the concatemer has a cross-sectional diameter greater than the diameter of a specific region, immobilizing the concatemer to the specific region to make an immobilized concatemer, and sequencing the immobilized concatemer.

  7. Pig genome sequence - analysis and publication strategy

    NARCIS (Netherlands)

    Archibald, A.L.; Bolund, L.; Churcher, C.; Fredholm, M.; Groenen, M.A.M.; Harlizius, B.

    2010-01-01

    Background - The pig genome is being sequenced and characterised under the auspices of the Swine Genome Sequencing Consortium. The sequencing strategy followed a hybrid approach combining hierarchical shotgun sequencing of BAC clones and whole genome shotgun sequencing. Results - Assemblies of the B

  8. Long-range barcode labeling-sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Feng; Zhang, Tao; Singh, Kanwar K.; Pennacchio, Len A.; Froula, Jeff L.; Eng, Kevin S.

    2016-10-18

    Methods for sequencing single large DNA molecules by clonal multiple displacement amplification using barcoded primers. Sequences are binned based on barcode sequences and sequenced using a microdroplet-based method for sequencing large polynucleotide templates to enable assembly of haplotype-resolved complex genomes and metagenomes.

  9. Sequencing and comparative analysis of the gorilla MHC genomic sequence.

    Science.gov (United States)

    Wilming, Laurens G; Hart, Elizabeth A; Coggill, Penny C; Horton, Roger; Gilbert, James G R; Clee, Chris; Jones, Matt; Lloyd, Christine; Palmer, Sophie; Sims, Sarah; Whitehead, Siobhan; Wiley, David; Beck, Stephan; Harrow, Jennifer L

    2013-01-01

    Major histocompatibility complex (MHC) genes play a critical role in vertebrate immune response and because the MHC is linked to a significant number of auto-immune and other diseases it is of great medical interest. Here we describe the clone-based sequencing and subsequent annotation of the MHC region of the gorilla genome. Because the MHC is subject to extensive variation, both structural and sequence-wise, it is not readily amenable to study in whole genome shotgun sequence such as the recently published gorilla genome. The variation of the MHC also makes it of evolutionary interest and therefore we analyse the sequence in the context of human and chimpanzee. In our comparisons with human and re-annotated chimpanzee MHC sequence we find that gorilla has a trimodular RCCX cluster, versus the reference human bimodular cluster, and additional copies of Class I (pseudo)genes between Gogo-K and Gogo-A (the orthologues of HLA-K and -A). We also find that Gogo-H (and Patr-H) is coding versus the HLA-H pseudogene and, conversely, there is a Gogo-DQB2 pseudogene versus the HLA-DQB2 coding gene. Our analysis, which is freely available through the VEGA genome browser, provides the research community with a comprehensive dataset for comparative and evolutionary research of the MHC.

  10. Using apatite fission track thermochronology to document the deformation sequence in an exhumed foreland basin: an example from the southern Pyrenees.

    Science.gov (United States)

    Meresse, F.; Labaume, P.; Jolivet, M.; Teixell, A.

    2009-04-01

    Université Montpellier 2, INSU-CNRS, Laboratoire Géosciences Montpellier, cc060, 34095 Montpellier Cedex 5, France florian.meresse@gm.univ-montp2.fr The study of foreland basins provides important constraints on the evolution of orogenic wedges. In particular, the study of tectonics-sedimentation relationships is essential to date the tectonic activity. However, processes linked to wedge growth are not always completely recorded by the tecto-sedimentary markers, and thermochronological study of the basin-fill can provide further insights. In this work, we have combined apatite fission track analysis (apatite FTA) with structural analysis to precise the timing of the deformation sequence and to characterise the coupling between thrust activity, burial and denudation in the south-Pyrenean foreland basin, a proximal foredeep of the Pyrenees that has been incorporated in the Pyrenean thrust wedge. We have focused the study on a NNE-SSW cross-section of the south-vergent thrust system from the southern flank of the Axial Zone to the South-Pyrenean Frontal Thrust (SPFT), in the west-central part of the belt. This section provides a complete transverse of the South-Pyrenean Zone, here corresponding to the Ainsa and Jaca basins. Apatite FTA provides important new constraints on the south-Pyrenean foreland basin evolution: (i) Data show the southward decrease of the fission track reset level, from a total reset (indicating heating at Tmax>110°C) in the Paleozoic of the Axial Zone, to a partial reset (110°C>Tmax>60°C) in the lower-middle Eocene Hecho Group turbidites in the northern part of the Jaca basin, and to the absence of reset (TmaxJaca basin. This indicates a decreasing amount of denudation going southwards, from more than 4.5 km in the north to less than 2.5 km in the south if we assume an average geothermal gradient around 25°/km. The structural setting of the Jaca basin attests that the burial of sediments was mainly due to sedimentary accumulation. (ii

  11. ARC Code TI: sequenceMiner

    Data.gov (United States)

    National Aeronautics and Space Administration — The sequenceMiner was developed to address the problem of detecting and describing anomalies in large sets of high-dimensional symbol sequences. sequenceMiner works...

  12. Sequencing Needs for Viral Diagnostics

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, S N; Lam, M; Mulakken, N J; Torres, C L; Smith, J R; Slezak, T

    2004-01-26

    We built a system to guide decisions regarding the amount of genomic sequencing required to develop diagnostic DNA signatures, which are short sequences that are sufficient to uniquely identify a viral species. We used our existing DNA diagnostic signature prediction pipeline, which selects regions of a target species genome that are conserved among strains of the target (for reliability, to prevent false negatives) and unique relative to other species (for specificity, to avoid false positives). We performed simulations, based on existing sequence data, to assess the number of genome sequences of a target species and of close phylogenetic relatives (''near neighbors'') that are required to predict diagnostic signature regions that are conserved among strains of the target species and unique relative to other bacterial and viral species. For DNA viruses such as variola (smallpox), three target genomes provide sufficient guidance for selecting species-wide signatures. Three near neighbor genomes are critical for species specificity. In contrast, most RNA viruses require four target genomes and no near neighbor genomes, since lack of conservation among strains is more limiting than uniqueness. SARS and Ebola Zaire are exceptional, as additional target genomes currently do not improve predictions, but near neighbor sequences are urgently needed. Our results also indicate that double stranded DNA viruses are more conserved among strains than are RNA viruses, since in most cases there was at least one conserved signature candidate for the DNA viruses and zero conserved signature candidates for the RNA viruses.

  13. Sequence-dependent nucleosome positioning.

    Science.gov (United States)

    Chung, Ho-Ryun; Vingron, Martin

    2009-03-13

    Eukaryotic DNA is organized into a macromolecular structure called chromatin. The basic repeating unit of chromatin is the nucleosome, which consists of two copies of each of the four core histones and DNA. The nucleosomal organization and the positions of nucleosomes have profound effects on all DNA-dependent processes. Understanding the factors that influence nucleosome positioning is therefore of general interest. Among the many determinants of nucleosome positioning, the DNA sequence has been proposed to have a major role. Here, we analyzed more than 860,000 nucleosomal DNA sequences to identify sequence features that guide the formation of nucleosomes in vivo. We found that both a periodic enrichment of AT base pairs and an out-of-phase oscillating enrichment of GC base pairs as well as the overall preference for GC base pairs are determinants of nucleosome positioning. The preference for GC pairs can be related to a lower energetic cost required for deformation of the DNA to wrap around the histones. In line with this idea, we found that only incorporation of both signal components into a sequence model for nucleosome formation results in maximal predictive performance on a genome-wide scale. In this manner, one achieves greater predictive power than published approaches. Our results confirm the hypothesis that the DNA sequence has a major role in nucleosome positioning in vivo.

  14. Explaining the harmonic sequence paradox.

    Science.gov (United States)

    Schmidt, Ulrich; Zimper, Alexander

    2012-05-01

    According to the harmonic sequence paradox, an expected utility decision maker's willingness to pay for a gamble whose expected payoffs evolve according to the harmonic series is finite if and only if his marginal utility of additional income becomes zero for rather low payoff levels. Since the assumption of zero marginal utility is implausible for finite payoff levels, expected utility theory - as well as its standard generalizations such as cumulative prospect theory - are apparently unable to explain a finite willingness to pay. This paper presents first an experimental study of the harmonic sequence paradox. Additionally, it demonstrates that the theoretical argument of the harmonic sequence paradox only applies to time-patient decision makers, whereas the paradox is easily avoided if time-impatience is introduced.

  15. Transgressive Surface as Sequence Boundary

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Analysis of the four cases of the sequence boundary (SB)-transgressive surface (TS) relation in nature shows that applying transgressive surfaces as sequence boundaries has the following merits: it improves the methodology of stratigraphic subdivision; the position of transgressive surface in a sea level curve is relatively fixed; the transgressive surface is a transforming surface of the stratal structure; in platforms or ramps, the transgressive surface is the only choice for determining the sequence boundary; the transgressive surface is a readily recognized physical surface reflected by seismic records in seismostratigraphy. The paper reaches a conclusion that to delineate a SB in terms of the TS is theoretically and practically better than to delineate it between highstand and lowstand sediments as has been done traditionally.

  16. On the base sequence conjecture

    CERN Document Server

    Djokovic, Dragomir Z

    2010-01-01

    Let BS(m,n) denote the set of base sequences (A;B;C;D), with A and B of length m and C and D of length n. The base sequence conjecture (BSC) asserts that BS(n+1,n) exist (i.e., are non-empty) for all n. This is known to be true for n <= 36 and when n is a Golay number. We show that it is also true for n=37 and n=38. It is worth pointing out that BSC is stronger than the famous Hadamard matrix conjecture. In order to demonstrate the abundance of base sequences, we have previously attached to BS(n+1,n) a graph Gamma_n and computed the Gamma_n for n <= 27. We now extend these computations and determine the Gamma_n for n=28,...,35. We also propose a conjecture describing these graphs in general.

  17. Comparative analysis of sequences from PT 2013

    DEFF Research Database (Denmark)

    Mikkelsen, Susie Sommer

    . All but one sequence mapped to the MCP gene while the last sequence mapped to the Neurofilament gene. Approx. half of the sequences contained no errors while the rest differed with 88-99 percent similarity with most having 99% similarity. One sequence, when BLASTed, showed most similarity to European...... Sheatfish and not EHNV. Generally, mistakes occurred at the ends of the sequences. This can be due to several factors. One is that the sequence has not been trimmed of the sequence primer sites. Another is the lack of quality control of the chromatogram. Finally, sequencing in just one direction can result...

  18. Sequence Patterns of Identity Authentication Protocols

    Institute of Scientific and Technical Information of China (English)

    Tao Hongcai; He Dake

    2006-01-01

    From the viewpoint of protocol sequence, analyses are made of the sequence patterns of possible identity authentication protocol under two cases: with or without the trusted third party (TTP). Ten feasible sequence patterns of authentication protocol with TTP and 5 sequence patterns without TTP are gained. These gained sequence patterns meet the requirements for identity authentication,and basically cover almost all the authentication protocols with TTP and without TTP at present. All of the sequence patterns gained are classified into unilateral or bilateral authentication. Then , according to the sequence symmetry, several good sequence patterns with TTP are evaluated. The accompolished results can provide a reference to design of new identity authentication protocols.

  19. KERNEL WORDS AND GAP SEQUENCE OF THE TRIBONACCI SEQUENCE

    Institute of Scientific and Technical Information of China (English)

    Yuke HUANG; Zhiying WEN

    2016-01-01

    In this paper, we investigate the factor properties and gap sequence of the Tri-bonacci sequence, the fixed point of the substitution σ(a, b, c) = (ab, ac, a). Let ωp be the p-th occurrence of ω and Gp(ω) be the gap between ωp and ωp+1. We introduce a notion of kernel for each factor ω, and then give the decomposition of the factor ω with respect to its kernel. Using the kernel and the decomposition, we prove the main result of this paper:for each factorω, the gap sequence{Gp(ω)}p≥1 is the Tribonacci sequence over the alphabet{G1(ω), G2(ω), G4(ω)}, and the expressions of gaps are determined completely. As an appli-cation, for each factorω and p∈N, we determine the position ofωp. Finally we introduce a notion of spectrum for studying some typical combinatorial properties, such as power, overlap and separate of factors.

  20. Sequences and series involving the sequence of composite numbers

    Directory of Open Access Journals (Sweden)

    Panayiotis Vlamos

    2002-01-01

    Full Text Available Denoting by pn and cn the nth prime number and the nth composite number, respectively, we prove that both the sequence (xnn≥1, defined by xn=∑k=1n (ck+1−ck / k−pn / n, and the series ∑n=1∞ (pcn−cpn / npn are convergent.

  1. Integrated sequence analysis. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, K.; Pyy, P

    1998-02-01

    The NKS/RAK subprojet 3 `integrated sequence analysis` (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term `methodology` denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  2. Network motifs in music sequences

    CERN Document Server

    Zanette, Damian H

    2010-01-01

    In this note, I summarize ongoing research on motif distribution in networks built up out of symbolic sequences of Western musical origin. Their motif significance profiles exhibit remarkable consistency over different styles and periods, and define a class that cannot be identified with any of the four "superfamilies" to which most real networks seem to belong. Networks from music sequences possess an unusual abundance of bidirectional connections, due to the inherent reversibility of short musical note patterns. This property contributes to motif significance from both local and large-scale features of musical structure.

  3. Convergence of Fuzzy Set Sequences

    Institute of Scientific and Technical Information of China (English)

    FENG Yu-hu

    2002-01-01

    There are more than one mode of convergence with respect to the fuzzy set sequences. In this paper,common six modes of convergence and their relationships are discussed. These six modes are convergence in uniform metric D, convergence in separable metric Dp or D*p, 1 ≤ p <∞, convergence in level set, strong convergence in level set and weak convergence. Suitable counterexamples are given. The necessary and sufficient conditions of convergence in uniform metric D are described. Some comme nts on the convergence of LRfuzzy number sequences are represented.

  4. DNA Sequencing Using capillary Electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Barry Karger

    2011-05-09

    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other

  5. The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing.

    Directory of Open Access Journals (Sweden)

    Toon Rosseel

    Full Text Available Sequence Independent Single Primer Amplification is one of the most widely used random amplification approaches in virology for sequencing template preparation. This technique relies on oligonucleotides consisting of a 3' random part used to prime complementary DNA synthesis and a 5' defined tag sequence for subsequent amplification. Recently, this amplification method was combined with next generation sequencing to obtain viral sequences. However, these studies showed a biased distribution of the resulting sequence reads over the analyzed genomes. The aim of this study was to elucidate the mechanisms that lead to biased sequence depth when using random amplification. Avian paramyxovirus type 8 was used as a model RNA virus to investigate these mechanisms. We showed, based on in silico analysis of the sequence depth in relation to GC-content, predicted RNA secondary structure and sequence complementarity to the 3' part of the tag sequence, that the tag sequence has the main contribution to the observed bias in sequence depth. We confirmed this finding experimentally using both fragmented and non-fragmented viral RNAs as well as primers differing in random oligomer length (6 or 12 nucleotides and in the sequence of the amplification tag. The observed oligonucleotide annealing bias can be reduced by extending the random oligomer sequence and by in silico combining sequence data from SISPA experiments using different 5' defined tag sequences. These findings contribute to the optimization of random nucleic acid amplification protocols that are currently required for downstream applications such as viral metagenomics and microarray analysis.

  6. Sequences in language and text

    CERN Document Server

    Mikros, George K

    2015-01-01

    The aim of this volume is to present the diverse but highly interesting area of the quantitative analysis of the sequence of various linguistic structures. The collected articles present a wide spectrum of quantitative analyses of linguistic syntagmatic structures and explore novel sequential linguistic entities. This volume will be interesting to all researchers studying linguistics using quantitative methods.

  7. Instruction Sequences for Computer Science

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    2012-01-01

    This book demonstrates that the concept of an instruction sequence offers a novel and useful viewpoint on issues relating to diverse subjects in computer science. Selected issues relating to well-known subjects from the theory of computation and the area of computer architecture are rigorously

  8. Single-primer fluorescent sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Ruth, J.L.; Morgan, C.A.; Middendorf, L.R.; Grone, D.L.; Brumbaugh, J.A.

    1987-05-01

    Modified linker arm oligonucleotides complementary to standard M13 priming sites were synthesized, labelled with either one, two, or three fluoresceins, and purified by reverse-phase HPLC. When used as primers in standard dideoxy M13 sequencing with /sup 32/P-dNTPs, normal autoradiographic patterns were obtained. To eliminate the radioactivity, direct on-line fluorescence detection was achieved by the use of a scanning 10 mW Argon laser emitting 488 nm light. Fluorescent bands were detected directly in standard 0.2 or 0.35 mm thick polyacrylamide gels at a distance of 24 cm from the loading wells by a photomultiplier tube filtered at 520 nm. Horizontal and temporal location of each band was displayed by computer as a band in real time, providing visual appearance similar to normal 4-lane autoradiograms. Using a single primer labelled with two fluoresceins, sequences of between 500 and 600 bases have been read in a single loading with better than 98% accuracy; up to 400 bases can be read reproducibly with no errors. More than 50 sequences have been determined by this method. This approach requires only 1-2 ug of cloned template, and produces continuous sequence data at about one band per minute.

  9. Multifractal analyses of music sequences

    Science.gov (United States)

    Su, Zhi-Yuan; Wu, Tzuyin

    2006-09-01

    Multifractal analysis is applied to study the fractal property of music. In this paper, a method is proposed to transform both the melody and rhythm of a music piece into individual sets of distributed points along a one-dimensional line. The structure of the musical composition is thus manifested and characterized by the local clustering pattern of these sequences of points. Specifically, the local Hölder exponent and the multifractal spectrum are calculated for the transformed music sequences according to the multifractal formalism. The observed fluctuations of the Hölder exponent along the music sequences confirm the non-uniformity feature in the structures of melodic and rhythmic motions of music. Our present result suggests that the shape and opening width of the multifractal spectrum plot can be used to distinguish different styles of music. In addition, a characteristic curve is constructed by mapping the point sequences converted from the melody and rhythm of a musical work into a two-dimensional graph. Each different pieces of music has its own unique characteristic curve. This characteristic curve, which also exhibits a fractal trait, unveils the intrinsic structure of music.

  10. Fractals in DNA sequence analysis

    Institute of Scientific and Technical Information of China (English)

    Yu Zu-Guo(喻祖国); Vo Anh; Gong Zhi-Min(龚志民); Long Shun-Chao(龙顺潮)

    2002-01-01

    Fractal methods have been successfully used to study many problems in physics, mathematics, engineering, finance,and even in biology. There has been an increasing interest in unravelling the mysteries of DNA; for example, how can we distinguish coding and noncoding sequences, and the problems of classification and evolution relationship of organisms are key problems in bioinformatics. Although much research has been carried out by taking into consideration the long-range correlations in DNA sequences, and the global fractal dimension has been used in these works by other people, the models and methods are somewhat rough and the results are not satisfactory. In recent years, our group has introduced a time series model (statistical point of view) and a visual representation (geometrical point of view)to DNA sequence analysis. We have also used fractal dimension, correlation dimension, the Hurst exponent and the dimension spectrum (multifractal analysis) to discuss problems in this field. In this paper, we introduce these fractal models and methods and the results of DNA sequence analysis.

  11. Farey Sequences and Resistor Networks

    Indian Academy of Sciences (India)

    Sameen Ahmed Khan

    2012-05-01

    In this article, we employ the Farey sequence and Fibonacci numbers to establish strict upper and lower bounds for the order of the set of equivalent resistances for a circuit constructed from equal resistors combined in series and in parallel. The method is applicable for networks involving bridge and non-planar circuits.

  12. Nd isotopic compositions of the Tethyan Himalayan Sequence in southeastern Tibet

    Institute of Scientific and Technical Information of China (English)

    DAI JinGen; YIN An; LIU WenCan; WANG ChengShan

    2008-01-01

    The Himalayan orogen consists of three major lithologic units that are separated by two major north-dipping faults: the Lesser Himalayan Sequence (LHS) below the Main Central Thrust (MCT), the Greater Himalayan Crystalline Complex (GHC) above the MCT, and the Tethyan Himalayan Sequence (THS) juxtaposed by the South Tibet Detachment fault (STD) over the GHC.Due to widespread meta-morphism and intense deformation, differentiating the above three lithologic units is often difficult.This problem has been overcome by the use of Sm-Nd isotopic analysis.The previous studies suggested that the LHS can be clearly distinguished from the GHC and THS by their Nd isotope compositions.However, the lack of detailed and systematic Sm-Nd isotopic studies of the THS across the Himalaya in general has made differentiation of this unit from the nearby GHC impossible, as the two appear to share overlapping Nd compositions and model ages.To address this problem, we systematically sampled and analyzed Nd isotopes of the THS in southeastern Tibet directly north of Bhutan.Our study identifies two distinctive fields in a εNd-TDM plot.The first is defined by the εNd(210 Ma) values of -3.45 to -7.34 and TDM values of 1.15 to 1.29 Ga from a Late Triassic turbidite sequence, which are broadly similar to those obtained from the Lhasa block.The second field is derived from the Early Cretaceous meta-sedimentary rocks with εNd(130 Ma) values from -15.24 to -16.61 and TDM values from 1.63 to 2.00 Ga; these values are similar to those obtained from the Greater Himalayan Crystalline Complex in Bhutan directly south of our sampling traverse, which has εNd(130 Ma) values of -10.89 to -16.32 and Nd model ages (TDM) of 1.73 to 2.20 Ga.From the above observations, we suggest that the Late Triassic strata of the southeast Tibetan THS were derived from the Lhasa block in the north, while the Early Cretaceous strata of the THS were derived from a source similar to the High Himalayan Crystalline Complex or

  13. The Toothpick Sequence and Other Sequences from Cellular Automata

    CERN Document Server

    Applegate, David; Sloane, N J A

    2010-01-01

    A two-dimensional arrangement of toothpicks is constructed by the following iterative procedure. At stage 1, place a single toothpick of length 1 on a square grid, aligned with the y-axis. At each subsequent stage, for every exposed toothpick end, place an orthogonal toothpick centered at that end. The resulting structure has a fractal-like appearance. We will analyze the toothpick sequence, which gives the total number of toothpicks after n steps. We also study several related sequences that arise from enumerating active cells in cellular automata. Some unusual recurrences appear: a typical example is that instead of the Fibonacci recurrence, which we may write as a(2+i) = a(i) + a(i+1), we set n = 2^k+i (0 = 0} (1+x^{2^k-1}+2x^{2^k}) and variations thereof.

  14. Algebraic divisibility sequences over function fields

    CERN Document Server

    Ingram, Patrick; Silverman, Joseph H; Stange, Katherine E; Streng, Marco

    2011-01-01

    We study the existence of primes and of primitive divisors in classical divisibility sequences defined over function fields. Under various hypotheses, we prove that Lucas sequences and elliptic divisibility sequences over function fields defined over number fields contain infinitely many irreducible elements. We also prove that an elliptic divisibility sequence over a function field has only finitely many terms lacking a primitive divisor.

