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Sample records for automated stratigraphic structural

  1. Directional structure tensors in estimating seismic structural and stratigraphic orientations

    NASA Astrophysics Data System (ADS)

    Wu, Xinming; Janson, Xavier

    2017-07-01

    Estimating orientations of seismic structures (reflections) and stratigraphic features (channels) is important for seismic interpretation, subsurface interpolation and geophysical inversion. Structure tensors, constructed as smoothed outer products of amplitude gradients, are commonly used to estimate seismic reflection normals, which uniquely define the reflection orientations. However, this conventional structure-tensor method often generates significant errors in estimating orientations of the reflections with steep and rapidly varying slopes. To better estimate reflection orientations, we propose to construct structure tensors in a new space, where the reflections are mostly flat or only slightly dipping and the variation of reflection slopes is reduced. We use these constructed structure tensors to compute reflection normals in this new space and then transform the normals back to obtain a better estimation of reflection orientations in the original space. Seismic stratigraphic features such as channels are often aligned within dipping reflections. It is not discussed previously by others to estimate orientations of such features directly from a seismic image. An ideal way to estimate stratigraphic orientations is to first extract a horizon surface with stratigraphic features, and then construct structure tensors with gradients on the surface to estimate the orientations of the features. However, extracting horizon surfaces can be a difficult and time-consuming task in practice. Fortunately, computing gradients on a horizon surface is only a local operation and is equivalent to directly compute directional derivatives along reflection slopes without picking horizons. Based on this observation, we propose to use an equivalent but more efficient way to estimate seismic stratigraphic orientations by using structure tensors constructed with the directional derivatives along reflections. We demonstrate the methods of estimating structural and stratigraphic

  2. Stratigraphic and structural interpretation with 3-D seismic coherence

    SciTech Connect

    Bahorich, M.; Lopez, J.; Haskell, N.

    1996-12-31

    3-D seismic discontinuity is useful for identifying faults, stratigraphic features and the relationship between them. This paper covers the application of coherence technology to three basins; the Gulf of Mexico, the North Sea, aid the Ardmore Basin of Oklahoma. In the Gulf of Mexico, 3-D coherence data may be used to simultaneously view faults and stratigraphic features and therefore see the relationship between them. Coherence data reveal channels that avoid a structural high generated by a salt dome, Channels that change direction as they cross faults, radial faults adjacent to a salt dome, and complex and en-echelon faults. Since the coherence process is applied to non- interpreted seismic data, these features are available for viewing without the time or bias of interpretation. Coherence time slices from the Ardmore Basin of Oklahoma were compared with a horizon-dip map and a discrepancy in the fault patterns was noted. Further analysis revealed that subtle errors in the autopicking had created a false bend in a fault trace seen on the horizon-dip map. After correction, the horizon-dip map and coherence time slice indicated similar fault patterns. Since the coherence method is run on the raw seismic data, it provides a view of the faults that is not biased by the interpreter or horizon autopicker. In the North Sea, faults may exhibit meandering patterns that are easy to interpret on traditional time-slices where they cut perpendicular to stratigraphic bedding but are difficult to recognize where they cut parallel to bedding. The coherence technique images faults in any orientation equally well.

  3. Stratigraphic and structural interpretation with 3-D seismic coherence

    SciTech Connect

    Bahorich, M.; Lopez, J.; Haskell, N.; Nissen, S.; Poole, A.

    1996-06-01

    3-D seismic discontinuity is useful for identifying faults, stratigraphic features and the relationship between them. This paper covers the application of coherence technology to three basins; the Gulf of Mexico, the North Sea, and the Ardmore Basin of Oklahoma. In the Gulf of Mexico, 3-D coherence data may be used to simultaneously view faults and stratigraphic features and therefore see the relationship between them. Coherence data reveal channels that avoid a structural high generated by a salt dome, channels that change direction as they cross faults, radial faults adjacent to a salt dome, and complex and en-echelon faults. Since the coherence process is applied to non-interpreted seismic data, these features are available for viewing without the time or bias of interpretation. Coherence time slices from the Ardmore Basin of Oklahoma were compared with a horizon-dip map and a discrepancy in the fault patterns was noted. Further analysis revealed that subtle errors in the autopicking had created a false bend in a fault trace seen on the horizon-dip map. After correction, the horizon-dip map and coherence time slice indicated similar fault patterns. Since the coherence method is run on the raw seismic data, it provides a view of the faults that is not biased by the interpreter or horizon autopicker. In the North Sea, faults may exhibit meandering patterns that are easy to interpret on traditional time-slices where they cut perpendicular to stratigraphic bedding but are difficult to recognize where they cut parallel to bedding. The coherence technique images faults in any orientation equally well.