  15. Stream cipher based on GSS sequences

    Institute of Scientific and Technical Information of China (English)

    HU Yupu; XIAO Guozhen

    2004-01-01

    Generalized self-shrinking sequences, simply named the GSS sequences,are novel periodic sequences that have many advantages in cryptography. In this paper,we give several results about GSS sequence's application to cryptography. First, we give a simple method for selecting those GSS sequences whose least periods reach the maximum. Second, we give a method for describing and computing the auto-correlation coefficients of GSS sequences. Finally, we point out that some GSS sequences, when used as stream ciphers, have a security weakness.

  16. Pig genome sequence - analysis and publication strategy

    DEFF Research Database (Denmark)

    Archibald, Alan L.; Bolund, Lars; Churcher, Carol;

    2010-01-01

    BACKGROUND: The pig genome is being sequenced and characterised under the auspices of the Swine Genome Sequencing Consortium. The sequencing strategy followed a hybrid approach combining hierarchical shotgun sequencing of BAC clones and whole genome shotgun sequencing. RESULTS: Assemblies......) is under construction and will incorporate whole genome shotgun sequence (WGS) data providing > 30x genome coverage. The WGS sequence, most of which comprise short Illumina/Solexa reads, were generated from DNA from the same single Duroc sow as the source of the BAC library from which clones were...

  17. Sequence-structure relations of biopolymers

    CERN Document Server

    Barrett, Christopher; Reidys, Christian M

    2015-01-01

    Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as structural semantics of sequence data that allows for a different interpretation than conventional sequence alignment. Structural semantics could enable us to identify more general embedded "patterns" in DNA and RNA sequences. Results: We compute the partition function of sequences with respect to a fixed structure and connect this computation to the mutual information of a sequence-structure pair for RNA secondary structures. We present a Boltzmann sampler and obtain the a priori probability of specific sequence patterns. We present a detailed analysis for the three PDB-structures, 2JXV (hairpin), 2N3R (3-branch multi-loop) and 1EHZ (tRNA). We localize specific sequence patterns, contrast the energy spectrum of the Boltzmann sampled sequences versus those sequences that refold ...

  18. Expressing stochastic filters via number sequences

    OpenAIRE

    Capponi, A.; Farina, A; Pilotto, C.

    2010-01-01

    We generalize the results presented in [1] regarding the relation between the Kalman filter and the Fibonacci sequence. We consider more general filtering models and relate the finite dimensional Kalman and Benes filters to the Fibonacci sequence and to the Golden Section. We also prove that Fibonacci numbers may be expressed as the convolution of the Fibonacci and Padovan sequence, thus extending the connection between stochastic filtering and Fibonacci sequence to the Padovan sequence.

  19. Cassini Mission Sequence Subsystem (MSS)

    Science.gov (United States)

    Alland, Robert

    2011-01-01

    This paper describes my work with the Cassini Mission Sequence Subsystem (MSS) team during the summer of 2011. It gives some background on the motivation for this project and describes the expected benefit to the Cassini program. It then introduces the two tasks that I worked on - an automatic system auditing tool and a series of corrections to the Cassini Sequence Generator (SEQ_GEN) - and the specific objectives these tasks were to accomplish. Next, it details the approach I took to meet these objectives and the results of this approach, followed by a discussion of how the outcome of the project compares with my initial expectations. The paper concludes with a summary of my experience working on this project, lists what the next steps are, and acknowledges the help of my Cassini colleagues.

  20. Nonparametric Inference for Periodic Sequences

    KAUST Repository

    Sun, Ying

    2012-02-01

    This article proposes a nonparametric method for estimating the period and values of a periodic sequence when the data are evenly spaced in time. The period is estimated by a "leave-out-one-cycle" version of cross-validation (CV) and complements the periodogram, a widely used tool for period estimation. The CV method is computationally simple and implicitly penalizes multiples of the smallest period, leading to a "virtually" consistent estimator of integer periods. This estimator is investigated both theoretically and by simulation.We also propose a nonparametric test of the null hypothesis that the data have constantmean against the alternative that the sequence of means is periodic. Finally, our methodology is demonstrated on three well-known time series: the sunspots and lynx trapping data, and the El Niño series of sea surface temperatures. © 2012 American Statistical Association and the American Society for Quality.

  1. Genome Sequence of Mycobacteriophage Momo.

    Science.gov (United States)

    Pope, Welkin H; Bina, Elizabeth A; Brahme, Indraneel S; Hill, Amy B; Himmelstein, Philip H; Hunsicker, Sara M; Ish, Amanda R; Le, Tinh S; Martin, Mary M; Moscinski, Catherine N; Shetty, Sameer A; Swierzewski, Tomasz; Iyengar, Varun B; Kim, Hannah; Schafer, Claire E; Grubb, Sarah R; Warner, Marcie H; Bowman, Charles A; Russell, Daniel A; Hatfull, Graham F

    2015-06-18

    Momo is a newly discovered phage of Mycobacterium smegmatis mc(2)155. Momo has a double-stranded DNA genome 154,553 bp in length, with 233 predicted protein-encoding genes, 34 tRNA genes, and one transfer-messenger RNA (tmRNA) gene. Momo has a myoviral morphology and shares extensive nucleotide sequence similarity with subcluster C1 mycobacteriophages. Copyright © 2015 Pope et al.

  2. Multiplicative LSTM for sequence modelling

    OpenAIRE

    Krause, Ben; Lu, Liang; Murray, Iain; Renals, Steve

    2016-01-01

    This paper introduces multiplicative LSTM, a novel hybrid recurrent neural network architecture for sequence modelling that combines the long short-term memory (LSTM) and multiplicative recurrent neural network architectures. Multiplicative LSTM is motivated by its flexibility to have very different recurrent transition functions for each possible input, which we argue helps make it more expressive in autoregressive density estimation. We show empirically that multiplicative LSTM outperforms ...

  3. Multineuronal Spike Sequences Repeat with Millisecond Precision

    Directory of Open Access Journals (Sweden)

    Koki eMatsumoto

    2013-06-01

    Full Text Available Cortical microcircuits are nonrandomly wired by neurons. As a natural consequence, spikes emitted by microcircuits are also nonrandomly patterned in time and space. One of the prominent spike organizations is a repetition of fixed patterns of spike series across multiple neurons. However, several questions remain unsolved, including how precisely spike sequences repeat, how the sequences are spatially organized, how many neurons participate in sequences, and how different sequences are functionally linked. To address these questions, we monitored spontaneous spikes of hippocampal CA3 neurons ex vivo using a high-speed functional multineuron calcium imaging technique that allowed us to monitor spikes with millisecond resolution and to record the location of spiking and nonspiking neurons. Multineuronal spike sequences were overrepresented in spontaneous activity compared to the statistical chance level. Approximately 75% of neurons participated in at least one sequence during our observation period. The participants were sparsely dispersed and did not show specific spatial organization. The number of sequences relative to the chance level decreased when larger time frames were used to detect sequences. Thus, sequences were precise at the millisecond level. Sequences often shared common spikes with other sequences; parts of sequences were subsequently relayed by following sequences, generating complex chains of multiple sequences.

  4. Method and apparatus for biological sequence comparison

    Science.gov (United States)

    Marr, T.G.; Chang, W.I.

    1997-12-23

    A method and apparatus are disclosed for comparing biological sequences from a known source of sequences, with a subject (query) sequence. The apparatus takes as input a set of target similarity levels (such as evolutionary distances in units of PAM), and finds all fragments of known sequences that are similar to the subject sequence at each target similarity level, and are long enough to be statistically significant. The invention device filters out fragments from the known sequences that are too short, or have a lower average similarity to the subject sequence than is required by each target similarity level. The subject sequence is then compared only to the remaining known sequences to find the best matches. The filtering member divides the subject sequence into overlapping blocks, each block being sufficiently large to contain a minimum-length alignment from a known sequence. For each block, the filter member compares the block with every possible short fragment in the known sequences and determines a best match for each comparison. The determined set of short fragment best matches for the block provide an upper threshold on alignment values. Regions of a certain length from the known sequences that have a mean alignment value upper threshold greater than a target unit score are concatenated to form a union. The current block is compared to the union and provides an indication of best local alignment with the subject sequence. 5 figs.

  5. Static multiplicities in heterogeneous azeotropic distillation sequences

    DEFF Research Database (Denmark)

    Esbjerg, Klavs; Andersen, Torben Ravn; Jørgensen, Sten Bay

    1998-01-01

    In this paper the results of a bifurcation analysis on heterogeneous azeotropic distillation sequences are given. Two sequences suitable for ethanol dehydration are compared: The 'direct' and the 'indirect' sequence. It is shown, that the two sequences, despite their similarities, exhibit very...... different static behavior. The method of Petlyuk and Avet'yan (1971), Bekiaris et al. (1993), which assumes infinite reflux and infinite number of stages, is extended to and applied on heterogeneous azeotropic distillation sequences. The predictions are substantiated through simulations. The static sequence...

  6. On Inclusion Relations between Some Sequence Spaces

    Directory of Open Access Journals (Sweden)

    R. Çolak

    2016-01-01

    Full Text Available We determine the relations between the classes S^λ of almost λ-statistically convergent sequences and the relations between the classes V^,λ of strongly almost V,λ-summable sequences for various sequences λ, μ in the class Λ. Furthermore we also give the relations between the classes S^λ of almost λ-statistically convergent sequences and the classes V^,λ of strongly almost V,λ-summable sequences for various sequences λ,μ∈Λ.

  7. Bernoulli measure of complex admissible kneading sequences

    CERN Document Server

    Bruin, Henk

    2012-01-01

    Iterated quadratic polynomials give rise to a rich collection of different dynamical systems that are parametrized by a simple complex parameter $c$. The different dynamical features are encoded by the \\emph{kneading sequence} which is an infinite sequence over $\\{0,\\1\\}$. Not every such sequence actually occurs in complex dynamics. The set of admissible kneading sequences was described by Milnor and Thurston for real quadratic polynomials, and by the authors in the complex case. We prove that the set of admissible kneading sequences has positive Bernoulli measure within the set of sequences over $\\{0,\\1\\}$.

  8. Blind sequence-length estimation of low-SNR cyclostationary sequences

    CSIR Research Space (South Africa)

    Vlok, JD

    2014-06-01

    Full Text Available Several existing direct-sequence spread spectrum (DSSS) detection and estimation algorithms assume prior knowledge of the symbol period or sequence length, although very few sequence-length estimation techniques are available in the literature...

  9. Modified Genetic Algorithm for DNA Sequence Assembly by Shotgun and Hybridization Sequencing Techniques

    Directory of Open Access Journals (Sweden)

    Prof.Narayan Kumar Sahu

    2012-09-01

    Full Text Available Since the advent of rapid DNA sequencing methods in 1976, scientists have had the problem of inferring DNA sequences from sequenced fragments. Shotgun sequencing is a well-established biological and computational method used in practice. Many conventional algorithms for shotgun sequencing are based on the notion of pair wise fragment overlap. While shotgun sequencing infers a DNA sequence given the sequences of overlapping fragments, a recent and complementary method, called sequencing by hybridization (SBH, infers a DNA sequence given the set of oligomers that represents all sub words of some fixed length, k. In this paper, we propose a new computer algorithm for DNA sequence assembly that combines in a novel way the techniques of both shotgun and SBH methods. Based on our preliminary investigations, the algorithm promises- to be very fast and practical for DNA sequence assembly [1].

  10. Biomolecule Sequencer: Nanopore Sequencing Technology for In-Situ Environmental Monitoring and Astrobiology

    Science.gov (United States)

    John, K. K.; Botkin, D. J.; Burton, A. S.; Castro-Wallace, S. L.; Chaput, J. D.; Dworkin, J. P.; Lupisella, M. L.; Mason, C. E.; Rubins, K. H.; Smith, D. J.; Stahl, S.; Switzer, C.

    2016-10-01

    Biomolecule Sequencer will demonstrate, for the first time, that DNA sequencing is feasible as a tool for in-situ environmental monitoring and astrobiology. A space-based sequencer could identify microbes, diseases, and help detect DNA-based life.

  11. Integration of retinal image sequences

    Science.gov (United States)

    Ballerini, Lucia

    1998-10-01

    In this paper a method for noise reduction in ocular fundus image sequences is described. The eye is the only part of the human body where the capillary network can be observed along with the arterial and venous circulation using a non invasive technique. The study of the retinal vessels is very important both for the study of the local pathology (retinal disease) and for the large amount of information it offers on systematic haemodynamics, such as hypertension, arteriosclerosis, and diabetes. In this paper a method for image integration of ocular fundus image sequences is described. The procedure can be divided in two step: registration and fusion. First we describe an automatic alignment algorithm for registration of ocular fundus images. In order to enhance vessel structures, we used a spatially oriented bank of filters designed to match the properties of the objects of interest. To evaluate interframe misalignment we adopted a fast cross-correlation algorithm. The performances of the alignment method have been estimated by simulating shifts between image pairs and by using a cross-validation approach. Then we propose a temporal integration technique of image sequences so as to compute enhanced pictures of the overall capillary network. Image registration is combined with image enhancement by fusing subsequent frames of a same region. To evaluate the attainable results, the signal-to-noise ratio was estimated before and after integration. Experimental results on synthetic images of vessel-like structures with different kind of Gaussian additive noise as well as on real fundus images are reported.

  12. Discrete low-discrepancy sequences

    CERN Document Server

    Angel, Omer; Martin, James B; Propp, James

    2009-01-01

    Holroyd and Propp used Hall's marriage theorem to show that, given a probability distribution pi on a finite set S, there exists an infinite sequence s_1,s_2,... in S such that for all integers k >= 1 and all s in S, the number of i in [1,k] with s_i = s differs from k pi(s) by at most 1. We prove a generalization of this result using a simple explicit algorithm. A special case of this algorithm yields an extension of Holroyd and Propp's result to the case of discrete probability distributions on infinite sets.

  13. Infinite matrices and sequence spaces

    CERN Document Server

    Cooke, Richard G

    2014-01-01

    This clear and correct summation of basic results from a specialized field focuses on the behavior of infinite matrices in general, rather than on properties of special matrices. Three introductory chapters guide students to the manipulation of infinite matrices, covering definitions and preliminary ideas, reciprocals of infinite matrices, and linear equations involving infinite matrices.From the fourth chapter onward, the author treats the application of infinite matrices to the summability of divergent sequences and series from various points of view. Topics include consistency, mutual consi

  14. Differential correlation for sequencing data.

    Science.gov (United States)

    Siska, Charlotte; Kechris, Katerina

    2017-01-19

    Several methods have been developed to identify differential correlation (DC) between pairs of molecular features from -omics studies. Most DC methods have only been tested with microarrays and other platforms producing continuous and Gaussian-like data. Sequencing data is in the form of counts, often modeled with a negative binomial distribution making it difficult to apply standard correlation metrics. We have developed an R package for identifying DC called Discordant which uses mixture models for correlations between features and the Expectation Maximization (EM) algorithm for fitting parameters of the mixture model. Several correlation metrics for sequencing data are provided and tested using simulations. Other extensions in the Discordant package include additional modeling for different types of differential correlation, and faster implementation, using a subsampling routine to reduce run-time and address the assumption of independence between molecular feature pairs. With simulations and breast cancer miRNA-Seq and RNA-Seq data, we find that Spearman's correlation has the best performance among the tested correlation methods for identifying differential correlation. Application of Spearman's correlation in the Discordant method demonstrated the most power in ROC curves and sensitivity/specificity plots, and improved ability to identify experimentally validated breast cancer miRNA. We also considered including additional types of differential correlation, which showed a slight reduction in power due to the additional parameters that need to be estimated, but more versatility in applications. Finally, subsampling within the EM algorithm considerably decreased run-time with negligible effect on performance. A new method and R package called Discordant is presented for identifying differential correlation with sequencing data. Based on comparisons with different correlation metrics, this study suggests Spearman's correlation is appropriate for sequencing data

  15. Asymptotics of Lagged Fibonacci Sequences

    CERN Document Server

    Mertens, Stephan

    2009-01-01

    Consider "lagged" Fibonacci sequences $a(n) = a(n-1)+a(\\lfloor n/k\\rfloor)$ for $k > 1$. We show that $\\lim_{n\\to\\infty} a(kn)/a(n)\\cdot\\ln n/n = k\\ln k$ and we demonstrate the slow numerical convergence to this limit and how to deal with this slow convergence. We also discuss the connection between two classical results of N.G. de Bruijn and K. Mahler on the asymptotics of $a(n)$.

  16. FOGSAA: Fast Optimal Global Sequence Alignment Algorithm

    Science.gov (United States)

    Chakraborty, Angana; Bandyopadhyay, Sanghamitra

    2013-04-01

    In this article we propose a Fast Optimal Global Sequence Alignment Algorithm, FOGSAA, which aligns a pair of nucleotide/protein sequences faster than any optimal global alignment method including the widely used Needleman-Wunsch (NW) algorithm. FOGSAA is applicable for all types of sequences, with any scoring scheme, and with or without affine gap penalty. Compared to NW, FOGSAA achieves a time gain of (70-90)% for highly similar nucleotide sequences (> 80% similarity), and (54-70)% for sequences having (30-80)% similarity. For other sequences, it terminates with an approximate score. For protein sequences, the average time gain is between (25-40)%. Compared to three heuristic global alignment methods, the quality of alignment is improved by about 23%-53%. FOGSAA is, in general, suitable for aligning any two sequences defined over a finite alphabet set, where the quality of the global alignment is of supreme importance.

  17. Genome Sequences of Eight Morphologically Diverse Alphaproteobacteria▿

    OpenAIRE

    Brown, Pamela J.B.; Kysela, David T.; Buechlein, Aaron; Hemmerich, Chris; Brun, Yves V

    2011-01-01

    The Alphaproteobacteriacomprise morphologically diverse bacteria, including many species of stalked bacteria. Here we announce the genome sequences of eight alphaproteobacteria, including the first genome sequences of species belonging to the genera Asticcacaulis, Hirschia, Hyphomicrobium, and Rhodomicrobium.

  18. Genome sequences of eight morphologically diverse Alphaproteobacteria.

    Science.gov (United States)

    Brown, Pamela J B; Kysela, David T; Buechlein, Aaron; Hemmerich, Chris; Brun, Yves V

    2011-09-01

    The Alphaproteobacteria comprise morphologically diverse bacteria, including many species of stalked bacteria. Here we announce the genome sequences of eight alphaproteobacteria, including the first genome sequences of species belonging to the genera Asticcacaulis, Hirschia, Hyphomicrobium, and Rhodomicrobium.

  19. Genome Sequences of Eight Morphologically Diverse Alphaproteobacteria▿

    Science.gov (United States)

    Brown, Pamela J. B.; Kysela, David T.; Buechlein, Aaron; Hemmerich, Chris; Brun, Yves V.

    2011-01-01

    The Alphaproteobacteriacomprise morphologically diverse bacteria, including many species of stalked bacteria. Here we announce the genome sequences of eight alphaproteobacteria, including the first genome sequences of species belonging to the genera Asticcacaulis, Hirschia, Hyphomicrobium, and Rhodomicrobium. PMID:21705585

  20. The Art of Gymnastics: Creating Sequences.

    Science.gov (United States)

    Rovegno, Inez

    1988-01-01

    Offering students opportunities for creating movement sequences in gymnastics allows them to understand the essence of gymnastics, have creative experiences, and learn about themselves. The process of creating sequences is described. (MT)

  1. CONSONANT SEQUENCE REDUCTION IN CHILD PHONOLOGY

    African Journals Online (AJOL)

    Dr Kola ADENIYI

    in children's developmental difficulties, it is apparent that their vocal tracts are not ... proper articulation of certain complex sounds or sound sequences. ...... the nasal-oral consonant sequence is even limited in Yoruba, it means the frequency of.

  2. On topological spaces possessing uniformly distributed sequences

    CERN Document Server

    Bogachev, V I

    2007-01-01

    Two classes of topological spaces are introduced on which every probability Radon measure possesses a uniformly distributed sequence or a uniformly tight uniformly distributed sequence. It is shown that these classes are stable under multiplication by completely regular Souslin spaces

  3. On General Fibonacci Sequences in Groups

    OpenAIRE

    Özkan, Engin

    2003-01-01

    In this paper, we have constituted 3-step general Fibonacci sequences in a nilpotent group with exponent p (p is a prime number) and nilpotency class 4 and given formulas to find the a term of the sequence.

  4. On Paranorm Zweier -Convergent Sequence Spaces

    Directory of Open Access Journals (Sweden)

    Vakeel A. Khan

    2013-01-01

    Full Text Available In this paper, we introduce the paranorm Zweier -convergent sequence spaces , , and , a sequence of positive real numbers. We study some topological properties, prove the decomposition theorem, and study some inclusion relations on these spaces.

  5. Strong sequences and independent sets

    Directory of Open Access Journals (Sweden)

    Joanna Jureczko

    2016-05-01

    Full Text Available A family $\\mathcal{S} \\in \\mathcal{P}(\\omega$ is \\textit{an independent family} if for each pair $\\mathcal{A, B}$ of disjoint finite subsets of $\\mathcal{S}$ the set $\\bigcap \\mathcal{A} \\cap (\\omega \\setminus \\bigcup \\mathcal{B}$ is nonempty. The fact that there is an independent family on $\\omega$ of size continuum was proved by Fichtenholz and Kantorowicz in \\cite{FK}. If we substitute $\\mathcal{P}(\\omega$ by a set $(X, r$ with arbitrary relation \\textit{r} it is natural question about existence and length of an independent set on $(X, r$. In this paper special assumptions of such existence will be considered. On the other hand in 60s' of the last century the strong sequences method was introduced by Efimov. He used it for proving some famous theorems in dyadic spaces like: Marczewski theorem on cellularity, Shanin theorem on a calibre, Esenin-Volpin theorem and others. In this paper there will be considered: length of strong sequences, the length of independent sets and other well known cardinal invariants and there will be examined inequalities among them.

  6. Sequence Analysis in Demographic Research

    Directory of Open Access Journals (Sweden)

    Billari, Francesco C.

    2001-01-01

    Full Text Available EnglishThis paper examines the salient features of sequence analysis in demogrpahicresearch. The new approach allows a holistic perspective on life course analysis and is based on arepresentation of lives as sequences of states. Some of the methods for analyzing such data aresketched, from complex description to optimal matching ot monoethetic divisive algorithms. Afer ashort ilustration of a demographically-relevant example, the needs in terms of data collection and theopportunities of applying the same aproach to synthetic data are discussed.FrenchOn examine ici les principaux éléments de l’analyse par séquence endémographie. Cette nouvelle technique permet une perspective unifiée del’analyse du cours de la vie, en représentant la vie comme une série d’états.Certaines des méthodes pour de telles analyses sont décrites, en commençant parla description complexe, pour considérer ensuite les alignements optimales, etles algorithmes de division. Après un court exemple en démographie, onconsidère les besoins en données et les possibilités d’application aux donnéessynthétique.