  4. Effects of Basement, Structure, and Stratigraphic Heritages on Volcano Behavior

    NASA Astrophysics Data System (ADS)

    Lagmay, Alfredo Mahar Francisco A.

    2006-06-01

    Effective natural hazard mitigation requires that the science surrounding geophysical events be thoroughly explored. With millions of people living on the flanks of volcanoes, understanding the parameters that effect volcanic behavior is critically important. In particular, basements can influence the occurrence of volcanic eruptions and landslides. This control by the substrate on volcano behavior usually has been considered questionable or less important than the conditions of the deep magma source. However, due to recent findings, this view is changing, specifically with regard to approaches in assessing volcanic hazards. The November 2005 AGU Chapman Conference ``Effects of Basement, Structure, and Stratigraphic Heritages on Volcano Behavior'' brought together geologists and geophysicists from North and South America, Europe, and Asia to discuss the results of their research on the reciprocal effects of the interaction between volcanos and their basements. The conference also highlighted the importance of holding Chapman conferences in developing countries such as the Philippines because many hazardous volcanos are situated in these countries. Apart from having natural field laboratories, these are the very same places that need to promote scientific discourse on volcano research, which can lead to more effective hazard mitigation programs.

  5. Stratigraphic and structural interpretation with 3-D coherence

    SciTech Connect

    Bahorich, M.S.; Lopez, J.; Haskell, N.L.

    1995-12-31

    3-D seismic coherence is useful for identifying faults, stratigraphic features and the relationship between them (Bahorich, and Farmer, 1994). This paper documents the use of this technology in three basins; the Gulf of Mexico, the North Sea, and the Ardmore Basin of Oklahoma.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  7. Automated design of aerospace structures

    NASA Technical Reports Server (NTRS)

    Fulton, R. E.; Mccomb, H. G.

    1974-01-01

    The current state-of-the-art in structural analysis of aerospace vehicles is characterized, automated design technology is discussed, and an indication is given of the future direction of research in analysis and automated design. Representative computer programs for analysis typical of those in routine use in vehicle design activities are described, and results are shown for some selected analysis problems. Recent and planned advances in analysis capability are indicated. Techniques used to automate the more routine aspects of structural design are discussed, and some recently developed automated design computer programs are described. Finally, discussion is presented of early accomplishments in interdisciplinary automated design systems, and some indication of the future thrust of research in this field is given.

  8. Structural-stratigraphic setting of LaFourche Crossing Prospect, Louisisana

    SciTech Connect

    Snyder, F.C.; Pilger, R.H. Jr.; Bebout, D.G.; Bachman, A.L.

    1981-01-01

    Detailed structural-stratigraphic analysis of LaFourche Crossing Prospect has delineated several fault blocks which place limits on the size of potential geopressured-geothermal reservoirs. The most attractive reservoir is located on the south flank of Rousseau Field, between two apparently south-dipping growth faults.

  9. Mars Structural and Stratigraphic Mapping along the Coprates Rise

    NASA Technical Reports Server (NTRS)

    Saunders, R Stephen

    2009-01-01

    This geologic mapping project supports a topical study of structures in east Thaumasia associated with the Coprates rise. The study examines cuesta-like features on the east flank of the Coprates rise first identified by Saunders et al. [1]. Mapping combines detailed local stratigraphy, structural geology and topography. Hogbacks and cuestas indicate erosion of tilted rock units. The extent of the erosion will be determined in the course of the mapping. The region of interest lies along the eastern margin of Thaumasia bounded by latitudes -15 and -35 and longitudes 50 to 70 W (Figure 1). Three MTM geologic quadrangles are being compiled for publication by the USGS (-20057, -25057, -30057). All existing data sources are used including THEMIS, MOC, CTX, HiRISE, MOLA and gravity, as well as higher level data available through the PDS data nodes at ASU, UA and Washington University. The extremely valuable ASU JMARS tools are used for analysis of many of the data sets. ArcGIS software has been obtained and is being learned for the map compilation.