  7. Information Analysis of DNA Sequences

    CERN Document Server

    Mohammed, Riyazuddin

    2010-01-01

    The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they do not seem to participate in the process of transcription of amino-acids, they have been termed "junk DNA." Although it is believed that the non-coding regions in genomes have no role in cell growth and evolution, demonstration that these regions carry useful information would tend to falsify this belief. In this paper, we consider entropy as a measure of information by modifying the entropy expression to take into account the varying length of these sequences. Exons are usually much shorter in length than introns; therefore the comparison of the entropy values needs to be normalized. A length correction strategy was employed using randomly generated nucleonic base strings built out of the alphabet of the same size as the exons under question. Our analysis shows that intron...

  8. Movement sequencing in Huntington disease.

    Science.gov (United States)

    Georgiou-Karistianis, Nellie; Long, Jeffrey D; Lourens, Spencer G; Stout, Julie C; Mills, James A; Paulsen, Jane S

    2014-08-01

    To examine longitudinal changes in movement sequencing in prodromal Huntington's disease (HD) participants (795 prodromal HD; 225 controls) from the PREDICT-HD study. Prodromal HD participants were tested over seven annual visits and were stratified into three groups (low, medium, high) based on their CAG-Age Product (CAP) score, which indicates likely increasing proximity to diagnosis. A cued movement sequence task assessed the impact of advance cueing on response initiation and execution via three levels of advance information. Compared to controls, all CAP groups showed longer initiation and movement times across all conditions at baseline, demonstrating a disease gradient for the majority of outcomes. Across all conditions, the high CAP group had the highest mean for baseline testing, but also demonstrated an increase in movement time across the study. For initiation time, the high CAP group showed the highest mean baseline time across all conditions, but also faster decreasing rates of change over time. With progress to diagnosis, participants may increasingly use compensatory strategies, as evidenced by faster initiation. However, this occurred in conjunction with slowed execution times, suggesting a decline in effectively accessing control processes required to translate movement into effective execution.

  9. Effects of Sequence Partitioning on Compression Rate

    CERN Document Server

    Alagoz, B Baykant

    2010-01-01

    In the paper, a theoretical work is done for investigating effects of splitting data sequence into packs of data set. We proved that a partitioning of data sequence is possible to find such that the entropy rate at each subsequence is lower than entropy rate of the source. Effects of sequence partitioning on overall compression rate are argued on the bases of partitioning statistics, and then, an optimization problem for an optimal partition is defined to improve overall compression rate of a sequence.

  10. Cross-correlation properties of cyclotomic sequences

    CERN Document Server

    Cai, Kai; Zheng, Zhiming

    2009-01-01

    Sequences with good correlation properties are widely used in engineering applications, especially in the area of communications. Among the known sequences, cyclotomic families have the optimal autocorrelation property. In this paper, we decide the cross-correlation function of the known cyclotomic sequences completely. Moreover, to get our results, the relations between the multiplier group and the decimations of the characteristic sequence are also established for an arbitrary difference set.

  11. 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...

  12. Incidental Sequence Learning across the Lifespan

    Science.gov (United States)

    Weiermann, Brigitte; Meier, Beat

    2012-01-01

    The purpose of the present study was to investigate incidental sequence learning across the lifespan. We tested 50 children (aged 7-16), 50 young adults (aged 20-30), and 50 older adults (aged >65) with a sequence learning paradigm that involved both a task and a response sequence. After several blocks of practice, all age groups slowed down…

  13. Hardware Acceleration of Bioinformatics Sequence Alignment Applications

    NARCIS (Netherlands)

    Hasan, L.

    2011-01-01

    Biological sequence alignment is an important and challenging task in bioinformatics. Alignment may be defined as an arrangement of two or more DNA or protein sequences to highlight the regions of their similarity. Sequence alignment is used to infer the evolutionary relationship between a set of pr

  14. Disease gene identification strategies for exome sequencing

    NARCIS (Netherlands)

    Gilissen, C.; Hoischen, A.; Brunner, H.G.; Veltman, J.A.

    2012-01-01

    Next generation sequencing can be used to search for Mendelian disease genes in an unbiased manner by sequencing the entire protein-coding sequence, known as the exome, or even the entire human genome. Identifying the pathogenic mutation amongst thousands to millions of genomic variants is a major c

  15. PacBio Sequencing and Its Applications

    Institute of Scientific and Technical Information of China (English)

    Anthony Rhoads; Kin Fai Au

    2015-01-01

    Single-molecule, real-time sequencing developed by Pacific BioSciences offers longer read lengths than the second-generation sequencing (SGS) technologies, making it well-suited for unsolved problems in genome, transcriptome, and epigenetics research. The highly-contiguous de novo assemblies using PacBio sequencing can close gaps in current reference assemblies and characterize structural variation (SV) in personal genomes. With longer reads, we can sequence through extended repetitive regions and detect mutations, many of which are associated with dis-eases. Moreover, PacBio transcriptome sequencing is advantageous for the identification of gene isoforms and facilitates reliable discoveries of novel genes and novel isoforms of annotated genes, due to its ability to sequence full-length transcripts or fragments with significant lengths. Addition-ally, PacBio’s sequencing technique provides information that is useful for the direct detection of base modifications, such as methylation. In addition to using PacBio sequencing alone, many hybrid sequencing strategies have been developed to make use of more accurate short reads in conjunction with PacBio long reads. In general, hybrid sequencing strategies are more affordable and scalable especially for small-size laboratories than using PacBio Sequencing alone. The advent of PacBio sequencing has made available much information that could not be obtained via SGS alone.

  16. Joint Sequence Analysis: Association and Clustering

    Science.gov (United States)

    Piccarreta, Raffaella

    2017-01-01

    In its standard formulation, sequence analysis aims at finding typical patterns in a set of life courses represented as sequences. Recently, some proposals have been introduced to jointly analyze sequences defined on different domains (e.g., work career, partnership, and parental histories). We introduce measures to evaluate whether a set of…

  17. RNAome sequencing delineates the complete RNA landscape

    NARCIS (Netherlands)

    K.W.J. Derks (Kasper); J. Pothof (Joris)

    2015-01-01

    textabstractStandard RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species. For example, small and large RNAs from the same sample cannot be sequenced in a single sequence run. We designed RNAome sequencing, which is a strand-specif

  18. The recurrence sequence via the Fibonacci groups

    Science.gov (United States)

    Aküzüm, Yeşim; Deveci, Ömür

    2016-04-01

    This work develops properties of the recurrence sequence defined by the aid of the relation matrix of the Fibonacci groups. The study of this sequence modulo m yields cyclic groups and semigroups from generating matrix. Finally, we extend the sequence defined to groups and then, we obtain its period in the Fibonacci groups.

  19. Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.

    Directory of Open Access Journals (Sweden)

    Leho Tedersoo

    Full Text Available Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/ for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/, the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.

  20. Exome sequencing: what clinicians need to know

    Directory of Open Access Journals (Sweden)

    Sastre L

    2014-03-01

    Full Text Available Leandro SastreInstituto de Investigaciones Biomédicas, CSIC/UAM, C/Arturo Duperier 4, Madrid, Spain; Terapias Experimentales y Biomarcadores en Cáncer, IdiPaz, Madrid, Spain; CIBER de Enfermedades Raras, CIBERER, Valencia, SpainAbstract: The recent development of high throughput methods of deoxyribonucleic acid (DNA sequencing has made it possible to determine individual genome sequences and their specific variations. A region of particular interest is the protein-coding part of the genome, or exome, which is composed of gene exons. The principles of exome purification and sequencing will be described in this review, as well as analyses of the data generated. Results will be discussed in terms of their possible functional and clinical significance. The advantages and limitations of exome sequencing will be compared to those of other massive sequencing approaches such as whole-genome sequencing, ribonucleic acid sequencing or selected DNA sequencing. Exome sequencing has been used recently in the study of various diseases. Monogenic diseases with Mendelian inheritance are among these, but studies have also been carried out on genetic variations that represent risk factors for complex diseases. Cancer is another intensive area for exome sequencing studies. Several examples of the use of exome sequencing in the diagnosis, prognosis, and treatment of these diseases will be described. Finally, remaining challenges and some practical and ethical considerations for the clinical application of exome sequencing will be discussed.Keywords: massively parallel sequencing, RNA sequencing, whole-genome sequencing, genetic variants, molecular diagnosis, pharmacogenomics, personalized medicine, NGS, SGS, SNP, SNV

  1. Chip-based sequencing nucleic acids

    Energy Technology Data Exchange (ETDEWEB)

    Beer, Neil Reginald

    2014-08-26

    A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.

  2. MatrixPlot: visualizing sequence constraints

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Stærfeldt, Hans Henrik; Lund, Ole

    1999-01-01

    MatrixPlot: visualizing sequence constraints. Sub-title Abstract Summary : MatrixPlot is a program for making high-quality matrix plots, such as mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional coordinates. The user can add information...... about the sequences (e.g. a sequence logo profile) along the edges of the plot, as well as zoom in on any region in the plot. Availability : MatrixPlot can be obtained on request, and can also be accessed online at http://www. cbs.dtu.dk/services/MatrixPlot. Contact : gorodkin@cbs.dtu.dk...

  3. Chip-based sequencing nucleic acids

    Science.gov (United States)

    Beer, Neil Reginald

    2014-08-26

    A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.

  4. MatrixPlot: visualizing sequence constraints

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Stærfeldt, Hans Henrik; Lund, Ole

    1999-01-01

    MatrixPlot: visualizing sequence constraints. Sub-title Abstract Summary : MatrixPlot is a program for making high-quality matrix plots, such as mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional coordinates. The user can add information...... about the sequences (e.g. a sequence logo profile) along the edges of the plot, as well as zoom in on any region in the plot. Availability : MatrixPlot can be obtained on request, and can also be accessed online at http://www. cbs.dtu.dk/services/MatrixPlot. Contact : gorodkin@cbs.dtu.dk...

  5. Permutation Entropy for Random Binary Sequences

    Directory of Open Access Journals (Sweden)

    Lingfeng Liu

    2015-12-01

    Full Text Available In this paper, we generalize the permutation entropy (PE measure to binary sequences, which is based on Shannon’s entropy, and theoretically analyze this measure for random binary sequences. We deduce the theoretical value of PE for random binary sequences, which can be used to measure the randomness of binary sequences. We also reveal the relationship between this PE measure with other randomness measures, such as Shannon’s entropy and Lempel–Ziv complexity. The results show that PE is consistent with these two measures. Furthermore, we use PE as one of the randomness measures to evaluate the randomness of chaotic binary sequences.

  6. Computing with Hereditarily Finite Sequences

    CERN Document Server

    Tarau, Paul

    2011-01-01

    e use Prolog as a flexible meta-language to provide executable specifications of some fundamental mathematical objects and their transformations. In the process, isomorphisms are unraveled between natural numbers and combinatorial objects (rooted ordered trees representing hereditarily finite sequences and rooted ordered binary trees representing G\\"odel's System {\\bf T} types). This paper focuses on an application that can be seen as an unexpected "paradigm shift": we provide recursive definitions showing that the resulting representations are directly usable to perform symbolically arbitrary-length integer computations. Besides the theoretically interesting fact of "breaking the arithmetic/symbolic barrier", the arithmetic operations performed with symbolic objects like trees or types turn out to be genuinely efficient -- we derive implementations with asymptotic performance comparable to ordinary bitstring implementations of arbitrary-length integer arithmetic. The source code of the paper, organized as a ...

  7. [DNA sequencing technology and automatization of it].

    Science.gov (United States)

    Kraev, A S

    1991-01-01

    Precise manipulations with genetic material, typical for modern experiments in molecular biology and in new biotechnology, require a capability to determine DNA base sequence. This capability enables today to exploit specific genetic knowledge for the dissection of complex cell processes and for modulation of cell metabolism in transgenic organisms. The review focuses on such DNA sequencing technologies that are widespread in general laboratory practice. They can safely be called, with the availability of commercial reagents, industrial techniques. Modern DNA sequencing requires recurrent breakdown of large genomic DNA into smaller pieces, that are then amplified, sequenced and the initial long stretch reconstructed via overlap of small pieces. The DNA sequencing process has several steps: a DNA fragment is obtained in sufficient quantity and purity, it is converted to a form suitable for a particular sequencing method, a sequencing reaction is performed and its products fractionated; and finally the resultant data are interpreted (i.e. an autoradiograph is read into a computer memory) and a long sequence in reconstructed via overlap of short stretches. These steps are considered in separate parts; an accent is made on sequencing strategies with respect to their biological task. In the last part, possibilities for automation of sequencing experiment are considered, followed by a discussion of domestic problems in DNA sequencing.

  8. Experimental investigation of an RNA sequence space

    Science.gov (United States)

    Lee, Youn-Hyung; Dsouza, Lisa; Fox, George E.

    1993-12-01

    Modern rRNAs are the historic consequence of an ongoing evolutionary exploration of a sequence space. These extant sequences belong to a special subset of the sequence space that is comprised only of those primary sequences that can validly perform the biological function(s) required of the particular RNA. If it were possible to readily identify all such valid sequences, stochastic predictions could be made about the relative likelihood of various evolutionary pathways available to an RNA. Herein an experimental system which can assess whether a particular sequence is likely to have validity as a eubacterial 5S rRNA is described. A total of ten naturally occurring, and hence known to be valid, sequences and two point mutants of unknown validity were used to test the usefulness of the approach. Nine of the ten valid sequences tested positive whereas both mutants tested as clearly defective. The tenth valid sequence gave results that would be interpreted as reflecting a borderline status were the answer not known. These results demonstrate that it is possible to experimentally determine which sequences in local regions of the sequence space are potentially valid 5S rRNAs. This approach will allow direct study of the constraints governing RNA evolution and allow inquiry into how the last common ancestor of extant life apparently came to have very complex ribosomal RNAs that subsequently were very conserved.

  9. Discovering novel sequence motifs with MEME.

    Science.gov (United States)

    Bailey, Timothy L

    2002-11-01

    This unit illustrates how to use MEME to discover motifs in a group of related nucleotide or peptide sequences. A MEME motif is a sequence pattern that occurs repeatedly in one or more sequences in the input group. MEME can be used to discover novel patterns because it bases its discoveries only on the input sequences, not on any prior knowledge (such as databases of known motifs). The input to MEME is a set of unaligned sequences of the same type (peptide or nucleotide). For each motif it discovers, MEME reports the occurrences (sites), consensus sequence, and the level of conservation (information content) at each position in the pattern. MEME also produces block diagrams showing where all of the discovered motifs occur in the training set sequences. MEME's hypertext (HTML) output also contains buttons that allow for the convenient use of the motifs in other searches.

  10. Design of Digital Hybrid Chaotic Sequence Generator

    Institute of Scientific and Technical Information of China (English)

    RAO Nini; ZENG Dong

    2004-01-01

    The feasibility of the hybrid chaotic sequences as the spreading codes in code divided multiple access(CDMA) system is analyzed.The design and realization of the digital hybrid chaotic sequence generator by very high speed integrated circuit hardware description language(VHDL) are described.A valid hazard canceledl method is presented.Computer simulations show that the stable digital sequence waveforms can be produced.The correlations of the digital hybrid chaotic sequences are compared with those of m-sequences.The results show that the correlations of the digital hybrid chaotic sequences are almost as good as those of m-sequences.The works in this paper explored a road for the practical applications of chaos.

  11. Sequencing technologies for animal cell culture research.

    Science.gov (United States)

    Kremkow, Benjamin G; Lee, Kelvin H

    2015-01-01

    Over the last 10 years, 2nd and 3rd generation sequencing technologies have made the use of genomic sequencing within the animal cell culture community increasingly commonplace. Each technology's defining characteristics are unique, including the cost, time, sequence read length, daily throughput, and occurrence of sequence errors. Given each sequencing technology's intrinsic advantages and disadvantages, the optimal technology for a given experiment depends on the particular experiment's objective. This review discusses the current characteristics of six next-generation sequencing technologies, compares the differences between them, and characterizes their relevance to the animal cell culture community. These technologies are continually improving, as evidenced by the recent achievement of the field's benchmark goal: sequencing a human genome for less than $1,000.

  12. Assembly Sequence Planning for Mechanical Products

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    A method for assembly sequence planning is proposed in this paper. First, two methods for assembly sequence planning are compared, which are indirect method and direct method. Then, the limits of the previous assembly planning system are pointed out. On the basis of indirect method, an improved method for assembly sequence planning is put forward. This method is composed of four parts, which are assembly modeling for products, assembly sequence representing, assembly sequence planning, and evaluation and optimization. The assembly model is established by human machine interaction, and the assembly model contains components' information and the assembly relation among the components. The assembly sequence planning is based on the breaking up of the assembly model. And/or graph is used to represent assembly sequence set. Every component which satisfies the disassembly condition is recorded as a node of an and/or graph. After the disassembly sequence and/or graph is generated, heuristic algorithm - AO* algorithm is used to search the disassembly sequence and/or graph, and the optimum assembly sequence planning is realized. This method is proved to be effective in a prototype system which is a sub-project of a state 863/CIMS research project of China - ‘Concurrent Engineering’.

  13. Randomness in Sequence Evolution Increases over Time.

    Directory of Open Access Journals (Sweden)

    Guangyu Wang

    Full Text Available The second law of thermodynamics states that entropy, as a measure of randomness in a system, increases over time. Although studies have investigated biological sequence randomness from different aspects, it remains unknown whether sequence randomness changes over time and whether this change consists with the second law of thermodynamics. To capture the dynamics of randomness in molecular sequence evolution, here we detect sequence randomness based on a collection of eight statistical random tests and investigate the randomness variation of coding sequences with an application to Escherichia coli. Given that core/essential genes are more ancient than specific/non-essential genes, our results clearly show that core/essential genes are more random than specific/non-essential genes and accordingly indicate that sequence randomness indeed increases over time, consistent well with the second law of thermodynamics. We further find that an increase in sequence randomness leads to increasing randomness of GC content and longer sequence length. Taken together, our study presents an important finding, for the first time, that sequence randomness increases over time, which may provide profound insights for unveiling the underlying mechanisms of molecular sequence evolution.

  14. Effects of an Additional Sequence of Color Stimuli on Visuomotor Sequence Learning

    Science.gov (United States)

    Tanaka, Kanji; Watanabe, Katsumi

    2017-01-01

    Through practice, people are able to integrate a secondary sequence (e.g., a stimulus-based sequence) into a primary sequence (e.g., a response-based sequence), but it is still controversial whether the integrated sequences lead to better learning than only the primary sequence. In the present study, we aimed to investigate the effects of a sequence that integrated space and color sequences on early and late learning phases (corresponding to effector-independent and effector-dependent learning, respectively) and how the effects differed in the integrated and primary sequences in each learning phase. In the task, the participants were required to learn a sequence of button presses using trial-and-error and to perform the sequence successfully for 20 trials (m × n task). First, in the baseline task, all participants learned a non-colored sequence, in which the response button always turned red. Then, in the learning task, the participants were assigned to two groups: a colored sequence group (i.e., space and color) or a non-colored sequence group (i.e., space). In the colored sequence, the response button turned a pre-determined color and the participants were instructed to attend to the sequences of both location and color as much as they could. The results showed that the participants who performed the colored sequence acquired the correct button presses of the sequence earlier, but showed a slower mean performance time than those who performed the non-colored sequence. Moreover, the slower performance time in the colored sequence group remained in a subsequent transfer task in which the spatial configurations of the buttons were vertically mirrored from the learning task. These results indicated that if participants explicitly attended to both the spatial response sequence and color stimulus sequence at the same time, they could develop their spatial representations of the sequence earlier (i.e., early development of the effector-independent learning), but might

  15. Comparison of sequence reads obtained from three next-generation sequencing platforms.

    Directory of Open Access Journals (Sweden)

    Shingo Suzuki

    Full Text Available Next-generation sequencing technologies enable the rapid cost-effective production of sequence data. To evaluate the performance of these sequencing technologies, investigation of the quality of sequence reads obtained from these methods is important. In this study, we analyzed the quality of sequence reads and SNP detection performance using three commercially available next-generation sequencers, i.e., Roche Genome Sequencer FLX System (FLX, Illumina Genome Analyzer (GA, and Applied Biosystems SOLiD system (SOLiD. A common genomic DNA sample obtained from Escherichia coli strain DH1 was applied to these sequencers. The obtained sequence reads were aligned to the complete genome sequence of E. coli DH1, to evaluate the accuracy and sequence bias of these sequence methods. We found that the fraction of "junk" data, which could not be aligned to the reference genome, was largest in the data set of SOLiD, in which about half of reads could not be aligned. Among data sets after alignment to the reference, sequence accuracy was poorest in GA data sets, suggesting relatively low fidelity of the elongation reaction in the GA method. Furthermore, by aligning the sequence reads to the E. coli strain W3110, we screened sequence differences between two E. coli strains using data sets of three different next-generation platforms. The results revealed that the detected sequence differences were similar among these three methods, while the sequence coverage required for the detection was significantly small in the FLX data set. These results provided valuable information on the quality of short sequence reads and the performance of SNP detection in three next-generation sequencing platforms.

  16. Continued fractions and heavy sequences

    CERN Document Server

    Boshernitzan, Michael

    2009-01-01

    We initiate the study of the sets $H(c)$, $0=x-[x]$ stands for the fractional part of $x\\in \\mathbb R$. We prove that, for rational $c$, the sets $H(c)$ are of positive Hausdorff dimension and, in particular, are uncountable. For integers $m\\geq1$, we obtain a surprising characterization of the numbers $\\alpha\\in H_m= H(\\frac1m)$ in terms of their continued fraction expansions: The odd entries (partial quotients) of these expansions are divisible by $m$. The characterization implies that $x\\in H_m$ if and only if $\\frac 1{mx} \\in H_m$, for $x>0$. We are unaware of a direct proof of this equivalence, without making a use of the mentioned characterization of the sets $H_m$. We also introduce the dual sets $\\hat H_m$ of reals $y$ for which the sequence of integers $\\big([ky]\\big)_{k\\geq1}$ consistently hits the set $m\\mathbb Z$ with the at least expected frequency $\\frac1m$ and establish the connection with the sets $H_m$: {2mm} If $xy=m$ for $x,y>0$, then $x\\in H_m$ if and only if $y\\in \\hat H_m$. The motivatio...

  17. Pareto optimal pairwise sequence alignment.

    Science.gov (United States)

    DeRonne, Kevin W; Karypis, George

    2013-01-01

    Sequence alignment using evolutionary profiles is a commonly employed tool when investigating a protein. Many profile-profile scoring functions have been developed for use in such alignments, but there has not yet been a comprehensive study of Pareto optimal pairwise alignments for combining multiple such functions. We show that the problem of generating Pareto optimal pairwise alignments has an optimal substructure property, and develop an efficient algorithm for generating Pareto optimal frontiers of pairwise alignments. All possible sets of two, three, and four profile scoring functions are used from a pool of 11 functions and applied to 588 pairs of proteins in the ce_ref data set. The performance of the best objective combinations on ce_ref is also evaluated on an independent set of 913 protein pairs extracted from the BAliBASE RV11 data set. Our dynamic-programming-based heuristic approach produces approximated Pareto optimal frontiers of pairwise alignments that contain comparable alignments to those on the exact frontier, but on average in less than 1/58th the time in the case of four objectives. Our results show that the Pareto frontiers contain alignments whose quality is better than the alignments obtained by single objectives. However, the task of identifying a single high-quality alignment among those in the Pareto frontier remains challenging.

  18. Comparison of next-generation sequencing systems.

    Science.gov (United States)

    Liu, Lin; Li, Yinhu; Li, Siliang; Hu, Ni; He, Yimin; Pong, Ray; Lin, Danni; Lu, Lihua; Law, Maggie

    2012-01-01

    With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence information is within reach to aid the achievement of goals to decode life mysteries, make better crops, detect pathogens, and improve life qualities. NGS systems are typically represented by SOLiD/Ion Torrent PGM from Life Sciences, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and GS FLX Titanium/GS Junior from Roche. Beijing Genomics Institute (BGI), which possesses the world's biggest sequencing capacity, has multiple NGS systems including 137 HiSeq 2000, 27 SOLiD, one Ion Torrent PGM, one MiSeq, and one 454 sequencer. We have accumulated extensive experience in sample handling, sequencing, and bioinformatics analysis. In this paper, technologies of these systems are reviewed, and first-hand data from extensive experience is summarized and analyzed to discuss the advantages and specifics associated with each sequencing system. At last, applications of NGS are summarized.

  19. The genome sequence of parrot bornavirus 5.

    Science.gov (United States)

    Guo, Jianhua; Tizard, Ian

    2015-12-01

    Although several new avian bornaviruses have recently been described, information on their evolution, virulence, and sequence are often limited. Here we report the complete genome sequence of parrot bornavirus 5 (PaBV-5) isolated from a case of proventricular dilatation disease in a Palm cockatoo (Probosciger aterrimus). The complete genome consists of 8842 nucleotides with distinct 5' and 3' end sequences. This virus shares nucleotide sequence identities of 69-74 % with other bornaviruses in the genomic regions excluding the 5' and 3' terminal sequences. Phylogenetic analysis based on the genomic regions demonstrated this new isolate is an isolated branch within the clade that includes the aquatic bird bornaviruses and the passerine bornaviruses. Based on phylogenetic analyses and its low nucleotide sequence identities with other bornavirus, we support the proposal that PaBV-5 be assigned to a new bornavirus species:- Psittaciform 2 bornavirus.

  20. Application of ecostratigraphy to sequences tratigraphy

    Institute of Scientific and Technical Information of China (English)

    殷鸿福; 童金南; 张克信; 吴顺宝

    1997-01-01

    The results of ecostratigraphy can directly serve sequence stratigraphy. The habitat type curve is useful not only in the analysis of sequences and parasequences, but also in demonstration of the process of regional sea level change. The various biological surfaces usually coincide with or relate to the boundaries of sequences or system tracts. The ecostratigraphic framework composed of coenozones, community sequences and ecotracts with good timing completely corresponds to the sequence stratigraphic framework of the sedimentary basin. Therefore, through establishment of the habitat type curve in individual section, recognition of the various biological surfaces, regional ecostratigraphic correlation and the formation of an ecostratigraphic framework of the sedimentary basin, ecostratigraphy plays an important role in the study of sequence stratigraphy and the reconstruction of regional and even global sea level changes.

  1. Sequencing intractable DNA to close microbial genomes.

    Science.gov (United States)

    Hurt, Richard A; Brown, Steven D; Podar, Mircea; Palumbo, Anthony V; Elias, Dwayne A

    2012-01-01

    Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  2. Some fundamenltal problems in outcrop sequence stratigraphy

    Institute of Scientific and Technical Information of China (English)

    王训练

    1999-01-01

    Some fundamental problems in outcrop sequence stratigraphy are discussed, and the following ideas are obtained: (i) Detailed sedimentary facies analysis and study on stacking pattern of parasequences, careful and accurate study of biostratigraphy, and stratigraphical correlation of different facies areas are the essential conditions for proper identification of sequences. (ii) The first flooding surface may be an ideal sequence boundary in outcrop sequence stratigraphy, where the most distinct palaeontological and sedimentary changes take place and make the surface readily recognizable in outcrop. (iii) The distribution in space, specially in different facies belts, is regarded as an important criterion for defining and recognizing the various orders of sequences. The third-order sequence is probably global in nature , which may be discerned in various depositional facies belts at least on one continental margin, and can be correlated over long distances, sometimes worldwide. (iv) The first flooding surf

  3. Sequencing intractable DNA to close microbial genomes.

    Directory of Open Access Journals (Sweden)

    Richard A Hurt

    Full Text Available Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps and the Desulfovibrio africanus genome (1 intractable gap. The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  4. Evolutionarily conserved sequences on human chromosome 21

    Energy Technology Data Exchange (ETDEWEB)

    Frazer, Kelly A.; Sheehan, John B.; Stokowski, Renee P.; Chen, Xiyin; Hosseini, Roya; Cheng, Jan-Fang; Fodor, Stephen P.A.; Cox, David R.; Patil, Nila

    2001-09-01

    Comparison of human sequences with the DNA of other mammals is an excellent means of identifying functional elements in the human genome. Here we describe the utility of high-density oligonucleotide arrays as a rapid approach for comparing human sequences with the DNA of multiple species whose sequences are not presently available. High-density arrays representing approximately 22.5 Mb of nonrepetitive human chromosome 21 sequence were synthesized and then hybridized with mouse and dog DNA to identify sequences conserved between humans and mice (human-mouse elements) and between humans and dogs (human-dog elements). Our data show that sequence comparison of multiple species provides a powerful empiric method for identifying actively conserved elements in the human genome. A large fraction of these evolutionarily conserved elements are present in regions on chromosome 21 that do not encode known genes.

  5. Predicting Contextual Sequences via Submodular Function Maximization

    CERN Document Server

    Dey, Debadeepta; Hebert, Martial; Bagnell, J Andrew

    2012-01-01

    Sequence optimization, where the items in a list are ordered to maximize some reward has many applications such as web advertisement placement, search, and control libraries in robotics. Previous work in sequence optimization produces a static ordering that does not take any features of the item or context of the problem into account. In this work, we propose a general approach to order the items within the sequence based on the context (e.g., perceptual information, environment description, and goals). We take a simple, efficient, reduction-based approach where the choice and order of the items is established by repeatedly learning simple classifiers or regressors for each "slot" in the sequence. Our approach leverages recent work on submodular function maximization to provide a formal regret reduction from submodular sequence optimization to simple cost-sensitive prediction. We apply our contextual sequence prediction algorithm to optimize control libraries and demonstrate results on two robotics problems: ...

  6. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

    DEFF Research Database (Denmark)

    de Souza, S J; Camargo, A A; Briones, M R;

    2000-01-01

    by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48......Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central...... coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1, 181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes...

  7. Preparing DNA libraries for multiplexed paired-end deep sequencing for Illumina GA sequencers.

    Science.gov (United States)

    Son, Mike S; Taylor, Ronald K

    2011-02-01

    Whole-genome sequencing, also known as deep sequencing, is becoming a more affordable and efficient way to identify SNP mutations, deletions, and insertions in DNA sequences across several different strains. Two major obstacles preventing the widespread use of deep sequencers are the costs involved in services used to prepare DNA libraries for sequencing and the overall accuracy of the sequencing data. This unit describes the preparation of DNA libraries for multiplexed paired-end sequencing using the Illumina GA series sequencer. Self-preparation of DNA libraries can help reduce overall expenses, especially if optimization is required for the different samples, and use of the Illumina GA Sequencer can improve the quality of the data.

  8. EGNAS: an exhaustive DNA sequence design algorithm

    Directory of Open Access Journals (Sweden)

    Kick Alfred

    2012-06-01

    Full Text Available Abstract Background The molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exhaustive DNA sequence design algorithm that allows to generate sets containing a maximum number of sequences with defined properties. EGNAS (Exhaustive Generation of Nucleic Acid Sequences offers the possibility of controlling both interstrand and intrastrand properties. The guanine-cytosine content can be adjusted. Sequences can be forced to start and end with guanine or cytosine. This option reduces the risk of “fraying” of DNA strands. It is possible to limit cross hybridizations of a defined length, and to adjust the uniqueness of sequences. Self-complementarity and hairpin structures of certain length can be avoided. Sequences and subsequences can optionally be forbidden. Furthermore, sequences can be designed to have minimum interactions with predefined strands and neighboring sequences. Results The algorithm is realized in a C++ program. TAG sequences can be generated and combined with primers for single-base extension reactions, which were described for multiplexed genotyping of single nucleotide polymorphisms. Thereby, possible foldback through intrastrand interaction of TAG-primer pairs can be limited. The design of sequences for specific attachment of molecular constructs to DNA origami is presented. Conclusions We developed a new software tool called EGNAS for the design of unique nucleic acid sequences. The presented exhaustive algorithm allows to generate greater sets of sequences than with previous software and equal constraints. EGNAS is freely available for noncommercial use at http://www.chm.tu-dresden.de/pc6/EGNAS.

  9. WEAK CONVERGENCE OF HENSTOCK INTEGRABLE SEQUENCES

    Institute of Scientific and Technical Information of China (English)

    LuisaDiPiazza

    1994-01-01

    Some relationships between pointwise and weak convergence of a sequence of Henstock integrable functions are studied, In particular it is provided an example of a sequence of Henstock integrable functions whose pointwise limit is different from the weak one. By introducing an asymptotic version of the Henstock equiintegrability notion it is given a necessary and sufficient condition in order that a pointwisely convergent sequence of Henstock integrable functions is weakly convergent to its pointwise limit.

  10. Exome sequencing and genetic testing for MODY.

    Directory of Open Access Journals (Sweden)

    Stefan Johansson

    Full Text Available CONTEXT: Genetic testing for monogenic diabetes is important for patient care. Given the extensive genetic and clinical heterogeneity of diabetes, exome sequencing might provide additional diagnostic potential when standard Sanger sequencing-based diagnostics is inconclusive. OBJECTIVE: The aim of the study was to examine the performance of exome sequencing for a molecular diagnosis of MODY in patients who have undergone conventional diagnostic sequencing of candidate genes with negative results. RESEARCH DESIGN AND METHODS: We performed exome enrichment followed by high-throughput sequencing in nine patients with suspected MODY. They were Sanger sequencing-negative for mutations in the HNF1A, HNF4A, GCK, HNF1B and INS genes. We excluded common, non-coding and synonymous gene variants, and performed in-depth analysis on filtered sequence variants in a pre-defined set of 111 genes implicated in glucose metabolism. RESULTS: On average, we obtained 45 X median coverage of the entire targeted exome and found 199 rare coding variants per individual. We identified 0-4 rare non-synonymous and nonsense variants per individual in our a priori list of 111 candidate genes. Three of the variants were considered pathogenic (in ABCC8, HNF4A and PPARG, respectively, thus exome sequencing led to a genetic diagnosis in at least three of the nine patients. Approximately 91% of known heterozygous SNPs in the target exomes were detected, but we also found low coverage in some key diabetes genes using our current exome sequencing approach. Novel variants in the genes ARAP1, GLIS3, MADD, NOTCH2 and WFS1 need further investigation to reveal their possible role in diabetes. CONCLUSION: Our results demonstrate that exome sequencing can improve molecular diagnostics of MODY when used as a complement to Sanger sequencing. However, improvements will be needed, especially concerning coverage, before the full potential of exome sequencing can be realized.

  11. cis sequence effects on gene expression

    Directory of Open Access Journals (Sweden)

    Jacobs Kevin

    2007-08-01

    Full Text Available Abstract Background Sequence and transcriptional variability within and between individuals are typically studied independently. The joint analysis of sequence and gene expression variation (genetical genomics provides insight into the role of linked sequence variation in the regulation of gene expression. We investigated the role of sequence variation in cis on gene expression (cis sequence effects in a group of genes commonly studied in cancer research in lymphoblastoid cell lines. We estimated the proportion of genes exhibiting cis sequence effects and the proportion of gene expression variation explained by cis sequence effects using three different analytical approaches, and compared our results to the literature. Results We generated gene expression profiling data at N = 697 candidate genes from N = 30 lymphoblastoid cell lines for this study and used available candidate gene resequencing data at N = 552 candidate genes to identify N = 30 candidate genes with sufficient variance in both datasets for the investigation of cis sequence effects. We used two additive models and the haplotype phylogeny scanning approach of Templeton (Tree Scanning to evaluate association between individual SNPs, all SNPs at a gene, and diplotypes, with log-transformed gene expression. SNPs and diplotypes at eight candidate genes exhibited statistically significant (p cis sequence effects in our study, respectively. Conclusion Based on analysis of our results and the extant literature, one in four genes exhibits significant cis sequence effects, and for these genes, about 30% of gene expression variation is accounted for by cis sequence variation. Despite diverse experimental approaches, the presence or absence of significant cis sequence effects is largely supported by previously published studies.

  12. Some properties of generalized Fibonacci sequence

    Science.gov (United States)

    Chong, Chin-Yoon; Ho, C. K.

    2015-12-01

    For all non-negative integer n and real constants a, b, p and q, the generalized Fibonacci sequence {U n } is defined by Un+2 = pUn+1 + qUn with the initial values U0 = a and U1 = b. Throughout the paper, we study some properties of the generalized Fibonacci sequence. Our results will motivate some new research problems concerning the contribution of the generalized sequence.

  13. Hardware Accelerated Sequence Alignment with Traceback

    Directory of Open Access Journals (Sweden)

    Scott Lloyd

    2009-01-01

    in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space-efficient, global sequence alignment algorithm and architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations. With 256 processing elements in FPGA technology, a performance gain over 300 times that of a desktop computer is demonstrated on sequence lengths of 16000. For greater performance, the architecture is scalable to more processing elements.

  14. Recursive sequences in first-year calculus

    Science.gov (United States)

    Krainer, Thomas

    2016-02-01

    This article provides ready-to-use supplementary material on recursive sequences for a second-semester calculus class. It equips first-year calculus students with a basic methodical procedure based on which they can conduct a rigorous convergence or divergence analysis of many simple recursive sequences on their own without the need to invoke inductive arguments as is typically required in calculus textbooks. The sequences that are accessible to this kind of analysis are predominantly (eventually) monotonic, but also certain recursive sequences that alternate around their limit point as they converge can be considered.

  15. Maize genome sequencing by methylation filtration.

    Science.gov (United States)

    Palmer, Lance E; Rabinowicz, Pablo D; O'Shaughnessy, Andrew L; Balija, Vivekanand S; Nascimento, Lidia U; Dike, Sujit; de la Bastide, Melissa; Martienssen, Robert A; McCombie, W Richard

    2003-12-19

    Gene enrichment strategies offer an alternative to sequencing large and repetitive genomes such as that of maize. We report the generation and analysis of nearly 100,000 undermethylated (or methylation filtration) maize sequences. Comparison with the rice genome reveals that methylation filtration results in a more comprehensive representation of maize genes than those that result from expressed sequence tags or transposon insertion sites sequences. About 7% of the repetitive DNA is unmethylated and thus selected in our libraries, but potentially active transposons and unmethylated organelle genomes can be identified. Reverse transcription polymerase chain reaction can be used to finish the maize transcriptome.

  16. Genomic sequencing of Pleistocene cave bears

    Energy Technology Data Exchange (ETDEWEB)

    Noonan, James P.; Hofreiter, Michael; Smith, Doug; Priest, JamesR.; Rohland, Nadin; Rabeder, Gernot; Krause, Johannes; Detter, J. Chris; Paabo, Svante; Rubin, Edward M.

    2005-04-01

    Despite the information content of genomic DNA, ancient DNA studies to date have largely been limited to amplification of mitochondrial DNA due to technical hurdles such as contamination and degradation of ancient DNAs. In this study, we describe two metagenomic libraries constructed using unamplified DNA extracted from the bones of two 40,000-year-old extinct cave bears. Analysis of {approx}1 Mb of sequence from each library showed that, despite significant microbial contamination, 5.8 percent and 1.1 percent of clones in the libraries contain cave bear inserts, yielding 26,861 bp of cave bear genome sequence. Alignment of this sequence to the dog genome, the closest sequenced genome to cave bear in terms of evolutionary distance, revealed roughly the expected ratio of cave bear exons, repeats and conserved noncoding sequences. Only 0.04 percent of all clones sequenced were derived from contamination with modern human DNA. Comparison of cave bear with orthologous sequences from several modern bear species revealed the evolutionary relationship of these lineages. Using the metagenomic approach described here, we have recovered substantial quantities of mammalian genomic sequence more than twice as old as any previously reported, establishing the feasibility of ancient DNA genomic sequencing programs.

  17. Detecting Emotions from Connected Action Sequences

    Science.gov (United States)

    Bernhardt, Daniel; Robinson, Peter

    In this paper we deal with the problem of detecting emotions from the body movements produced by naturally connected action sequences. Although action sequences are one of the most common forms of body motions in everyday scenarios their potential for emotion recognition has not been explored in the past. We show that there are fundamental differences between actions recorded in isolation and in natural sequences and demonstrate a number of techniques which allow us to correctly label action sequences with one of four emotions up to 86% of the time. Our results bring us an important step closer to recognizing emotions from body movements in natural scenarios.

  18. Researches on Sequence of Plant Cystatin: Phytocystatin

    Institute of Scientific and Technical Information of China (English)

    QINQingfeng; HEWei; LIANGJun; ZHANGXingyao

    2005-01-01

    Plant cystatins or phytocystatins are cysteine proteinase inhibitors exist widely in different plant species. Because they can kill insects by inhibiting the digestive function of the cysteine proteinase in gut, they are believed to play an important role in plant's defense against pests. Phytocystatins contain the conserved QXVXG motif and show some features on their sequence different to animal cystatins.After sequencing the protein directly and the cDNA clone, a large number of plant cystatins have been characterized. A multialignment with BLAST software and a detail analysis of 38 phytocystatins show that phytocystatins possess a specific conserved amino acid sequence [LRVI]-[AGT]-[RQKE]-[FY]-[AS]-[VI]-X-[EGHDQV]-[HYFQ]-N different to the conserved sequence demonstrated by Margis in 1998. This conserved sequence can be enough to detect with exclusivity phytocystatin sequences on protein data banks. A classification of these phytocystatins is performed and they can be divided into 3 groups according to their features on amino acid sequence, and the group-I can be still divided into 3 subgroups based on the feature of their amino acid and genomic sequence. By the CLUSTALX software,the most conserved nucleotide sequences of phytocystatins were found, which could be used to design the degenerate premiers to search new phytocystatins with PCR reaction.

  19. Massively parallel sequencing of forensic STRs

    DEFF Research Database (Denmark)

    Parson, Walther; Ballard, David; Budowle, Bruce

    2016-01-01

    The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data...... accessible genome assembly, and in place before the uptake of MPS by the general forensic community starts to generate sequence data on a large scale. While the established nomenclature for CE-based STR analysis will remain unchanged in the future, the nomenclature of sequence-based STR genotypes will need...

  20. Visible periodicity of strong nucleosome DNA sequences.

    Science.gov (United States)

    Salih, Bilal; Tripathi, Vijay; Trifonov, Edward N

    2015-01-01

    Fifteen years ago, Lowary and Widom assembled nucleosomes on synthetic random sequence DNA molecules, selected the strongest nucleosomes and discovered that the TA dinucleotides in these strong nucleosome sequences often appear at 10-11 bases from one another or at distances which are multiples of this period. We repeated this experiment computationally, on large ensembles of natural genomic sequences, by selecting the strongest nucleosomes--i.e. those with such distances between like-named dinucleotides, multiples of 10.4 bases, the structural and sequence period of nucleosome DNA. The analysis confirmed the periodicity of TA dinucleotides in the strong nucleosomes, and revealed as well other periodic sequence elements, notably classical AA and TT dinucleotides. The matrices of DNA bendability and their simple linear forms--nucleosome positioning motifs--are calculated from the strong nucleosome DNA sequences. The motifs are in full accord with nucleosome positioning sequences derived earlier, thus confirming that the new technique, indeed, detects strong nucleosomes. Species- and isochore-specific variations of the matrices and of the positioning motifs are demonstrated. The strong nucleosome DNA sequences manifest the highest hitherto nucleosome positioning sequence signals, showing the dinucleotide periodicities in directly observable rather than in hidden form.

  1. Multiplexed microsatellite recovery using massively parallel sequencing.

    Science.gov (United States)

    Jennings, T N; Knaus, B J; Mullins, T D; Haig, S M; Cronn, R C

    2011-11-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356,958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5 M (USD).

  2. Locomotor sequence learning in visually guided walking.

    Science.gov (United States)

    Choi, Julia T; Jensen, Peter; Nielsen, Jens Bo

    2016-04-01

    Voluntary limb modifications must be integrated with basic walking patterns during visually guided walking. In this study we tested whether voluntary gait modifications can become more automatic with practice. We challenged walking control by presenting visual stepping targets that instructed subjects to modify step length from one trial to the next. Our sequence learning paradigm is derived from the serial reaction-time (SRT) task that has been used in upper limb studies. Both random and ordered sequences of step lengths were used to measure sequence-specific and sequence-nonspecific learning during walking. In addition, we determined how age (i.e., healthy young adults vs. children) and biomechanical factors (i.e., walking speed) affected the rate and magnitude of locomotor sequence learning. The results showed that healthy young adults (age 24 ± 5 yr,n= 20) could learn a specific sequence of step lengths over 300 training steps. Younger children (age 6-10 yr,n= 8) had lower baseline performance, but their magnitude and rate of sequence learning were the same compared with those of older children (11-16 yr,n= 10) and healthy adults. In addition, learning capacity may be more limited at faster walking speeds. To our knowledge, this is the first study to demonstrate that spatial sequence learning can be integrated with a highly automatic task such as walking. These findings suggest that adults and children use implicit knowledge about the sequence to plan and execute leg movement during visually guided walking.

  3. A measurement of disorder in binary sequences

    Science.gov (United States)

    Gong, Longyan; Wang, Haihong; Cheng, Weiwen; Zhao, Shengmei

    2015-03-01

    We propose a complex quantity, AL, to characterize the degree of disorder of L-length binary symbolic sequences. As examples, we respectively apply it to typical random and deterministic sequences. One kind of random sequences is generated from a periodic binary sequence and the other is generated from the logistic map. The deterministic sequences are the Fibonacci and Thue-Morse sequences. In these analyzed sequences, we find that the modulus of AL, denoted by |AL | , is a (statistically) equivalent quantity to the Boltzmann entropy, the metric entropy, the conditional block entropy and/or other quantities, so it is a useful quantitative measure of disorder. It can be as a fruitful index to discern which sequence is more disordered. Moreover, there is one and only one value of |AL | for the overall disorder characteristics. It needs extremely low computational costs. It can be easily experimentally realized. From all these mentioned, we believe that the proposed measure of disorder is a valuable complement to existing ones in symbolic sequences.