  10. Stratigraphic and structural distribution of reservoirs in Romania

    SciTech Connect

    Stefanescu, M.O. )

    1991-08-01

    In Romania, there are reservoirs at different levels of the whole Cambrian-Pliocene interval, but only some of these levels have the favorable structural conditions to accumulate hydrocarbons in commercial quantities. These levels are the Devonian, Triassic, Middle Jurassic, Lower Cretaceous (locally including the uppermost Jurassic), Eocene, Oligocene-lower Miocene, middle and upper Miocene, and Pliocene. The productive reservoirs are represented either by carbonate rocks (in Devonian, Middle Triassic and uppermost Jurassic-Lower Cretaceous) or by detrital rocks (in Lower and Upper Triassic, Middle Jurassic, Eocene, Oligocene, Miocene, and Pliocene). From the structural point of view, the Romanian territory is characterized by the coexistence both of platforms (East European, Scythian, and Moesian platforms) and of the strongly tectonized orogenes (North Dobrogea and Carpathian orogenes). Each importance crust shortening was followed by the accumulation of post-tectonic covers, some of them being folded during subsequently tectonic movements. The youngest post-tectonic cover is common both for the platforms (foreland) and Carpathian orogene, representing the Carpathian foredeep. Producing reservoirs are present in the East European and Moesian platforms, in the outer Carpathian units (Tarcau and Marginal folds nappes) and in certain post-tectonic covers which fill the Carpathian foredeep and the Transylvanian and Pannonian basins. In the platforms, hydrocarbons accumulated both in calcareous and detrital reservoirs, whereas in the Carpathian units and in their reservoirs, whereas in the Carpathian units and in their post-tectonic covers, hydrocarbons accumulated only in detrital reservoirs.

  11. Structural and stratigraphic controls on cave development in the Oak Ridge area, Tennessee

    SciTech Connect

    Rubin, P A; Lemiszki, P J

    1992-01-01

    The Oak Ridge Reservation (ORR) is located in the northwestern part of the Valley and Ridge province in east Tennessee. The Valley and Ridge province is the topographic expression of the southern Appalachian foreland fold-thrust belt, which formed during the late Paleozoic Alleghanian orogeny. In the Oak Ridge area, three major northwest verging thrust faults (Kingston, Whiteoak Mountain, and Copper Creek) imbricate and juxtapose carbonate and clastic stratigraphic units that range in age from the lower Cambrian to the lower Mississippian. The carbonate stratigraphic units range in thickness from 1278 to 1748 m and include the Maynardville Limestone in the Conasauga Group (hereby included as part of the Knox Group), the Knox Group, and the Chickamauga Group. Stratigraphic relationships and repetition of units by thrust faulting has produced three northeast striking and southeast dipping carbonate bands bounded to the northwest and southeast by noncarbonate units. Preliminary results indicate that within two of these carbonate bands, formations composed of mudstone and argillaceous limestone appear to further subdivide groundwater basins. Our efforts have focused on relating the stratigraphic and structural characteristics of these rock units with cave development in the region.

  12. Using 3D visualization and seismic attributes to improve structural and stratigraphic resolution of reservoirs

    SciTech Connect

    Kerr, J. ); Jones, G.L. )

    1996-01-01

    Recent advances in hardware and software have given the interpreter and engineer new ways to view 3D seismic data and well bore information. Recent papers have also highlighted the use of various statistics and seismic attributes. By combining new 3D rendering technologies with recent trends in seismic analysis, the interpreter can improve the structural and stratigraphic resolution of hydrocarbon reservoirs. This paper gives several examples using 3D visualization to better define both the structural and stratigraphic aspects of several different structural types from around the world. Statistics, 3D visualization techniques and rapid animation are used to show complex faulting and detailed channel systems. These systems would be difficult to map using either 2D or 3D data with conventional interpretation techniques.

  13. Using 3D visualization and seismic attributes to improve structural and stratigraphic resolution of reservoirs

    SciTech Connect

    Kerr, J.; Jones, G.L.

    1996-12-31

    Recent advances in hardware and software have given the interpreter and engineer new ways to view 3D seismic data and well bore information. Recent papers have also highlighted the use of various statistics and seismic attributes. By combining new 3D rendering technologies with recent trends in seismic analysis, the interpreter can improve the structural and stratigraphic resolution of hydrocarbon reservoirs. This paper gives several examples using 3D visualization to better define both the structural and stratigraphic aspects of several different structural types from around the world. Statistics, 3D visualization techniques and rapid animation are used to show complex faulting and detailed channel systems. These systems would be difficult to map using either 2D or 3D data with conventional interpretation techniques.

  14. Structural and tectonic setting of the Charleston, South Carolina, region: Evidence from the Tertiary stratigraphic record

    USGS Publications Warehouse

    Weems, R.E.; Lewis, W.C.