  4. Strebel differentials and Hamilton sequences

    Institute of Scientific and Technical Information of China (English)

    LI; Zhong(

    2001-01-01

    [1]Strebel, K., Point shift differentials and extremal quasiconformal mappings, Annale Acad. Scle. Fenn. Math., 1998, 23: 475 -494.[2]Gardiner, F. P., Approximation of infinite dimensional Teichmutller space, Trans. Amer. Soc., 1999, 282: 367-383.[3]Lakic, N. , The Strebel points, Comptemp. Math. , 1997, 211: 417-431.[4]Wu Sheng jian, Hamilton sequences for extremal quasiconformal mappings of the unit disc, Science in China, Ser. A, 1999,42(10): 1033-1042.[5]Li Zhong, Qi Yi, A note on point shift differentials, Science in China, Ser. A, 1999, 42(5): 449-455.[6]Hamilton, R. S., Extremal quasiconformal mappings with prescribed boundary values, Trans. Amer. Math. Soc. , 1969,138: 399-406.[7]Krushkal, S. , Extremal quasiconformal mappings, Sirbirsk. Mat. Zh., 1969, 10: 573-583.[8]Reich, E., Strebel, K., Extremal quasiconformal mappings with given boundary values, Contributions to Analysis, New York: Academic Press, 1974, 375-391.[9]Strebel, K. , On quasiconformal mappings of open Riemann surfaces, Commemt. Math. Helr., 1978, 53: 301-321.[10]Earle, C., Li Zhong, Extremal quasiconformal mappings in plane domains, Quasiconformal Mappings and Analysis A Col-lection of Papers Honoring F. W. Gehring, New York: Springer-Verlag, 1998, 141-158.[11]Strebel, K., On quadratic differentials and extremal quasiconforrnal mappings, in Proc. of the Intern. Congress of Math.,Vancouver, 1974.[12]Li Zhong, Some new results on the geometry of infinite dimensional Teichmuller space, in Proceedings of the 3rd International Colloquium on Finite or Infinite Dimensional Complex Analysis, 1995, 369-378.

  5. Compressing DNA sequence databases with coil

    Directory of Open Access Journals (Sweden)

    Hendy Michael D

    2008-05-01

    Full Text Available Abstract Background Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.

  6. Timing-Sequence Testing of Parallel Programs

    Institute of Scientific and Technical Information of China (English)

    LIANG Yu; LI Shu; ZHANG Hui; HAN Chengde

    2000-01-01

    Testing of parallel programs involves two parts-testing of controlflow within the processes and testing of timing-sequence.This paper focuses on the latter, particularly on the timing-sequence of message-passing paradigms.Firstly the coarse-grained SYN-sequence model is built up to describe the execution of distributed programs. All of the topics discussed in this paper are based on it. The most direct way to test a program is to run it. A fault-free parallel program should be of both correct computing results and proper SYN-sequence. In order to analyze the validity of observed SYN-sequence, this paper presents the formal specification (Backus Normal Form) of the valid SYN-sequence. Till now there is little work about the testing coverage for distributed programs. Calculating the number of the valid SYN-sequences is the key to coverage problem, while the number of the valid SYN-sequences is terribly large and it is very hard to obtain the combination law among SYN-events. In order to resolve this problem, this paper proposes an efficient testing strategy-atomic SYN-event testing, which is to linearize the SYN-sequence (making it only consist of serial atomic SYN-events) first and then test each atomic SYN-event independently. This paper particularly provides the calculating formula about the number of the valid SYN-sequences for tree-topology atomic SYN-event (broadcast and combine). Furthermore,the number of valid SYN-sequences also,to some degree, mirrors the testability of parallel programs. Taking tree-topology atomic SYN-event as an example, this paper demonstrates the testability and communication speed of the tree-topology atomic SYN-event under different numbers of branches in order to achieve a more satisfactory tradeoff between testability and communication efficiency.

  7. Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.

    Directory of Open Access Journals (Sweden)

    Marta Brozynska

    Full Text Available Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina and Ion Torrent (Life Technology sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare. Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.

  8. Generalized Identities of Companion Fibonacci-Like Sequences

    OpenAIRE

    Shikha Bhatnagar; Bijendra Singh; Omprakash Sikhwal

    2013-01-01

    The Fibonacci sequence, Lucas sequence, Pell sequence, Pell-Lucas sequence, Jacobsthalsequence and Jacobsthal-Lucas sequence are most prominent examples of second order recursivesequences. In this paper, we deal with two companion Fibonacci- Like sequences which aregeneralization of Fibonacci-Like sequence. Further we obtain some generalized identities amongthe terms of companion Fibonacci-Like sequences, Jacobsthal and Jacobsthal-Lucas sequencesthrough Binet’s formulae.

  9. Sequencing the Cotton Genomes-Gossypium spp.

    Institute of Scientific and Technical Information of China (English)

    PATERSON Andrew H

    2008-01-01

    @@ The genomes of most major crops,including cotton,will be fully sequenced in the next fewyears.Cotton is unusual,although not unique,in that we will need to sequence not only cultivated(tetraploid) genotypes but their diploid progenitors,to understand how elite cottons have surpassedthe productivity and quality of their progenitors.

  10. Convergence of a Linear Recursive Sequence

    Science.gov (United States)

    Tay, E. G.; Toh, T. L.; Dong, F. M.; Lee, T. Y.

    2004-01-01

    A necessary and sufficient condition is found for a linear recursive sequence to be convergent, no matter what initial values are given. Its limit is also obtained when the sequence is convergent. Methods from various areas of mathematics are used to obtain the results.

  11. Novel algorithms for protein sequence analysis

    NARCIS (Netherlands)

    Ye, Kai

    2008-01-01

    Each protein is characterized by its unique sequential order of amino acids, the so-called protein sequence. Biology”s paradigm is that this order of amino acids determines the protein”s architecture and function. In this thesis, we introduce novel algorithms to analyze protein sequences. Chapter 1

  12. Sequencing for the cream of the crop

    Science.gov (United States)

    In this invited commentary, we discuss how next-generation sequencing methods are beginning to find their way into plant genetics, promising substantial improvements in crop yields over the coming decades. Next-generation sequencing facilitates the construction of high-resolution variation maps, whi...

  13. Sequencing Events: Exploring Art and Art Jobs.

    Science.gov (United States)

    Stephens, Pamela Geiger; Shaddix, Robin K.

    2000-01-01

    Presents an activity for upper-elementary students that correlates the actions of archaeologists, patrons, and artists with the sequencing of events in a logical order. Features ancient Egyptian art images. Discusses the preparation of materials, motivation, a pre-writing activity, and writing a story in sequence. (CMK)

  14. Pig genome sequence - analysis and publication strategy

    DEFF Research Database (Denmark)

    Archibald, Alan L.; Bolund, Lars; Churcher, Carol

    2010-01-01

    preferentially selected for sequencing. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement the data have been released into public sequence repositories (Genbank/EMBL, NCBI/Ensembl trace repositories) in a timely manner and in advance of publication. CONCLUSIONS...

  15. Sequence Comparison: Close and Open problems

    NARCIS (Netherlands)

    Lenzini, Gabriele; Cerrai, P.; Freguglia, P.

    1997-01-01

    Comparing sequences is a very important activity both in computer science and in a many other areas as well. For example thank to text editors, everyone knows the particular instance of a sequence comparison problem knonw as ``string mathcing problem''. It consists in searching a given work eventual

  16. Stochastic modelling of daily rainfall sequences

    NARCIS (Netherlands)

    Buishand, T.A.

    1977-01-01

    Rainfall series of different climatic regions were analysed with the aim of generating daily rainfall sequences. A survey of the data is given in I, 1. When analysing daily rainfall sequences one must be aware of the following points:
    a. Seasonality. Because of seasonal variation

  17. Genome Sequence of Lactobacillus rhamnosus ATCC 8530

    OpenAIRE

    Pittet, Vanessa; Ewen, Emily; Bushell, Barry R.; Ziola, Barry

    2012-01-01

    Lactobacillus rhamnosus is found in the human gastrointestinal tract and is important for probiotics. We became interested in L. rhamnosus isolate ATCC 8530 in relation to beer spoilage and hops resistance. We report here the genome sequence of this isolate, along with a brief comparison to other available L. rhamnosus genome sequences.

  18. SEQUENCE IN LEARNING--FACT OR FICTION.

    Science.gov (United States)

    MIEL, ALICE

    SEQUENCE IN LEARNING IS USEFUL ONLY AS IT CONTRIBUTES TO THE CONTINUITY OF A CHILD'S OVERALL DEVELOPMENT. CHILDREN MAY NOT GO THROUGH THE SAME SEQUENCE TO ARRIVE AT A SIMILAR POINT OF UNDERSTANDING. EDUCATIONAL PROGRESS IS INDICATED BY A CHILD'S GROWTH IN THE DEVELOPMENT OF STRATEGIC CONCEPTS, IN WAYS OF PROCESSING INFORMATION, AND IN WAYS OF…

  19. Controlling monomer-sequence using supramolecular templates

    OpenAIRE

    ten Brummelhuis, Niels

    2014-01-01

    The transcription and translation of information contained in nucleic acids that has been perfected by nature serves as inspiration for chemists to devise strategies for the creation of polymers with welldefined monomer sequences. In this review the various approaches in which templates (either biopolymers or synthetic ones) are used to influence the monomer-sequence are discussed.

  20. What's Next? Judging Sequences of Binary Events

    Science.gov (United States)

    Oskarsson, An T.; Van Boven, Leaf; McClelland, Gary H.; Hastie, Reid

    2009-01-01

    The authors review research on judgments of random and nonrandom sequences involving binary events with a focus on studies documenting gambler's fallacy and hot hand beliefs. The domains of judgment include random devices, births, lotteries, sports performances, stock prices, and others. After discussing existing theories of sequence judgments,…

  1. SPARSE SEQUENCE CONSTRUCTION OF LDPC CODES

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    This letter proposes a novel and simple construction of regular Low-Density Parity-Check (LDPC) codes using sparse binary sequences. It utilizes the cyclic cross correlation function of sparse sequences to generate codes with girth8. The new codes perform well using the sumproduct decoding. Low encodingcomplexity can also be achieved due to the inherent quasi-cyclic structure of the codes.

  2. Sequence Comparison: Close and Open problems

    NARCIS (Netherlands)

    Lenzini, Gabriele; Cerrai, P.; Freguglia, P.

    Comparing sequences is a very important activity both in computer science and in a many other areas as well. For example thank to text editors, everyone knows the particular instance of a sequence comparison problem knonw as ``string mathcing problem''. It consists in searching a given work

  3. Archaebacterial rhodopsin sequences: Implications for evolution

    Science.gov (United States)

    Lanyi, J. K.

    1991-01-01

    It was proposed over 10 years ago that the archaebacteria represent a separate kingdom which diverged very early from the eubacteria and eukaryotes. It follows that investigations of archaebacterial characteristics might reveal features of early evolution. So far, two genes, one for bacteriorhodopsin and another for halorhodopsin, both from Halobacterium halobium, have been sequenced. We cloned and sequenced the gene coding for the polypeptide of another one of these rhodopsins, a halorhodopsin in Natronobacterium pharaonis. Peptide sequencing of cyanogen bromide fragments, and immuno-reactions of the protein and synthetic peptides derived from the C-terminal gene sequence, confirmed that the open reading frame was the structural gene for the pharaonis halorhodopsin polypeptide. The flanking DNA sequences of this gene, as well as those of other bacterial rhodopsins, were compared to previously proposed archaebacterial consensus sequences. In pairwise comparisons of the open reading frame with DNA sequences for bacterio-opsin and halo-opsin from Halobacterium halobium, silent divergences were calculated. These indicate very considerable evolutionary distance between each pair of genes, even in the dame organism. In spite of this, three protein sequences show extensive similarities, indicating strong selective pressures.

  4. Bonobos extract meaning from call sequences.

    Directory of Open Access Journals (Sweden)

    Zanna Clay

    Full Text Available Studies on language-trained bonobos have revealed their remarkable abilities in representational and communication tasks. Surprisingly, however, corresponding research into their natural communication has largely been neglected. We address this issue with a first playback study on the natural vocal behaviour of bonobos. Bonobos produce five acoustically distinct call types when finding food, which they regularly mix together into longer call sequences. We found that individual call types were relatively poor indicators of food quality, while context specificity was much greater at the call sequence level. We therefore investigated whether receivers could extract meaning about the quality of food encountered by the caller by integrating across different call sequences. We first trained four captive individuals to find two types of foods, kiwi (preferred and apples (less preferred at two different locations. We then conducted naturalistic playback experiments during which we broadcasted sequences of four calls, originally produced by a familiar individual responding to either kiwi or apples. All sequences contained the same number of calls but varied in the composition of call types. Following playbacks, we found that subjects devoted significantly more search effort to the field indicated by the call sequence. Rather than attending to individual calls, bonobos attended to the entire sequences to make inferences about the food encountered by a caller. These results provide the first empirical evidence that bonobos are able to extract information about external events by attending to vocal sequences of other individuals and highlight the importance of call combinations in their natural communication system.

  5. What's Next? Judging Sequences of Binary Events

    Science.gov (United States)

    Oskarsson, An T.; Van Boven, Leaf; McClelland, Gary H.; Hastie, Reid

    2009-01-01

    The authors review research on judgments of random and nonrandom sequences involving binary events with a focus on studies documenting gambler's fallacy and hot hand beliefs. The domains of judgment include random devices, births, lotteries, sports performances, stock prices, and others. After discussing existing theories of sequence judgments,…

  6. Wolbachia Sequence Typing in Butterflies Using Pyrosequencing.

    Science.gov (United States)

    Choi, Sungmi; Shin, Su-Kyoung; Jeong, Gilsang; Yi, Hana

    2015-09-01

    Wolbachia is an obligate symbiotic bacteria that is ubiquitous in arthropods, with 25-70% of insect species estimated to be infected. Wolbachia species can interact with their insect hosts in a mutualistic or parasitic manner. Sequence types (ST) of Wolbachia are determined by multilocus sequence typing (MLST) of housekeeping genes. However, there are some limitations to MLST with respect to the generation of clone libraries and the Sanger sequencing method when a host is infected with multiple STs of Wolbachia. To assess the feasibility of massive parallel sequencing, also known as next-generation sequencing, we used pyrosequencing for sequence typing of Wolbachia in butterflies. We collected three species of butterflies (Eurema hecabe, Eurema laeta, and Tongeia fischeri) common to Korea and screened them for Wolbachia STs. We found that T. fischeri was infected with a single ST of Wolbachia, ST41. In contrast, E. hecabe and E. laeta were each infected with two STs of Wolbachia, ST41 and ST40. Our results clearly demonstrate that pyrosequencing-based MLST has a higher sensitivity than cloning and Sanger sequencing methods for the detection of minor alleles. Considering the high prevalence of infection with multiple Wolbachia STs, next-generation sequencing with improved analysis would assist with scaling up approaches to Wolbachia MLST.

  7. Value of a newly sequenced bacterial genome

    DEFF Research Database (Denmark)

    Barbosa, Eudes; Aburjaile, Flavia F; Ramos, Rommel Tj

    2014-01-01

    and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses...

  8. Discrepancy of LS-sequences of partitions

    CERN Document Server

    Carbone, Ingrid

    2010-01-01

    In this paper we give a precise estimate of the discrepancy of a class of uniformly distributed sequences of partitions. Among them we found a large class having low discrepancy (which means of order 1/N. One of them is the Kakutani-Fibonacci sequence.

  9. Some identities of generalized Fibonacci sequence

    Science.gov (United States)

    Chong, Chin-Yoon; Cheah, C. L.; Ho, C. K.

    2014-07-01

    We introduced the generalized Fibonacci sequence {Un} defined by U0 = 0, U1 = 1, and Un+2 = pUn+1+qUn for all p, q∈Z+ and for all non-negative integers n. In this paper, we obtained some recursive formulas of the sequence.

  10. On the sum of generalized Fibonacci sequence

    Science.gov (United States)

    Chong, Chin-Yoon; Ho, C. K.

    2014-06-01

    We consider the generalized Fibonacci sequence {Un defined by U0 = 0, U1 = 1, and Un+2 = pUn+1+qUn for all n∈Z0+ and p, q∈Z+. In this paper, we derived various sums of the generalized Fibonacci sequence from their recursive relations.

  11. Regular Pentagons and the Fibonacci Sequence.

    Science.gov (United States)

    French, Doug

    1989-01-01

    Illustrates how to draw a regular pentagon. Shows the sequence of a succession of regular pentagons formed by extending the sides. Calculates the general formula of the Lucas and Fibonacci sequences. Presents a regular icosahedron as an example of the golden ratio. (YP)

  12. GENE SEQUENCE HOMOLOGY OF CHEMOKINES ACROSS SPECIES

    Science.gov (United States)

    The abundance of expressed gene and protein sequences available in the biological information databases facilitates comparison of protein homologies. A high degree of sequence similarity typically implies homology regarding structure and function and may provide clues to antibody cross-react...

  13. Concept For Generation Of Long Pseudorandom Sequences

    Science.gov (United States)

    Wang, C. C.

    1990-01-01

    Conceptual very-large-scale integrated (VLSI) digital circuit performs exponentiation in finite field. Algorithm that generates unusually long sequences of pseudorandom numbers executed by digital processor that includes such circuits. Concepts particularly advantageous for such applications as spread-spectrum communications, cryptography, and generation of ranging codes, synthetic noise, and test data, where usually desirable to make pseudorandom sequences as long as possible.

  14. Using Conventional Sequences in L2 French

    Science.gov (United States)

    Forsberg, Fanny

    2010-01-01

    By means of a phraseological identification method, this study provides a general description of the use of conventional sequences (CSs) in interviews at four different levels of spoken L2 French as well as in interviews with native speakers. Use of conventional sequences is studied with regard to overall quantity, category distribution and type…

  15. Fibonacci-triple sequences and some fundamental properties

    Directory of Open Access Journals (Sweden)

    Bijendra Singh

    2010-12-01

    Full Text Available Fibonacci sequence stands as a kind of super sequence with fabulous properties. This note presents Fibonacci-Triple sequences that may also be called 3-F sequences. This is the explosive development in the region of Fibonacci sequence. Our purpose of this paper is to demonstrate fundamental properties of Fibonacci-Triple sequence.

  16. Fibonacci-triple sequences and some fundamental properties

    OpenAIRE

    Bijendra Singh; Omprakash Sikhwal

    2010-01-01

    Fibonacci sequence stands as a kind of super sequence with fabulous properties. This note presents Fibonacci-Triple sequences that may also be called 3-F sequences. This is the explosive development in the region of Fibonacci sequence. Our purpose of this paper is to demonstrate fundamental properties of Fibonacci-Triple sequence.

  17. Conserved Sequence Processing in Primate Frontal Cortex.

    Science.gov (United States)

    Wilson, Benjamin; Marslen-Wilson, William D; Petkov, Christopher I

    2017-02-01

    An important aspect of animal perception and cognition is learning to recognize relationships between environmental events that predict others in time, a form of relational knowledge that can be assessed using sequence-learning paradigms. Humans are exquisitely sensitive to sequencing relationships, and their combinatorial capacities, most saliently in the domain of language, are unparalleled. Recent comparative research in human and nonhuman primates has obtained behavioral and neuroimaging evidence for evolutionarily conserved substrates involved in sequence processing. The findings carry implications for the origins of domain-general capacities underlying core language functions in humans. Here, we synthesize this research into a 'ventrodorsal gradient' model, where frontal cortex engagement along this axis depends on sequencing complexity, mapping onto the sequencing capacities of different species. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Sequencing and comparing whole mitochondrial genomes ofanimals

    Energy Technology Data Exchange (ETDEWEB)

    Boore, Jeffrey L.; Macey, J. Robert; Medina, Monica

    2005-04-22

    Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning,sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences to date with determining and comparing complete mtDNA sequences.

  19. NGS-based deep bisulfite sequencing.

    Science.gov (United States)

    Lee, Suman; Kim, Joomyeong

    2016-01-01

    We have developed an NGS-based deep bisulfite sequencing protocol for the DNA methylation analysis of genomes. This approach allows the rapid and efficient construction of NGS-ready libraries with a large number of PCR products that have been individually amplified from bisulfite-converted DNA. This approach also employs a bioinformatics strategy to sort the raw sequence reads generated from NGS platforms and subsequently to derive DNA methylation levels for individual loci. The results demonstrated that this NGS-based deep bisulfite sequencing approach provide not only DNA methylation levels but also informative DNA methylation patterns that have not been seen through other existing methods.•This protocol provides an efficient method generating NGS-ready libraries from individually amplified PCR products.•This protocol provides a bioinformatics strategy sorting NGS-derived raw sequence reads.•This protocol provides deep bisulfite sequencing results that can measure DNA methylation levels and patterns of individual loci.

  20. Locomotor sequence learning in visually guided walking

    DEFF Research Database (Denmark)

    Choi, Julia T; Jensen, Peter; Nielsen, Jens Bo

    2016-01-01

    walking. In addition, we determined how age (i.e., healthy young adults vs. children) and biomechanical factors (i.e., walking speed) affected the rate and magnitude of locomotor sequence learning. The results showed that healthy young adults (age 24 ± 5 years, N = 20) could learn a specific sequence...... of step lengths over 300 training steps. Younger children (age 6-10 years, N = 8) have lower baseline performance, but their magnitude and rate of sequence learning was the same compared to older children (11-16 years, N = 10) and healthy adults. In addition, learning capacity may be more limited...... at faster walking speeds. To our knowledge, this is the first study to demonstrate that spatial sequence learning can be integrated with a highly automatic task like walking. These findings suggest that adults and children use implicit knowledge about the sequence to plan and execute leg movement during...

  1. Spiking neuron model for temporal sequence recognition.

    Science.gov (United States)

    Byrnes, Sean; Burkitt, Anthony N; Grayden, David B; Meffin, Hamish

    2010-01-01

    A biologically inspired neuronal network that stores and recognizes temporal sequences of symbols is described. Each symbol is represented by excitatory input to distinct groups of neurons (symbol pools). Unambiguous storage of multiple sequences with common subsequences is ensured by partitioning each symbol pool into subpools that respond only when the current symbol has been preceded by a particular sequence of symbols. We describe synaptic structure and neural dynamics that permit the selective activation of subpools by the correct sequence. Symbols may have varying durations of the order of hundreds of milliseconds. Physiologically plausible plasticity mechanisms operate on a time scale of tens of milliseconds; an interaction of the excitatory input with periodic global inhibition bridges this gap so that neural events representing successive symbols occur on this much faster timescale. The network is shown to store multiple overlapping sequences of events. It is robust to variation in symbol duration, it is scalable, and its performance degrades gracefully with perturbation of its parameters.

  2. Aligning Sequences by Minimum Description Length

    Directory of Open Access Journals (Sweden)

    John S. Conery

    2008-01-01

    Full Text Available This paper presents a new information theoretic framework for aligning sequences in bioinformatics. A transmitter compresses a set of sequences by constructing a regular expression that describes the regions of similarity in the sequences. To retrieve the original set of sequences, a receiver generates all strings that match the expression. An alignment algorithm uses minimum description length to encode and explore alternative expressions; the expression with the shortest encoding provides the best overall alignment. When two substrings contain letters that are similar according to a substitution matrix, a code length function based on conditional probabilities defined by the matrix will encode the substrings with fewer bits. In one experiment, alignments produced with this new method were found to be comparable to alignments from CLUSTALW. A second experiment measured the accuracy of the new method on pairwise alignments of sequences from the BAliBASE alignment benchmark.

  3. Metagenomics using next-generation sequencing.

    Science.gov (United States)

    Bragg, Lauren; Tyson, Gene W

    2014-01-01

    Traditionally, microbial genome sequencing has been restricted to the small number of species that can be grown in pure culture. The progressive development of culture-independent methods over the last 15 years now allows researchers to sequence microbial communities directly from environmental samples. This approach is commonly referred to as "metagenomics" or "community genomics". However, the term metagenomics is applied liberally in the literature to describe any culture-independent analysis of microbial communities. Here, we define metagenomics as shotgun ("random") sequencing of the genomic DNA of a sample taken directly from the environment. The metagenome can be thought of as a sampling of the collective genome of the microbial community. We outline the considerations and analyses that should be undertaken to ensure the success of a metagenomic sequencing project, including the choice of sequencing platform and methods for assembly, binning, annotation, and comparative analysis.

  4. Strategies for complete plastid genome sequencing.

    Science.gov (United States)

    Twyford, Alex D; Ness, Rob W

    2016-10-28

    Plastid sequencing is an essential tool in the study of plant evolution. This high-copy organelle is one of the most technically accessible regions of the genome, and its sequence conservation makes it a valuable region for comparative genome evolution, phylogenetic analysis and population studies. Here, we discuss recent innovations and approaches for de novo plastid assembly that harness genomic tools. We focus on technical developments including low-cost sequence library preparation approaches for genome skimming, enrichment via hybrid baits and methylation-sensitive capture, sequence platforms with higher read outputs and longer read lengths, and automated tools for assembly. These developments allow for a much more streamlined assembly than via conventional short-range PCR. Although newer methods make complete plastid sequencing possible for any land plant or green alga, there are still challenges for producing finished plastomes particularly from herbarium material or from structurally divergent plastids such as those of parasitic plants.

  5. Reading biological processes from nucleotide sequences

    Science.gov (United States)

    Murugan, Anand

    Cellular processes have traditionally been investigated by techniques of imaging and biochemical analysis of the molecules involved. The recent rapid progress in our ability to manipulate and read nucleic acid sequences gives us direct access to the genetic information that directs and constrains biological processes. While sequence data is being used widely to investigate genotype-phenotype relationships and population structure, here we use sequencing to understand biophysical mechanisms. We present work on two different systems. First, in chapter 2, we characterize the stochastic genetic editing mechanism that produces diverse T-cell receptors in the human immune system. We do this by inferring statistical distributions of the underlying biochemical events that generate T-cell receptor coding sequences from the statistics of the observed sequences. This inferred model quantitatively describes the potential repertoire of T-cell receptors that can be produced by an individual, providing insight into its potential diversity and the probability of generation of any specific T-cell receptor. Then in chapter 3, we present work on understanding the functioning of regulatory DNA sequences in both prokaryotes and eukaryotes. Here we use experiments that measure the transcriptional activity of large libraries of mutagenized promoters and enhancers and infer models of the sequence-function relationship from this data. For the bacterial promoter, we infer a physically motivated 'thermodynamic' model of the interaction of DNA-binding proteins and RNA polymerase determining the transcription rate of the downstream gene. For the eukaryotic enhancers, we infer heuristic models of the sequence-function relationship and use these models to find synthetic enhancer sequences that optimize inducibility of expression. Both projects demonstrate the utility of sequence information in conjunction with sophisticated statistical inference techniques for dissecting underlying biophysical

  6. GASP: Gapped Ancestral Sequence Prediction for proteins

    Directory of Open Access Journals (Sweden)

    Shields Denis C

    2004-09-01

    Full Text Available Abstract Background The prediction of ancestral protein sequences from multiple sequence alignments is useful for many bioinformatics analyses. Predicting ancestral sequences is not a simple procedure and relies on accurate alignments and phylogenies. Several algorithms exist based on Maximum Parsimony or Maximum Likelihood methods but many current implementations are unable to process residues with gaps, which may represent insertion/deletion (indel events or sequence fragments. Results Here we present a new algorithm, GASP (Gapped Ancestral Sequence Prediction, for predicting ancestral sequences from phylogenetic trees and the corresponding multiple sequence alignments. Alignments may be of any size and contain gaps. GASP first assigns the positions of gaps in the phylogeny before using a likelihood-based approach centred on amino acid substitution matrices to assign ancestral amino acids. Important outgroup information is used by first working down from the tips of the tree to the root, using descendant data only to assign probabilities, and then working back up from the root to the tips using descendant and outgroup data to make predictions. GASP was tested on a number of simulated datasets based on real phylogenies. Prediction accuracy for ungapped data was similar to three alternative algorithms tested, with GASP performing better in some cases and worse in others. Adding simple insertions and deletions to the simulated data did not have a detrimental effect on GASP accuracy. Conclusions GASP (Gapped Ancestral Sequence Prediction will predict ancestral sequences from multiple protein alignments of any size. Although not as accurate in all cases as some of the more sophisticated maximum likelihood approaches, it can process a wide range of input phylogenies and will predict ancestral sequences for gapped and ungapped residues alike.

  7. GASP: Gapped Ancestral Sequence Prediction for proteins.

    Science.gov (United States)

    Edwards, Richard J; Shields, Denis C

    2004-09-06

    The prediction of ancestral protein sequences from multiple sequence alignments is useful for many bioinformatics analyses. Predicting ancestral sequences is not a simple procedure and relies on accurate alignments and phylogenies. Several algorithms exist based on Maximum Parsimony or Maximum Likelihood methods but many current implementations are unable to process residues with gaps, which may represent insertion/deletion (indel) events or sequence fragments. Here we present a new algorithm, GASP (Gapped Ancestral Sequence Prediction), for predicting ancestral sequences from phylogenetic trees and the corresponding multiple sequence alignments. Alignments may be of any size and contain gaps. GASP first assigns the positions of gaps in the phylogeny before using a likelihood-based approach centred on amino acid substitution matrices to assign ancestral amino acids. Important outgroup information is used by first working down from the tips of the tree to the root, using descendant data only to assign probabilities, and then working back up from the root to the tips using descendant and outgroup data to make predictions. GASP was tested on a number of simulated datasets based on real phylogenies. Prediction accuracy for ungapped data was similar to three alternative algorithms tested, with GASP performing better in some cases and worse in others. Adding simple insertions and deletions to the simulated data did not have a detrimental effect on GASP accuracy. GASP (Gapped Ancestral Sequence Prediction) will predict ancestral sequences from multiple protein alignments of any size. Although not as accurate in all cases as some of the more sophisticated maximum likelihood approaches, it can process a wide range of input phylogenies and will predict ancestral sequences for gapped and ungapped residues alike.

  8. On some difference sequence spaces defined by a sequence of Orlicz functions

    Institute of Scientific and Technical Information of China (English)

    ASMA BEKTA(S) (C)i(g)dem

    2006-01-01

    The idea of difference sequence spaces was introduced in (Kizmaz, 1981) and this concept was generalized in (Et and Colak, 1995). In this paper we define some difference sequence spaces by a sequence of Orlicz functions and establish some inclusion relations.

  9. Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.

    Science.gov (United States)

    Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

    2017-07-01

    PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

  10. Finding Common Sequence and Structure Motifs in a set of RNA sequences

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Heyer, Laurie J.; Stormo, Gary D.

    1997-01-01

    We present a computational scheme to search for the most common motif, composed of a combination of sequence and structure constraints, among a collection of RNA sequences. The method uses a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences...

  11. SOME GEOMETRIC PROPERTIES OF A NEW DIFFERENCE SEQUENCE SPACE INVOLVING LACUNARY SEQUENCES

    Institute of Scientific and Technical Information of China (English)

    Murat KARAKAŞ; Mikail ET; Vatan KARAKAYA

    2013-01-01

    In this paper, we define a new generalized difference sequence space involving lacunary sequence. Then, we examine k-NUC property and property (β) for this space and also show that it is not rotund where p=(pr) is a bounded sequence of positive real numbers with pr ≥1 for all r∈N.

  12. Targeted next-generation sequencing can replace Sanger sequencing in clinical diagnostics

    NARCIS (Netherlands)

    Sikkema-Raddatz, B.; Johansson, L.F.; de Boer, E.N.; Almomani, R.; Boven, L.G.; van den Berg, M.P.; van Spaendonck-Zwarts, K.Y.; van Tintelen, J.P.; Sijmons, R.H.; Jongbloed, J.D.H.; Sinke, R.J.

    2013-01-01

    Mutation detection through exome sequencing allows simultaneous analysis of all coding sequences of genes. However, it cannot yet replace Sanger sequencing (SS) in diagnostics because of incomplete representation and coverage of exons leading to missing clinically relevant mutations. Targeted next-g

  13. Sequencing and Analysis of a Genomic Fragment Provide an Insight into the Dunaliella viridis Genomic Sequence

    Institute of Scientific and Technical Information of China (English)

    Xiao-Ming SUN; Yuan-Ping TANG; Xiang-Zong MENG; Wen-Wen ZHANG; Shan LI; Zhi-Rui DENG; Zheng-Kai XU; Ren-Tao SONG

    2006-01-01

    Dunaliella is a genus of wall-less unicellular eukaryotic green alga. Its exceptional resistances to salt and various other stresses have made it an ideal model for stress tolerance study. However, very little is known about its genome and genomic sequences. In this study, we sequenced and analyzed a 29,268 bp genomic fragment from Dunaliella viridis. The fragment showed low sequence homology to the GenBank database. At the nucleotide level, only a segment with significant sequence homology to 18S rRNA was found. The fragment contained six putative genes, but only one gene showed significant homology at the protein level to GenBank database. The average GC content of this sequence was 51.1%, which was much lower than that of close related green algae Chlamydomonas (65.7%). Significant segmental duplications were found within this fragment. The duplicated sequences accounted for about 35.7% of the entire region. Large amounts of simple sequence repeats (microsatellites) were found, with strong bias towards (AC)n type (76%). Analysis of other Dunaliella genomic sequences in the GenBank database (total 25,749 bp) was in agreement with these findings. These sequence features made it difficult to sequence Dunaliella genomic sequences. Further investigation should be made to reveal the biological significance of these unique sequence features.

  14. Gelada vocal sequences follow Menzerath's linguistic law.

    Science.gov (United States)

    Gustison, Morgan L; Semple, Stuart; Ferrer-I-Cancho, Ramon; Bergman, Thore J

    2016-05-10

    Identifying universal principles underpinning diverse natural systems is a key goal of the life sciences. A powerful approach in addressing this goal has been to test whether patterns consistent with linguistic laws are found in nonhuman animals. Menzerath's law is a linguistic law that states that, the larger the construct, the smaller the size of its constituents. Here, to our knowledge, we present the first evidence that Menzerath's law holds in the vocal communication of a nonhuman species. We show that, in vocal sequences of wild male geladas (Theropithecus gelada), construct size (sequence size in number of calls) is negatively correlated with constituent size (duration of calls). Call duration does not vary significantly with position in the sequence, but call sequence composition does change with sequence size and most call types are abbreviated in larger sequences. We also find that intercall intervals follow the same relationship with sequence size as do calls. Finally, we provide formal mathematical support for the idea that Menzerath's law reflects compression-the principle of minimizing the expected length of a code. Our findings suggest that a common principle underpins human and gelada vocal communication, highlighting the value of exploring the applicability of linguistic laws in vocal systems outside the realm of language.

  15. De novo peptide sequencing by deep learning.

    Science.gov (United States)

    Tran, Ngoc Hieu; Zhang, Xianglilan; Xin, Lei; Shan, Baozhen; Li, Ming

    2017-07-18

    De novo peptide sequencing from tandem MS data is the key technology in proteomics for the characterization of proteins, especially for new sequences, such as mAbs. In this study, we propose a deep neural network model, DeepNovo, for de novo peptide sequencing. DeepNovo architecture combines recent advances in convolutional neural networks and recurrent neural networks to learn features of tandem mass spectra, fragment ions, and sequence patterns of peptides. The networks are further integrated with local dynamic programming to solve the complex optimization task of de novo sequencing. We evaluated the method on a wide variety of species and found that DeepNovo considerably outperformed state of the art methods, achieving 7.7-22.9% higher accuracy at the amino acid level and 38.1-64.0% higher accuracy at the peptide level. We further used DeepNovo to automatically reconstruct the complete sequences of antibody light and heavy chains of mouse, achieving 97.5-100% coverage and 97.2-99.5% accuracy, without assisting databases. Moreover, DeepNovo is retrainable to adapt to any sources of data and provides a complete end-to-end training and prediction solution to the de novo sequencing problem. Not only does our study extend the deep learning revolution to a new field, but it also shows an innovative approach in solving optimization problems by using deep learning and dynamic programming.

  16. Fungal genome sequencing: basic biology to biotechnology.

    Science.gov (United States)

    Sharma, Krishna Kant

    2016-08-01

    The genome sequences provide a first glimpse into the genomic basis of the biological diversity of filamentous fungi and yeast. The genome sequence of the budding yeast, Saccharomyces cerevisiae, with a small genome size, unicellular growth, and rich history of genetic and molecular analyses was a milestone of early genomics in the 1990s. The subsequent completion of fission yeast, Schizosaccharomyces pombe and genetic model, Neurospora crassa initiated a revolution in the genomics of the fungal kingdom. In due course of time, a substantial number of fungal genomes have been sequenced and publicly released, representing the widest sampling of genomes from any eukaryotic kingdom. An ambitious genome-sequencing program provides a wealth of data on metabolic diversity within the fungal kingdom, thereby enhancing research into medical science, agriculture science, ecology, bioremediation, bioenergy, and the biotechnology industry. Fungal genomics have higher potential to positively affect human health, environmental health, and the planet's stored energy. With a significant increase in sequenced fungal genomes, the known diversity of genes encoding organic acids, antibiotics, enzymes, and their pathways has increased exponentially. Currently, over a hundred fungal genome sequences are publicly available; however, no inclusive review has been published. This review is an initiative to address the significance of the fungal genome-sequencing program and provides the road map for basic and applied research.

  17. CATEGORIZATION OF EVENT SEQUENCES FOR LICENSE APPLICATION

    Energy Technology Data Exchange (ETDEWEB)

    G.E. Ragan; P. Mecheret; D. Dexheimer

    2005-04-14

    The purposes of this analysis are: (1) Categorize (as Category 1, Category 2, or Beyond Category 2) internal event sequences that may occur before permanent closure of the repository at Yucca Mountain. (2) Categorize external event sequences that may occur before permanent closure of the repository at Yucca Mountain. This includes examining DBGM-1 seismic classifications and upgrading to DBGM-2, if appropriate, to ensure Beyond Category 2 categorization. (3) State the design and operational requirements that are invoked to make the categorization assignments valid. (4) Indicate the amount of material put at risk by Category 1 and Category 2 event sequences. (5) Estimate frequencies of Category 1 event sequences at the maximum capacity and receipt rate of the repository. (6) Distinguish occurrences associated with normal operations from event sequences. It is beyond the scope of the analysis to propose design requirements that may be required to control radiological exposure associated with normal operations. (7) Provide a convenient compilation of the results of the analysis in tabular form. The results of this analysis are used as inputs to the consequence analyses in an iterative design process that is depicted in Figure 1. Categorization of event sequences for permanent retrieval of waste from the repository is beyond the scope of this analysis. Cleanup activities that take place after an event sequence and other responses to abnormal events are also beyond the scope of the analysis.

  18. Exploration of noncoding sequences in metagenomes.

    Directory of Open Access Journals (Sweden)

    Fabián Tobar-Tosse

    Full Text Available Environment-dependent genomic features have been defined for different metagenomes, whose genes and their associated processes are related to specific environments. Identification of ORFs and their functional categories are the most common methods for association between functional and environmental features. However, this analysis based on finding ORFs misses noncoding sequences and, therefore, some metagenome regulatory or structural information could be discarded. In this work we analyzed 23 whole metagenomes, including coding and noncoding sequences using the following sequence patterns: (G+C content, Codon Usage (Cd, Trinucleotide Usage (Tn, and functional assignments for ORF prediction. Herein, we present evidence of a high proportion of noncoding sequences discarded in common similarity-based methods in metagenomics, and the kind of relevant information present in those. We found a high density of trinucleotide repeat sequences (TRS in noncoding sequences, with a regulatory and adaptive function for metagenome communities. We present associations between trinucleotide values and gene function, where metagenome clustering correlate with microorganism adaptations and kinds of metagenomes. We propose here that noncoding sequences have relevant information to describe metagenomes that could be considered in a whole metagenome analysis in order to improve their organization, classification protocols, and their relation with the environment.

  19. Value of a newly sequenced bacterial genome

    Institute of Scientific and Technical Information of China (English)

    Eudes; GV; Barbosa; Flavia; F; Aburjaile; Rommel; TJ; Ramos; Adriana; R; Carneiro; Yves; Le; Loir; Jan; Baumbach; Anderson; Miyoshi; Artur; Silva; Vasco; Azevedo

    2014-01-01

    Next-generation sequencing(NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft(partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information.

  20. Revisiting Mendelian disorders through exome sequencing.

    Science.gov (United States)

    Ku, Chee-Seng; Naidoo, Nasheen; Pawitan, Yudi

    2011-04-01

    Over the past several years, more focus has been placed on dissecting the genetic basis of complex diseases and traits through genome-wide association studies. In contrast, Mendelian disorders have received little attention mainly due to the lack of newer and more powerful methods to study these disorders. Linkage studies have previously been the main tool to elucidate the genetics of Mendelian disorders; however, extremely rare disorders or sporadic cases caused by de novo variants are not amendable to this study design. Exome sequencing has now become technically feasible and more cost-effective due to the recent advances in high-throughput sequence capture methods and next-generation sequencing technologies which have offered new opportunities for Mendelian disorder research. Exome sequencing has been swiftly applied to the discovery of new causal variants and candidate genes for a number of Mendelian disorders such as Kabuki syndrome, Miller syndrome and Fowler syndrome. In addition, de novo variants were also identified for sporadic cases, which would have not been possible without exome sequencing. Although exome sequencing has been proven to be a promising approach to study Mendelian disorders, several shortcomings of this method must be noted, such as the inability to capture regulatory or evolutionary conserved sequences in non-coding regions and the incomplete capturing of all exons.

  1. Identification of ancient remains through genomic sequencing

    Science.gov (United States)

    Blow, Matthew J.; Zhang, Tao; Woyke, Tanja; Speller, Camilla F.; Krivoshapkin, Andrei; Yang, Dongya Y.; Derevianko, Anatoly; Rubin, Edward M.

    2008-01-01

    Studies of ancient DNA have been hindered by the preciousness of remains, the small quantities of undamaged DNA accessible, and the limitations associated with conventional PCR amplification. In these studies, we developed and applied a genomewide adapter-mediated emulsion PCR amplification protocol for ancient mammalian samples estimated to be between 45,000 and 69,000 yr old. Using 454 Life Sciences (Roche) and Illumina sequencing (formerly Solexa sequencing) technologies, we examined over 100 megabases of DNA from amplified extracts, revealing unbiased sequence coverage with substantial amounts of nonredundant nuclear sequences from the sample sources and negligible levels of human contamination. We consistently recorded over 500-fold increases, such that nanogram quantities of starting material could be amplified to microgram quantities. Application of our protocol to a 50,000-yr-old uncharacterized bone sample that was unsuccessful in mitochondrial PCR provided sufficient nuclear sequences for comparison with extant mammals and subsequent phylogenetic classification of the remains. The combined use of emulsion PCR amplification and high-throughput sequencing allows for the generation of large quantities of DNA sequence data from ancient remains. Using such techniques, even small amounts of ancient remains with low levels of endogenous DNA preservation may yield substantial quantities of nuclear DNA, enabling novel applications of ancient DNA genomics to the investigation of extinct phyla. PMID:18426903

  2. Enhanced Dynamic Algorithm of Genome Sequence Alignments

    Directory of Open Access Journals (Sweden)

    Arabi E. keshk

    2014-05-01

    Full Text Available The merging of biology and computer science has created a new field called computational biology that explore the capacities of computers to gain knowledge from biological data, bioinformatics. Computational biology is rooted in life sciences as well as computers, information sciences, and technologies. The main problem in computational biology is sequence alignment that is a way of arranging the sequences of DNA, RNA or protein to identify the region of similarity and relationship between sequences. This paper introduces an enhancement of dynamic algorithm of genome sequence alignment, which called EDAGSA. It is filling the three main diagonals without filling the entire matrix by the unused data. It gets the optimal solution with decreasing the execution time and therefore the performance is increased. To illustrate the effectiveness of optimizing the performance of the proposed algorithm, it is compared with the traditional methods such as Needleman-Wunsch, Smith-Waterman and longest common subsequence algorithms. Also, database is implemented for using the algorithm in multi-sequence alignments for searching the optimal sequence that matches the given sequence.

  3. Large Zero Autocorrelation Zone of Golay Sequences and $4^q$-QAM Golay Complementary Sequences

    CERN Document Server

    Gong, Guang; Yang, Yang

    2011-01-01

    Sequences with good correlation properties have been widely adopted in modern communications, radar and sonar applications. In this paper, we present our new findings on some constructions of single $H$-ary Golay sequence and $4^q$-QAM Golay complementary sequence with a large zero autocorrelation zone, where $H\\ge 2$ is an arbitrary even integer and $q\\ge 2$ is an arbitrary integer. Those new results on Golay sequences and QAM Golay complementary sequences can be explored during synchronization and detection at the receiver end and thus improve the performance of the communication system.

  4. Identification of 10 882 porcine microsatellite sequences and virtual mapping of 4528 of these sequences

    DEFF Research Database (Denmark)

    Karlskov-Mortensen, Peter; Hu, Z.L.; Gorodkin, Jan

    2007-01-01

    the human genome (BLAST cut-off threshold = 1 x 10-5). All microsatellite sequences placed on the comparative map are accessible at http://www.animalgenome.org/QTLdb/pig.html . These sequences increase the number of identified microsatellites in the porcine genome by several orders of magnitude......A total of 10 882 porcine microsatelite repeats were identified in genomic shotgun sequences from the Sino-Danish Pig Genome Sequencing Consortium ( http://piggenome.dk ). Of these, 4528 microsatellites were placed on a pig-human comparative map by BLAST analysis of porcine sequences against...