    2002-01-01

    Eleven upper Eocene through Pliocene stratigraphic units occur in the subsurface of the region surrounding Charleston, South Carolina. These units contain a wealth of information concerning the long-term tectonic and structural setting of that area. These stratigraphic units have a mosaic pattern of distribution, rather than a simple layered pattern, because deposition, erosion, and tectonic warping have interacted in a complex manner through time. By generating separate structure-contour maps for the base of each stratigraphic unit, an estimate of the original basal surface of each unit can be reconstructed over wide areas. Changes in sea level over geologic time generate patterns of deposition and erosion that are geographically unique for the time of each transgression. Such patterns fail to persist when compared sequentially over time. In some areas, however, there has been persistent, repetitive net downward of upward movement over the past 34 m.y. These repetitive patterns of persistent motion are most readily attributable to tectonism. The spatial pattern of these high and low areas is complex, but it appears to correlate well with known tectonic features of the region. This correlation suggests that the tectonic setting of the Charleston region is controlled by scissors-like compression on a crustal block located between the north-trending Adams Run fault and the northwest-trending Charleston fault. Tectonism is localized in the Charleston region because it lies within a discrete hinge zone that accommodates structural movement between the Cape Fear arch and the Southeast Georgia embayment.

  15. Structural and Sequence Stratigraphic Analysis of the Onshore Nile Delta, Egypt.

    NASA Astrophysics Data System (ADS)

    Barakat, Moataz; Dominik, Wilhelm

    2010-05-01

    The Nile Delta is considered the earliest known delta in the world. It was already described by Herodotus in the 5th Century AC. Nowadays; the Nile Delta is an emerging giant gas province in the Middle East with proven gas reserves which have more than doubled in size in the last years. The Nile Delta basin contains a thick sedimentary sequence inferred to extend from Jurassic to recent time. Structural styles and depositional environments varied during this period. Facies architecture and sequence stratigraphy of the Nile Delta are resolved using seismic stratigraphy based on (2D seismic lines) including synthetic seismograms and tying in well log data. Synthetic seismograms were constructed using sonic and density logs. The combination of structural interpretation and sequence stratigraphy of the development of the basin was resolved. Seven chrono-stratigraphic boundaries have been identified and correlated on seismic and well log data. Several unconformity boundaries also identified on seismic lines range from angular to disconformity type. Furthermore, time structure maps, velocity maps, depth structure maps as well as Isopach maps were constructed using seismic lines and log data. Several structural features were identified: normal faults, growth faults, listric faults, secondary antithetic faults and large rotated fault blocks of manly Miocene age. In some cases minor rollover structures could be identified. Sedimentary features such as paleo-channels were distinctively recognized. Typical Sequence stratigraphic features such as incised valley, clinoforms, topsets, offlaps and onlaps are identified and traced on the seismic lines allowing a good insight into sequence stratigraphic history of the Nile Delta most especially in the Miocene to Pliocene clastic sedimentary succession.

  16. North African petroleum geology: regional structure and stratigraphic overview of a hydrocarbon-rich cratonic area

    SciTech Connect

    O'Connor, T.E.; Kanes, W.H.

    1985-02-01

    North Africa, including Sinai, contains some of the most important hydrocarbon-producing basins in the world. The North African Symposium is devoted to examining the exploration potential of the North African margin in light of the most recent and promising exploration discoveries. The geologic variety of the region is extraordinary and can challenge any exploration philosophy. Of primary interest are the Sirte basin of Libya, which has produced several billion barrels of oil, and the Gulf of Suez, a narrow, evaporite-capped trough with five fields that will produce more than 5 billion bbl. Both are extensional basins with minimal lateral movement and with good source rocks in direct proximity to reservoirs. Structural models of these basins give firm leads for future exploration. More difficult to evaluate are the Tethyan realm basins of the northern Sinai, and the Western Desert of Egypt, the Cyrenaican Platform of Libya, and the Tunisia-Sicily shelf area, where there are only limited subsurface data. These basins are extensional in origin also, but have been influenced by lateral tectonics. Favorable reservoirs exist, but source rocks have been a problem locally. Structural models with strong stratigraphic response offer several favorable play concepts. The Paleozoic Ghadames basin in Libya, Tunisia, and Algeria has the least complex structural history, and production appears to be limited to small structures. A series of stratigraphic models indicates additional areas with exploration potential. The Paleozoic megabasin of Morocco, with its downfaulted Triassic grabens, remains an untested but attractive area.