  5. Robot Sequencing and Visualization Program (RSVP)

    Science.gov (United States)

    Cooper, Brian K.; Maxwell,Scott A.; Hartman, Frank R.; Wright, John R.; Yen, Jeng; Toole, Nicholas T.; Gorjian, Zareh; Morrison, Jack C

    2013-01-01

    The Robot Sequencing and Visualization Program (RSVP) is being used in the Mars Science Laboratory (MSL) mission for downlink data visualization and command sequence generation. RSVP reads and writes downlink data products from the operations data server (ODS) and writes uplink data products to the ODS. The primary users of RSVP are members of the Rover Planner team (part of the Integrated Planning and Execution Team (IPE)), who use it to perform traversability/articulation analyses, take activity plan input from the Science and Mission Planning teams, and create a set of rover sequences to be sent to the rover every sol. The primary inputs to RSVP are downlink data products and activity plans in the ODS database. The primary outputs are command sequences to be placed in the ODS for further processing prior to uplink to each rover. RSVP is composed of two main subsystems. The first, called the Robot Sequence Editor (RoSE), understands the MSL activity and command dictionaries and takes care of converting incoming activity level inputs into command sequences. The Rover Planners use the RoSE component of RSVP to put together command sequences and to view and manage command level resources like time, power, temperature, etc. (via a transparent realtime connection to SEQGEN). The second component of RSVP is called HyperDrive, a set of high-fidelity computer graphics displays of the Martian surface in 3D and in stereo. The Rover Planners can explore the environment around the rover, create commands related to motion of all kinds, and see the simulated result of those commands via its underlying tight coupling with flight navigation, motor, and arm software. This software is the evolutionary replacement for the Rover Sequencing and Visualization software used to create command sequences (and visualize the Martian surface) for the Mars Exploration Rover mission.

  6. Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology

    Directory of Open Access Journals (Sweden)

    Jian eWu

    2012-11-01

    Full Text Available Sequencing of the chloroplast genome using traditional sequencing methods has been difficult because of its size (>120 kb and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the chloroplast genome using DNA extracted from whole cells and Solexa sequencing technology, we sequenced whole cellular DNA isolated from leaves of three Brassica rapa accessions with one lane per accession. In total, 246 Mb, 362Mb, 361 Mb sequence data were generated for the three accessions Chiifu-401-42, Z16 and FT, respectively. Microreads were assembled by reference-guided assembly using the cpDNA sequences of B. rapa, Arabidopsis thaliana, and Nicotiana tabacum. We achieved coverage of more than 99.96% of the cp genome in the three tested accessions using the B. rapa sequence as the reference. When A. thaliana or N. tabacum sequences were used as references, 99.7–99.8% or 95.5–99.7% of the B. rapa chloroplast genome was covered, respectively. These results demonstrated that sequencing of whole cellular DNA isolated from young leaves using the Illumina Genome Analyzer is an efficient method for high-throughput sequencing of chloroplast genome.

  7. Effects of the Ion PGM™ Hi-Q™ sequencing chemistry on sequence data quality.

    Science.gov (United States)

    Churchill, Jennifer D; King, Jonathan L; Chakraborty, Ranajit; Budowle, Bruce

    2016-09-01

    Massively parallel sequencing (MPS) offers substantial improvements over current forensic DNA typing methodologies such as increased resolution, scalability, and throughput. The Ion PGM™ is a promising MPS platform for analysis of forensic biological evidence. The system employs a sequencing-by-synthesis chemistry on a semiconductor chip that measures a pH change due to the release of hydrogen ions as nucleotides are incorporated into the growing DNA strands. However, implementation of MPS into forensic laboratories requires a robust chemistry. Ion Torrent's Hi-Q™ Sequencing Chemistry was evaluated to determine if it could improve on the quality of the generated sequence data in association with selected genetic marker targets. The whole mitochondrial genome and the HID-Ion STR 10-plex panel were sequenced on the Ion PGM™ system with the Ion PGM™ Sequencing 400 Kit and the Ion PGM™ Hi-Q™ Sequencing Kit. Concordance, coverage, strand balance, noise, and deletion ratios were assessed in evaluating the performance of the Ion PGM™ Hi-Q™ Sequencing Kit. The results indicate that reliable, accurate data are generated and that sequencing through homopolymeric regions can be improved with the use of Ion Torrent's Hi-Q™ Sequencing Chemistry. Overall, the quality of the generated sequencing data supports the potential for use of the Ion PGM™ in forensic genetic laboratories.

  8. Statistical properties of filtered pseudorandom digital sequences formed from the sum of maximum-length sequences

    Science.gov (United States)

    Wallace, G. R.; Weathers, G. D.; Graf, E. R.

    1973-01-01

    The statistics of filtered pseudorandom digital sequences called hybrid-sum sequences, formed from the modulo-two sum of several maximum-length sequences, are analyzed. The results indicate that a relation exists between the statistics of the filtered sequence and the characteristic polynomials of the component maximum length sequences. An analysis procedure is developed for identifying a large group of sequences with good statistical properties for applications requiring the generation of analog pseudorandom noise. By use of the analysis approach, the filtering process is approximated by the convolution of the sequence with a sum of unit step functions. A parameter reflecting the overall statistical properties of filtered pseudorandom sequences is derived. This parameter is called the statistical quality factor. A computer algorithm to calculate the statistical quality factor for the filtered sequences is presented, and the results for two examples of sequence combinations are included. The analysis reveals that the statistics of the signals generated with the hybrid-sum generator are potentially superior to the statistics of signals generated with maximum-length generators. Furthermore, fewer calculations are required to evaluate the statistics of a large group of hybrid-sum generators than are required to evaluate the statistics of the same size group of approximately equivalent maximum-length sequences.

  9. How Long is an Aftershock Sequence?

    Science.gov (United States)

    Godano, Cataldo; Tramelli, Anna

    2016-07-01

    The occurrence of a mainschok is always followed by aftershocks spatially distributed within the fault area. The aftershocks rate decay with time is described by the empirical Omori law which was inferred by catalogues analysis. The sequences discrimination within catalogues is not a straightforward operation, especially for low-magnitude mainshocks. Here, we describe the rate decay of the Omori law obtained using different sequence discrimination tools and we discover that, when the background seismicity is excluded, the sequences tend to last for the temporal extension of the catalogue.

  10. Nanopore-CMOS Interfaces for DNA Sequencing.

    Science.gov (United States)

    Magierowski, Sebastian; Huang, Yiyun; Wang, Chengjie; Ghafar-Zadeh, Ebrahim

    2016-08-06

    DNA sequencers based on nanopore sensors present an opportunity for a significant break from the template-based incumbents of the last forty years. Key advantages ushered by nanopore technology include a simplified chemistry and the ability to interface to CMOS technology. The latter opportunity offers substantial promise for improvement in sequencing speed, size and cost. This paper reviews existing and emerging means of interfacing nanopores to CMOS technology with an emphasis on massively-arrayed structures. It presents this in the context of incumbent DNA sequencing techniques, reviews and quantifies nanopore characteristics and models and presents CMOS circuit methods for the amplification of low-current nanopore signals in such interfaces.

  11. Initial retrieval sequence and blending strategy

    Energy Technology Data Exchange (ETDEWEB)

    Pemwell, D.L.; Grenard, C.E.

    1996-09-01

    This report documents the initial retrieval sequence and the methodology used to select it. Waste retrieval, storage, pretreatment and vitrification were modeled for candidate single-shell tank retrieval sequences. Performance of the sequences was measured by a set of metrics (for example,high-level waste glass volume, relative risk and schedule).Computer models were used to evaluate estimated glass volumes,process rates, retrieval dates, and blending strategy effects.The models were based on estimates of component inventories and concentrations, sludge wash factors and timing, retrieval annex limitations, etc.

  12. The double main sequence of Omega Centauri

    CERN Document Server

    Bedin, L R

    2004-01-01

    Recent, high precision photometry of Omega Centauri, the biggest Galactic globular cluster, has been obtained with Hubble Space Telescope. The color magnitude diagram reveals an unexpected bifurcation of colors in the main sequence (MS). The newly found double MS, the multiple turnoffs and subgiant branches, and other sequences discovered in the past along the red giant branch of this cluster add up to a fascinating but frustrating puzzle. Among the possible explanations for the blue main sequence an anomalous overabundance of helium is suggested. The hypothesis will be tested with a set of FLAMES@VLT data we have recently obtained (ESO DDT program), and with forthcoming ACS@HST images.

  13. Association Claims in the Sequencing Era

    Directory of Open Access Journals (Sweden)

    Sara L. Pulit

    2014-03-01

    Full Text Available Since the completion of the Human Genome Project, the field of human genetics has been in great flux, largely due to technological advances in studying DNA sequence variation. Although community-wide adoption of statistical standards was key to the success of genome-wide association studies, similar standards have not yet been globally applied to the processing and interpretation of sequencing data. It has proven particularly challenging to pinpoint unequivocally disease variants in sequencing studies of polygenic traits. Here, we comment on a number of factors that may contribute to irreproducible claims of association in scientific literature and discuss possible steps that we can take towards cultural change.

  14. Persistence and NIP in the characteristic sequence

    CERN Document Server

    Malliaris, M E

    2009-01-01

    For a first-order formula $\\phi(x;y)$ we introduce and study the characteristic sequence $$ of hypergraphs defined by $P_n(y_1,...,y_n) := (\\exists x) \\bigwedge_{i \\leq n} \\phi(x;y_i)$. We show that combinatorial and classification theoretic properties of the characteristic sequence reflect classification theoretic properties of $\\varphi$ and vice versa. Specifically, we show that some tree properties are detected by the presence of certain combinatorial configurations in the characteristic sequence while other properties such as instability and the independence property manifest themselves in the persistence of complicated configurations under localization.

  15. Scale-PC shielding analysis sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bowman, S.M.

    1996-05-01

    The SCALE computational system is a modular code system for analyses of nuclear fuel facility and package designs. With the release of SCALE-PC Version 4.3, the radiation shielding analysis community now has the capability to execute the SCALE shielding analysis sequences contained in the control modules SAS1, SAS2, SAS3, and SAS4 on a MS- DOS personal computer (PC). In addition, SCALE-PC includes two new sequences, QADS and ORIGEN-ARP. The capabilities of each sequence are presented, along with example applications.

  16. Spreadsheet macros for coloring sequence alignments.

    Science.gov (United States)

    Haygood, M G

    1993-12-01

    This article describes a set of Microsoft Excel macros designed to color amino acid and nucleotide sequence alignments for review and preparation of visual aids. The colored alignments can then be modified to emphasize features of interest. Procedures for importing and coloring sequences are described. The macro file adds a new menu to the menu bar containing sequence-related commands to enable users unfamiliar with Excel to use the macros more readily. The macros were designed for use with Macintosh computers but will also run with the DOS version of Excel.

  17. Microbial genomics: from sequence to function.

    OpenAIRE

    Schwartz, I

    2000-01-01

    The era of genomics (the study of genes and their function) began a scant dozen years ago with a suggestion by James Watson that the complete DNA sequence of the human genome be determined. Since that time, the human genome project has attracted a great deal of attention in the scientific world and the general media; the scope of the sequencing effort, and the extraordinary value that it will provide, has served to mask the enormous progress in sequencing other genomes. Microbial genome seque...

  18. Deep-sequencing protocols influence the results obtained in small-RNA sequencing.

    Directory of Open Access Journals (Sweden)

    Joern Toedling

    Full Text Available Second-generation sequencing is a powerful method for identifying and quantifying small-RNA components of cells. However, little attention has been paid to the effects of the choice of sequencing platform and library preparation protocol on the results obtained. We present a thorough comparison of small-RNA sequencing libraries generated from the same embryonic stem cell lines, using different sequencing platforms, which represent the three major second-generation sequencing technologies, and protocols. We have analysed and compared the expression of microRNAs, as well as populations of small RNAs derived from repetitive elements. Despite the fact that different libraries display a good correlation between sequencing platforms, qualitative and quantitative variations in the results were found, depending on the protocol used. Thus, when comparing libraries from different biological samples, it is strongly recommended to use the same sequencing platform and protocol in order to ensure the biological relevance of the comparisons.

  19. DNA Sequence Determination by Hybridization: A Strategy for Efficient Large-Scale Sequencing

    Science.gov (United States)

    Drmanac, R.; Drmanac, S.; Strezoska, Z.; Paunesku, T.; Labat, I.; Zeremski, M.; Snoddy, J.; Funkhouser, W. K.; Koop, B.; Hood, L.; Crkvenjakov, R.

    1993-06-01

    The concept of sequencing by hybridization (SBH) makes use of an array of all possible n-nucleotide oligomers (n-mers) to identify n-mers present in an unknown DNA sequence. Computational approaches can then be used to assemble the complete sequence. As a validation of this concept, the sequences of three DNA fragments, 343 base pairs in length, were determined with octamer oligonucleotides. Possible applications of SBH include physical mapping (ordering) of overlapping DNA clones, sequence checking, DNA fingerprinting comparisons of normal and disease-causing genes, and the identification of DNA fragments with particular sequence motifs in complementary DNA and genomic libraries. The SBH techniques may accelerate the mapping and sequencing phases of the human genome project.

  20. Optimization of a sequence of reactors

    DEFF Research Database (Denmark)

    Vidal, Rene Victor Valqui

    1991-01-01

    Concerns the optimal production of sulphuric acid in a sequence of reactors. Using a suitable approximation to the objective function, this problem can easily be solved using the maximum principle. A numerical example documents the applicability of the suggested approach...

  1. Network of tRNA Gene Sequences

    Institute of Scientific and Technical Information of China (English)

    WEI Fang-ping; LI Sheng; MA Hong-ru

    2008-01-01

    A network of 3719 tRNA gene sequences was constructed using simplest alignment. Its topology, degree distribution and clustering coefficient were studied. The behaviors of the network shift from fluctuated distribution to scale-free distribution when the similarity degree of the tRNA gene sequences increases. The tRNA gene sequences with the same anticodon identity are more self-organized than those with different anticodon identities and form local clusters in the network. Some vertices of the local cluster have a high connection with other local clusters, and the probable reason was given. Moreover, a network constructed by the same number of random tRNA sequences was used to make comparisons. The relationships between the properties of the tRNA similarity network and the characters of tRNA evolutionary history were discussed.

  2. Female-specific DNA sequences in geese.

    Science.gov (United States)

    Huang, M C; Lin, W C; Horng, Y M; Rouvier, R; Huang, C W

    2003-07-01

    1. The OPAE random primers (Operon Technologies, Inc., CA) were used for random amplified polymorphic DNA (RAPD) fingerprinting in Chinese, White Roman and Landaise geese. One of these primers, OPAE-06, produced a 938-bp sex-specific fragment in all females and in no males of Chinese geese only. 2. A novel female-specific DNA sequence in Chinese goose was cloned and sequenced. Two primers, CGSex-F and CGSex-R, were designed in order to amplify a 912-bp sex-specific polymerase chain reaction (PCR) fragment on genomic DNA from female geese. 3. It was shown that a simple and effective PCR-based sexing technique could be used in the three goose breeds studied. 4. Nucleotide sequencing of the sex-specific fragments in White Roman and Landaise geese was performed and sequence differences were observed among these three breeds.

  3. New stopping criteria for segmenting DNA sequences

    CERN Document Server

    Li, W

    2001-01-01

    We propose a solution on the stopping criterion in segmenting inhomogeneous DNA sequences with complex statistical patterns. This new stopping criterion is based on Bayesian Information Criterion (BIC) in the model selection framework. When this stopping criterion is applied to a left telomere sequence of yeast Saccharomyces cerevisiae and the complete genome sequence of bacterium Escherichia coli, borders of biologically meaningful units were identified (e.g. subtelomeric units, replication origin, and replication terminus), and a more reasonable number of domains was obtained. We also introduce a measure called segmentation strength which can be used to control the delineation of large domains. The relationship between the average domain size and the threshold of segmentation strength is determined for several genome sequences.

  4. Sequence Matching Analysis for Curriculum Development

    National Research Council Canada - National Science Library

    Liem Yenny Bendatu; Bernardo Nugroho Yahya

    2015-01-01

    .... This study attempts to develop a sequence matching analysis. Considering conformance checking as the basis of this approach, this proposed approach utilizes the current control flow technique in process mining domain...

  5. Supervised Sequence Labelling with Recurrent Neural Networks

    CERN Document Server

    Graves, Alex

    2012-01-01

    Supervised sequence labelling is a vital area of machine learning, encompassing tasks such as speech, handwriting and gesture recognition, protein secondary structure prediction and part-of-speech tagging. Recurrent neural networks are powerful sequence learning tools—robust to input noise and distortion, able to exploit long-range contextual information—that would seem ideally suited to such problems. However their role in large-scale sequence labelling systems has so far been auxiliary.    The goal of this book is a complete framework for classifying and transcribing sequential data with recurrent neural networks only. Three main innovations are introduced in order to realise this goal. Firstly, the connectionist temporal classification output layer allows the framework to be trained with unsegmented target sequences, such as phoneme-level speech transcriptions; this is in contrast to previous connectionist approaches, which were dependent on error-prone prior segmentation. Secondly, multidimensional...

  6. Characterizing leader sequences of CRISPR loci

    DEFF Research Database (Denmark)

    Alkhnbashi, Omer; Shah, Shiraz Ali; Garrett, Roger Antony

    2016-01-01

    The CRISPR-Cas system is an adaptive immune system in many archaea and bacteria, which provides resistance against invading genetic elements. The first phase of CRISPR-Cas immunity is called adaptation, in which small DNA fragments are excised from genetic elements and are inserted into a CRISPR...... array generally adjacent to its so called leader sequence at one end of the array. It has been shown that transcription initiation and adaptation signals of the CRISPR array are located within the leader. However, apart from promoters, there is very little knowledge of sequence or structural motifs...... sequences by focusing on the consensus repeat of the adjacent CRISPR array and weak upstream conservation signals. We applied our tool to the analysis of a comprehensive genomic database and identified several characteristic properties of leader sequences specific to archaea and bacteria, ranging from...

  7. Nanopore DNA sequencing using kinetic proofreading

    Science.gov (United States)

    Ling, Xinsheng

    We propose a method of DNA sequencing by combining the physical method of nanopore electrical measurements and Southern's sequencing-by-hybridization. The new key ingredient, essential to both lowering the costs and increasing the precision, is an asymmetric nanopore sandwich device capable of measuring the DNA hybridization probe twice separated by a designed waiting time. Those incorrect probes appearing only once in nanopore ionic current traces are discriminated from the correct ones that appear twice. This method of discrimination is similar to the principle of kinetic proofreading proposed by Hopfield and Ninio in gene transcription and translation processes. An error analysis is of this nanopore kinetic proofreading (nKP) technique for DNA sequencing is carried out in comparison with the most precise 3' dideoxy termination method developed by Sanger. Nanopore DNA sequencing using kinetic proofreading.

  8. Improved polynomial remainder sequences for Ore polynomials.

    Science.gov (United States)

    Jaroschek, Maximilian

    2013-11-01

    Polynomial remainder sequences contain the intermediate results of the Euclidean algorithm when applied to (non-)commutative polynomials. The running time of the algorithm is dependent on the size of the coefficients of the remainders. Different ways have been studied to make these as small as possible. The subresultant sequence of two polynomials is a polynomial remainder sequence in which the size of the coefficients is optimal in the generic case, but when taking the input from applications, the coefficients are often larger than necessary. We generalize two improvements of the subresultant sequence to Ore polynomials and derive a new bound for the minimal coefficient size. Our approach also yields a new proof for the results in the commutative case, providing a new point of view on the origin of the extraneous factors of the coefficients.

  9. Generalized locally Toeplitz sequences theory and applications

    CERN Document Server

    Garoni, Carlo

    2017-01-01

    Based on their research experience, the authors propose a reference textbook in two volumes on the theory of generalized locally Toeplitz sequences and their applications. This first volume focuses on the univariate version of the theory and the related applications in the unidimensional setting, while the second volume, which addresses the multivariate case, is mainly devoted to concrete PDE applications. This book systematically develops the theory of generalized locally Toeplitz (GLT) sequences and presents some of its main applications, with a particular focus on the numerical discretization of differential equations (DEs). It is the first book to address the relatively new field of GLT sequences, which occur in numerous scientific applications and are especially dominant in the context of DE discretizations. Written for applied mathematicians, engineers, physicists, and scientists who (perhaps unknowingly) encounter GLT sequences in their research, it is also of interest to those working in the fields of...

  10. Extracting biological knowledge from DNA sequences

    Energy Technology Data Exchange (ETDEWEB)

    De La Vega, F.M. [CINVESTAV-IPN (Mexico); Thieffry, D. [Universite Libre de Bruxelles, Rhode-Saint-Genese (Belgium)]|[Universidad Nacional Autonoma de Mexico, Morelos (Mexico); Collado-Vides, J. [Universidad Nacional Autonoma de Mexico, Morelos (Mexico)

    1996-12-31

    This session describes the elucidation of information from dna sequences and what challenges computational biologists face in their task of summarizing and deciphering the human genome. Techniques discussed include methods from statistics, information theory, artificial intelligence and linguistics. 1 ref.

  11. Genetics Home Reference: isolated lissencephaly sequence

    Science.gov (United States)

    ... Facebook Share on Twitter Your Guide to Understanding Genetic Conditions Search MENU Toggle navigation Home Page Search ... Conditions Genes Chromosomes & mtDNA Resources Help Me Understand Genetics Home Health Conditions isolated lissencephaly sequence isolated lissencephaly ...

  12. GASSST: global alignment short sequence search tool

    National Research Council Canada - National Science Library

    Rizk, Guillaume; Lavenier, Dominique

    2010-01-01

    .... Our goal with our new aligner GASSST (Global Alignment Short Sequence Search Tool) is thus 2-fold-achieving high performance with no restrictions on the number of indels with a design that is still effective on long reads...

  13. Long range correlations in DNA sequences

    CERN Document Server

    Mohanty, A K

    2002-01-01

    The so called long range correlation properties of DNA sequences are studied using the variance analyses of the density distribution of a single or a group of nucleotides in a model independent way. This new method which was suggested earlier has been applied to extract slope parameters that characterize the correlation properties for several intron containing and intron less DNA sequences. An important aspect of all the DNA sequences is the properties of complimentarity by virtue of which any two complimentary distributions (like GA is complimentary to TC or G is complimentary to ATC) have identical fluctuations at all scales although their distribution functions need not be identical. Due to this complimentarity, the famous DNA walk representation whose statistical interpretation is still unresolved is shown to be a special case of the present formalism with a density distribution corresponding to a purine or a pyrimidine group. Another interesting aspect of most of the DNA sequences is that the factorial m...

  14. Glycome mapping on DNA sequencing equipment.

    Science.gov (United States)

    Laroy, Wouter; Contreras, Roland; Callewaert, Nico

    2006-01-01

    Here we provide a detailed protocol for the analysis of protein-linked glycans on DNA sequencing equipment. This protocol satisfies the glyco-analytical needs of many projects and can form the basis of 'glycomics' studies, in which robustness, high throughput, high sensitivity and reliable quantification are of paramount importance. The protocol routinely resolves isobaric glycan stereoisomers, which is much more difficult by mass spectrometry (MS). Earlier methods made use of polyacrylamide gel-based sequencers, but we have now adapted the technique to multicapillary DNA sequencers, which represent the state of the art today. In addition, we have integrated an option for HPLC-based fractionation of highly anionic 8-amino-1,3,6-pyrenetrisulfonic acid (APTS)-labeled glycans before rapid capillary electrophoretic profiling. This option facilitates either two-dimensional profiling of complex glycan mixtures and exoglycosidase sequencing, or MS analysis of particular compounds of interest rather than of the total pool of glycans in a sample.

  15. Simultaneous sensorimotor adaptation and sequence learning.

    Science.gov (United States)

    Overduin, Simon A; Richardson, Andrew G; Bizzi, Emilio; Press, Daniel Z

    2008-01-01

    Sensorimotor adaptation and sequence learning have often been treated as distinct forms of motor learning. But frequently the motor system must acquire both types of experience simultaneously. Here, we investigated the interaction of these two forms of motor learning by having subjects adapt to predictable forces imposed by a robotic manipulandum while simultaneously reaching to an implicit sequence of targets. We show that adaptation to novel dynamics and learning of a sequence of movements can occur simultaneously and without significant interference or facilitation. When both conditions were presented simultaneously to subjects, their trajectory error and reaction time decreased to the same extent as those of subjects who experienced the force field or sequence independently.

  16. Sequencing Information Management System (SIMS). Final report

    Energy Technology Data Exchange (ETDEWEB)

    Fields, C.

    1996-02-15

    A feasibility study to develop a requirements analysis and functional specification for a data management system for large-scale DNA sequencing laboratories resulted in a functional specification for a Sequencing Information Management System (SIMS). This document reports the results of this feasibility study, and includes a functional specification for a SIMS relational schema. The SIMS is an integrated information management system that supports data acquisition, management, analysis, and distribution for DNA sequencing laboratories. The SIMS provides ad hoc query access to information on the sequencing process and its results, and partially automates the transfer of data between laboratory instruments, analysis programs, technical personnel, and managers. The SIMS user interfaces are designed for use by laboratory technicians, laboratory managers, and scientists. The SIMS is designed to run in a heterogeneous, multiplatform environment in a client/server mode. The SIMS communicates with external computational and data resources via the internet.

  17. The DWPF Melter proposed heat up sequence

    Energy Technology Data Exchange (ETDEWEB)

    Smith, M.E.

    1989-08-11

    Per the request of DWPT supervision, a proposed heatup sequence for the DWPF Melter has been documented in this report. DWPF personnel will use this report as a guide to write the detailed DWPF Melter startup plan. 6 refs.

  18. Identifying driver mutations in sequenced cancer genomes

    DEFF Research Database (Denmark)

    Raphael, Benjamin J; Dobson, Jason R; Oesper, Layla

    2014-01-01

    High-throughput DNA sequencing is revolutionizing the study of cancer and enabling the measurement of the somatic mutations that drive cancer development. However, the resulting sequencing datasets are large and complex, obscuring the clinically important mutations in a background of errors, noise......, and random mutations. Here, we review computational approaches to identify somatic mutations in cancer genome sequences and to distinguish the driver mutations that are responsible for cancer from random, passenger mutations. First, we describe approaches to detect somatic mutations from high-throughput DNA...... sequencing data, particularly for tumor samples that comprise heterogeneous populations of cells. Next, we review computational approaches that aim to predict driver mutations according to their frequency of occurrence in a cohort of samples, or according to their predicted functional impact on protein...

  19. A disruptive sequencer meets disruptive publishing.

    Science.gov (United States)

    Loman, Nick; Goodwin, Sarah; Jansen, Hans; Loose, Matt

    2015-01-01

    Nanopore sequencing was recently made available to users in the form of the Oxford Nanopore MinION. Released to users through an early access programme, the MinION is made unique by its tiny form factor and ability to generate very long sequences from single DNA molecules. The platform is undergoing rapid evolution with three distinct nanopore types and five updates to library preparation chemistry in the last 18 months. To keep pace with the rapid evolution of this sequencing platform, and to provide a space where new analysis methods can be openly discussed, we present a new F1000Research channel devoted to updates to and analysis of nanopore sequence data.

  20. "X"-tending the Fibonacci Sequence.

    Science.gov (United States)

    Moran, Glenn T.

    2002-01-01

    Outlines a lesson on the Fibonacci and Lucas sequences that captures student interest by presenting the opportunity for computation practice, mental mathematics, and proof for algebra students. Discusses an extension for solving simultaneous equations. (YDS)

  1. Fibonacci Sequence and Supramolecular Structure of DNA.

    Science.gov (United States)

    Shabalkin, I P; Grigor'eva, E Yu; Gudkova, M V; Shabalkin, P I

    2016-05-01

    We proposed a new model of supramolecular DNA structure. Similar to the previously developed by us model of primary DNA structure [11-15], 3D structure of DNA molecule is assembled in accordance to a mathematic rule known as Fibonacci sequence. Unlike primary DNA structure, supramolecular 3D structure is assembled from complex moieties including a regular tetrahedron and a regular octahedron consisting of monomers, elements of the primary DNA structure. The moieties of the supramolecular DNA structure forming fragments of regular spatial lattice are bound via linker (joint) sequences of the DNA chain. The lattice perceives and transmits information signals over a considerable distance without acoustic aberrations. Linker sequences expand conformational space between lattice segments allowing their sliding relative to each other under the action of external forces. In this case, sliding is provided by stretching of the stacked linker sequences.

  2. Sequence finishing and mapping of Drosophila melanogasterheterochromatin

    Energy Technology Data Exchange (ETDEWEB)

    Hoskins, Roger A.; Carlson, Joseph W.; Kennedy, Cameron; Acevedo,David; Evans-Holm, Martha; Frise, Erwin; Wan, Kenneth H.; Park, Soo; Mendez-Lago, Maria; Rossi, Fabrizio; Villasante, Alfredo; Dimitri,Patrizio; Karpen, Gary H.; Celniker, Susan E.

    2007-06-15

    Genome sequences for most metazoans are incomplete due tothe presence of repeated DNA in the pericentromeric heterochromatin. Theheterochromatic regions of D. melanogaster contain 20 Mb of sequenceamenable to mapping, sequence assembly and finishing. Here we describethe generation of 15 Mb of finished or improved heterochromatic sequenceusing available clone resources and assembly and mapping methods. We alsoconstructed a BAC-based physical map that spans approximately 13 Mb ofthe pericentromeric heterochromatin, and a cytogenetic map that positionsapproximately 11 Mb of BAC contigs and sequence scaffolds in specificchromosomal locations. The integrated sequence assembly and maps greatlyimprove our understanding of the structure and composition of this poorlyunderstood fraction of a metazoan genome and provide a framework forfunctional analyses.

  3. The complete DNA sequence of vaccinia virus.

    Science.gov (United States)

    Goebel, S J; Johnson, G P; Perkus, M E; Davis, S W; Winslow, J P; Paoletti, E

    1990-11-01

    The complete DNA sequence of the genome of vaccinia virus has been determined. The genome consisted of 191,636 bp with a base composition of 66.6% A + T. We have identified 198 "major" protein-coding regions and 65 overlapping "minor" regions, for a total of 263 potential genes. Genes encoded by the virus were located by examination of DNA sequence characteristics and compared with existing vaccinia virus mapping analyses, sequence data, and transcription data. These genes were found to be compactly organized along the genome with relatively few regions of noncoding sequences. Whereas several similarities to proteins of known function were discerned, the function of the majority of proteins encoded by these open reading frames is as yet undetermined.

  4. ASAP: Amplification, sequencing & annotation of plastomes

    Directory of Open Access Journals (Sweden)

    Folta Kevin M

    2005-12-01

    Full Text Available Abstract Background Availability of DNA sequence information is vital for pursuing structural, functional and comparative genomics studies in plastids. Traditionally, the first step in mining the valuable information within a chloroplast genome requires sequencing a chloroplast plasmid library or BAC clones. These activities involve complicated preparatory procedures like chloroplast DNA isolation or identification of the appropriate BAC clones to be sequenced. Rolling circle amplification (RCA is being used currently to amplify the chloroplast genome from purified chloroplast DNA and the resulting products are sheared and cloned prior to sequencing. Herein we present a universal high-throughput, rapid PCR-based technique to amplify, sequence and assemble plastid genome sequence from diverse species in a short time and at reasonable cost from total plant DNA, using the large inverted repeat region from strawberry and peach as proof of concept. The method exploits the highly conserved coding regions or intergenic regions of plastid genes. Using an informatics approach, chloroplast DNA sequence information from 5 available eudicot plastomes was aligned to identify the most conserved regions. Cognate primer pairs were then designed to generate ~1 – 1.2 kb overlapping amplicons from the inverted repeat region in 14 diverse genera. Results 100% coverage of the inverted repeat region was obtained from Arabidopsis, tobacco, orange, strawberry, peach, lettuce, tomato and Amaranthus. Over 80% coverage was obtained from distant species, including Ginkgo, loblolly pine and Equisetum. Sequence from the inverted repeat region of strawberry and peach plastome was obtained, annotated and analyzed. Additionally, a polymorphic region identified from gel electrophoresis was sequenced from tomato and Amaranthus. Sequence analysis revealed large deletions in these species relative to tobacco plastome thus exhibiting the utility of this method for structural and

  5. Sequencing and Analysis of Neanderthal Genomic DNA

    OpenAIRE

    Noonan, James P.; Coop, Graham; Kudaravalli, Sridhar; Smith, Doug; Krause, Johannes; Alessi, Joe; Chen, Feng; Platt, Darren; Paabo, Svante; Pritchard, Jonathan K; Rubin, Edward M.

    2006-01-01

    Our knowledge of Neanderthals is based on a limited number of remains and artifacts from which we must make inferences about their biology, behavior, and relationship to ourselves. Here, we describe the characterization of these extinct hominids from a new perspective, based on the development of a Neanderthal metagenomic library and its high-throughput sequencing and analysis. Several lines of evidence indicate that the 65,250 base pairs of hominid sequence so far identified in the library a...

  6. Inconsistencies in Neanderthal genomic DNA sequences.

    Directory of Open Access Journals (Sweden)

    Jeffrey D Wall

    2007-10-01

    Full Text Available Two recently published papers describe nuclear DNA sequences that were obtained from the same Neanderthal fossil. Our reanalyses of the data from these studies show that they are not consistent with each other and point to serious problems with the data quality in one of the studies, possibly due to modern human DNA contaminants and/or a high rate of sequencing errors.

  7. Recursive Polynomial Remainder Sequence and its Subresultants

    OpenAIRE

    Terui, Akira

    2008-01-01

    We introduce concepts of "recursive polynomial remainder sequence (PRS)" and "recursive subresultant," along with investigation of their properties. A recursive PRS is defined as, if there exists the GCD (greatest common divisor) of initial polynomials, a sequence of PRSs calculated "recursively" for the GCD and its derivative until a constant is derived, and recursive subresultants are defined by determinants representing the coefficients in recursive PRS as functions of coefficients of init...

  8. Inferring phylogenies from RAD sequence data.

    Directory of Open Access Journals (Sweden)

    Benjamin E R Rubin

    Full Text Available Reduced-representation genome sequencing represents a new source of data for systematics, and its potential utility in interspecific phylogeny reconstruction has not yet been explored. One approach that seems especially promising is the use of inexpensive short-read technologies (e.g., Illumina, SOLiD to sequence restriction-site associated DNA (RAD--the regions of the genome that flank the recognition sites of restriction enzymes. In this study, we simulated the collection of RAD sequences from sequenced genomes of different taxa (Drosophila, mammals, and yeasts and developed a proof-of-concept workflow to test whether informative data could be extracted and used to accurately reconstruct "known" phylogenies of species within each group. The workflow consists of three basic steps: first, sequences are clustered by similarity to estimate orthology; second, clusters are filtered by taxonomic coverage; and third, they are aligned and concatenated for "total evidence" phylogenetic analysis. We evaluated the performance of clustering and filtering parameters by comparing the resulting topologies with well-supported reference trees and we were able to identify conditions under which the reference tree was inferred with high support. For Drosophila, whole genome alignments allowed us to directly evaluate which parameters most consistently recovered orthologous sequences. For the parameter ranges explored, we recovered the best results at the low ends of sequence similarity and taxonomic representation of loci; these generated the largest supermatrices with the highest proportion of missing data. Applications of the method to mammals and yeasts were less successful, which we suggest may be due partly to their much deeper evolutionary divergence times compared to Drosophila (crown ages of approximately 100 and 300 versus 60 Mya, respectively. RAD sequences thus appear to hold promise for reconstructing phylogenetic relationships in younger clades in

  9. Inferring phylogenies from RAD sequence data.

    Science.gov (United States)

    Rubin, Benjamin E R; Ree, Richard H; Moreau, Corrie S

    2012-01-01

    Reduced-representation genome sequencing represents a new source of data for systematics, and its potential utility in interspecific phylogeny reconstruction has not yet been explored. One approach that seems especially promising is the use of inexpensive short-read technologies (e.g., Illumina, SOLiD) to sequence restriction-site associated DNA (RAD)--the regions of the genome that flank the recognition sites of restriction enzymes. In this study, we simulated the collection of RAD sequences from sequenced genomes of different taxa (Drosophila, mammals, and yeasts) and developed a proof-of-concept workflow to test whether informative data could be extracted and used to accurately reconstruct "known" phylogenies of species within each group. The workflow consists of three basic steps: first, sequences are clustered by similarity to estimate orthology; second, clusters are filtered by taxonomic coverage; and third, they are aligned and concatenated for "total evidence" phylogenetic analysis. We evaluated the performance of clustering and filtering parameters by comparing the resulting topologies with well-supported reference trees and we were able to identify conditions under which the reference tree was inferred with high support. For Drosophila, whole genome alignments allowed us to directly evaluate which parameters most consistently recovered orthologous sequences. For the parameter ranges explored, we recovered the best results at the low ends of sequence similarity and taxonomic representation of loci; these generated the largest supermatrices with the highest proportion of missing data. Applications of the method to mammals and yeasts were less successful, which we suggest may be due partly to their much deeper evolutionary divergence times compared to Drosophila (crown ages of approximately 100 and 300 versus 60 Mya, respectively). RAD sequences thus appear to hold promise for reconstructing phylogenetic relationships in younger clades in which sufficient

  10. Task sequencing for autonomous robotic vacuum cleaners

    Science.gov (United States)

    Gorbenko, Anna; Popov, Vladimir

    2017-07-01

    Various planning problems for robotic systems are of considerable interest. One of such problems is the problem of task sequencing. In this paper, we consider the problem of task sequencing for autonomous vacuum floor cleaning robots. We consider a graph model for the problem. We propose an efficient approach to solve the problem. In particular, we use an explicit reduction from the decision version of the problem to the satisfiability problem. We present the results of computational experiments for different satisfiability algorithms.

  11. Optimization of a sequence of reactors

    DEFF Research Database (Denmark)

    Vidal, Rene Victor Valqui

    1991-01-01

    Concerns the optimal production of sulphuric acid in a sequence of reactors. Using a suitable approximation to the objective function, this problem can easily be solved using the maximum principle. A numerical example documents the applicability of the suggested approach......Concerns the optimal production of sulphuric acid in a sequence of reactors. Using a suitable approximation to the objective function, this problem can easily be solved using the maximum principle. A numerical example documents the applicability of the suggested approach...

  12. Parallel motif extraction from very long sequences

    KAUST Repository

    Sahli, Majed

    2013-01-01

    Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern applications require mining of motifs in one very long sequence (i.e., in the order of several gigabytes). For this case, there exist statistical approaches that are fast but inaccurate; or combinatorial methods that are sound and complete. Unfortunately, existing combinatorial methods are serial and very slow. Consequently, they are limited to very short sequences (i.e., a few megabytes), small alphabets (typically 4 symbols for DNA sequences), and restricted types of motifs. This paper presents ACME, a combinatorial method for extracting motifs from a single very long sequence. ACME arranges the search space in contiguous blocks that take advantage of the cache hierarchy in modern architectures, and achieves almost an order of magnitude performance gain in serial execution. It also decomposes the search space in a smart way that allows scalability to thousands of processors with more than 90% speedup. ACME is the only method that: (i) scales to gigabyte-long sequences; (ii) handles large alphabets; (iii) supports interesting types of motifs with minimal additional cost; and (iv) is optimized for a variety of architectures such as multi-core systems, clusters in the cloud, and supercomputers. ACME reduces the extraction time for an exact-length query from 4 hours to 7 minutes on a typical workstation; handles 3 orders of magnitude longer sequences; and scales up to 16, 384 cores on a supercomputer. Copyright is held by the owner/author(s).

  13. A Method to Construct Generalized Fibonacci Sequences

    Directory of Open Access Journals (Sweden)

    Adalberto García-Máynez

    2016-01-01

    Full Text Available The main purpose of this paper is to study the convergence properties of Generalized Fibonacci Sequences and the series of partial sums associated with them. When the proper values of an s×s real matrix A are real and different, we give a necessary and sufficient condition for the convergence of the matrix sequence A,A2,A3,… to a matrix B.

  14. A Method to Construct Generalized Fibonacci Sequences

    OpenAIRE

    Adalberto García-Máynez; Adolfo Pimienta Acosta

    2016-01-01

    The main purpose of this paper is to study the convergence properties of Generalized Fibonacci Sequences and the series of partial sums associated with them. When the proper values of an $s\\timess$ real matrix $A$ are real and different, we give a necessary and sufficient condition for the convergence of the matrix sequence $A,{A}^{\\mathrm{2}},{A}^{\\mathrm{3}},\\dots $ to a matrix $B$ .

  15. Cactus: Algorithms for genome multiple sequence alignment

    OpenAIRE

    Paten, Benedict; Earl, Dent; Nguyen, Ngan; Diekhans, Mark; Zerbino, Daniel; Haussler, David

    2011-01-01

    Much attention has been given to the problem of creating reliable multiple sequence alignments in a model incorporating substitutions, insertions, and deletions. Far less attention has been paid to the problem of optimizing alignments in the presence of more general rearrangement and copy number variation. Using Cactus graphs, recently introduced for representing sequence alignments, we describe two complementary algorithms for creating genomic alignments. We have implemented these algorithms...

  16. Fibonacci difference sequence spaces for modulus functions

    Directory of Open Access Journals (Sweden)

    Kuldip Raj

    2015-05-01

    Full Text Available In the present paper we introduce Fibonacci difference sequence spaces l(F, Ƒ, p, u and  l_∞(F, Ƒ, p, u by using a sequence of modulus functions and a new band matrix F. We also make an effort to study some inclusion relations, topological and geometric properties of these spaces. Furthermore, the alpha, beta, gamma duals and matrix transformation of the space l(F, Ƒ, p, u are determined.

  17. Determinant Representations of Sequences: A Survey

    Directory of Open Access Journals (Sweden)

    Moghaddamfar A. R.

    2014-01-01

    Full Text Available This is a survey of recent results concerning (integer matrices whose leading principal minors are well-known sequences such as Fibonacci, Lucas, Jacobsthal and Pell (subsequences. There are different ways for constructing such matrices. Some of these matrices are constructed by homogeneous or nonhomogeneous recurrence relations, and others are constructed by convolution of two sequences. In this article, we will illustrate the idea of these methods by constructing some integer matrices of this type.

  18. Probabilistic motor sequence yields greater offline and less online learning than fixed sequence

    Directory of Open Access Journals (Sweden)

    Yue eDu

    2016-03-01

    Full Text Available It is well acknowledged that motor sequences can be learned quickly through online learning. Subsequently, the initial acquisition of a motor sequence is boosted or consolidated by offline learning. However, little is known whether offline learning can drive the fast learning of motor sequences (i.e., initial sequence learning in the first training session. To examine offline learning in the fast learning stage, we asked four groups of young adults to perform the serial reaction time (SRT task with either a fixed or probabilistic sequence and with or without preliminary knowledge of the presence of a sequence. The sequence and instruction types were manipulated to emphasize either procedural (probabilistic sequence; no preliminary knowledge or declarative (fixed sequence; with preliminary knowledge memory that were found to either facilitate or inhibit offline learning. In the SRT task, there were six learning blocks with a two-minute break between each consecutive block. Throughout the session, stimuli followed the same fixed or probabilistic pattern except in Block 5, in which stimuli appeared in a random order. We found that preliminary knowledge facilitated the learning of a fixed sequence, but not a probabilistic sequence. In addition to overall learning measured by the mean reaction time (RT, we examined the progressive changes in RT within and between blocks (i.e., online and offline learning, respectively. It was found that the two groups who performed the fixed sequence, regardless of preliminary knowledge, showed greater online learning than the other two groups who performed the probabilistic sequence. The groups who performed the probabilistic sequence, regardless of preliminary knowledge, did not display online learning, as indicated by a decline in performance within the learning blocks. However, they did demonstrate remarkably greater offline improvement in RT, which suggests that they are learning the probabilistic sequence

  19. A Unified Theoretical Framework for Cognitive Sequencing.

    Science.gov (United States)

    Savalia, Tejas; Shukla, Anuj; Bapi, Raju S

    2016-01-01

    The capacity to sequence information is central to human performance. Sequencing ability forms the foundation stone for higher order cognition related to language and goal-directed planning. Information related to the order of items, their timing, chunking and hierarchical organization are important aspects in sequencing. Past research on sequencing has emphasized two distinct and independent dichotomies: implicit vs. explicit and goal-directed vs. habits. We propose a theoretical framework unifying these two streams. Our proposal relies on brain's ability to implicitly extract statistical regularities from the stream of stimuli and with attentional engagement organizing sequences explicitly and hierarchically. Similarly, sequences that need to be assembled purposively to accomplish a goal require engagement of attentional processes. With repetition, these goal-directed plans become habits with concomitant disengagement of attention. Thus, attention and awareness play a crucial role in the implicit-to-explicit transition as well as in how goal-directed plans become automatic habits. Cortico-subcortical loops basal ganglia-frontal cortex and hippocampus-frontal cortex loops mediate the transition process. We show how the computational principles of model-free and model-based learning paradigms, along with a pivotal role for attention and awareness, offer a unifying framework for these two dichotomies. Based on this framework, we make testable predictions related to the potential influence of response-to-stimulus interval (RSI) on developing awareness in implicit learning tasks.

  20. A Unified Theoretical Framework for Cognitive Sequencing

    Directory of Open Access Journals (Sweden)

    Tejas Savalia

    2016-11-01

    Full Text Available The capacity to sequence information is central to human performance. Sequencing ability forms the foundation stone for higher order cognition related to language and goal-directed planning. Information related to the order of items, their timing, chunking and hierarchical organization are important aspects in sequencing. Past research on sequencing has emphasized two distinct and independent dichotomies: implicit versus explicit and goal-directed versus habits. We propose a theoretical framework unifying these two streams. Our proposal relies on brain's ability to implicitly extract statistical regularities from the stream of stimuli and with attentional engagement organizing sequences explicitly and hierarchically. Similarly, sequences that need to be assembled purposively to accomplish a goal require engagement of attentional processes. With repetition, these goal-directed plans become habits with concomitant disengagement of attention. Thus attention and awareness play a crucial role in the implicit-to-explicit transition as well as in how goal-directed plans become automatic habits. Cortico-subcortical loops ─ basal ganglia-frontal cortex and hippocampus-frontal cortex loops ─ mediate the transition process. We show how the computational principles of model-free and model-based learning paradigms, along with a pivotal role for attention and awareness, offer a unifying framework for these two dichotomies. Based on this framework, we make testable predictions related to the potential influence of response-to-stimulus interval (RSI on developing awareness in implicit learning tasks.