  17. Tectonic reconstructions of the southwestern Great Basin: Stratigraphic tests of structural models

    SciTech Connect

    Prave, A.R. . Dept. of Earth and Atmospheric Sciences); Snow, J.K. . Division of Geology and Planetary Sciences)

    1993-04-01

    Accurate paleogeographic reconstruction of the tectonically dismembered southwestern Great Basin is in large part dependent on the validity of the Wernicke et al. (1988) and Snow and Wernicke (1989) correlations of Mesozoic (pre-Tertiary) contractile deformational features. In order to independently assess these structurally based models and their predictions, carefully chosen stratigraphic data were used as tests. In the northern Death Valley region, sediment dispersal trends in two regionally developed facies of the Lower Cambrian Wood Canyon Formation and Zabriskie Quartzite suggest that otherwise uniformly northwest-directed paleocurrent indicators have undergone vertical axis rotations comparable in direction and magnitude to those predicted for anti-clockwise rotation of the Grapevine Mountains structural block. In the central Death Valley region, stratigraphic differences in upper plate rocks in the proposed Tucki Mountain-northern Nopah Range pierce point prevent the adjacent juxtaposition of those rocks but are permissive of such a correlation. Finally, in the southern Death Valley region, the Levy and Christie-Blick (1989) pre-Mesozoic reconstruction results in overlap of range blocks and juxtaposition of disparate facies in the Proterozoic Pahrump Group rocks. This implies that the Cenozoic deformational vector displacement paths, determined for elsewhere in the southern Great Basin, are not applicable to southern Death Valley and must be reassessed.

  18. Cambrian-Ordovician Knox production in Ohio: Three case studies of structural-stratigraphic traps

    USGS Publications Warehouse

    Riley, R.A.; Wicks, J.; Thomas, Joan

    2002-01-01

    The Knox Dolomite (Cambrian-Ordovician) in Ohio consists of a mixed carbonate-siliciclastic sequence deposited in a tidal-flat to shallow-marine environment along a broad continental shelf. Knox hydrocarbon production occurs in porous sandstone and dolomite reservoirs in the Copper Ridge dolomite, Rose Run sandstone, and Beekmantown dolomite. In Ohio, historical Knox exploration and development have been focused on paleogeomorphic traps within the prolific Morrow Consolidated field, and more recently, within and adjacent to the Rose Run subcrop. Although these paleogeomorphic traps have yielded significant Knox production, structural and stratigraphic traps are being largely ignored. Three Knox-producing pools demonstrate structural and stratigraphic traps: the Birmingham-Erie pool in southern Erie and southwestern Lorain counties, the South Canaan pool in northern Wayne County, and the East Randolph pool in south-central Portage County. Enhanced porosity and permeability from fractures, as evident in the East Randolph pool, are also an underexplored mechanism for Knox hydrocarbon accumulation. An estimated 800 bcf of gas from undiscovered Knox resources makes the Knox one of the most attractive plays in the Appalachian basin.

  19. Cenozoic structural evolution and tectono-stratigraphic framework of the northern Gulf Coast continental margin

    SciTech Connect

    Diegel, F.A.; Karlo, J.F.; Shoup, R.C.; Schuster, D.C.

    1996-12-31

    The Cenozoic structural evolution of the northern Gulf of Mexico Basin is controlled by progradation over deforming, largely allochthonous salt structures derived from an underlying autochthonous Jurassic salt. The wide variety of structural styles is due to a combination of (1) original distribution of Jurassic and Mesozoic salt structures, (2) different slope depositional environments during the Cenozoic, and (3) varying degrees of salt withdrawal from allochthonous salt sheets. Tectono-stratigraphic provinces describe regions of contrasting structural styles and ages. Provinces include (1) a contractional foldbelt province, (2) a tabular salt-minibasin-province, (3) a Pliocene-Pleistocene detachment province, (4) a salt dome-minibasin province, (5) an Oligocene-Miocene detachment province, (6) a lower Oligocene Vicksburg detachment province, (7) an upper Eocene detachment province, and (8) the Wilcox growth fault province of Paleocene-Eocene age. Within several tectono-stratigraphic provinces, shale-based detachment systems, dominated by lateral extension, and allochthonous salt-based detachment systems, dominated by subsidence, can be distinguished by geometry, palinspastic reconstructions, and subsidence analysis. Many shale-based detachments are linked downdip to deeper salt-based detachments. Large extensions above detachments are typically balanced by salt withdrawal. Salt-withdrawal minibasins with flanking salt bodies occur as both isolated structural systems and components of salt-based detachment systems. During progradation, progressive salt withdrawal from tabular salt bodies on the slope formed salt-bounded minibasins which, on the shelf, evolved into minibasins bounded by arcuate growth faults and remnant salt bodies. Associated secondary salt bodies above allochthonous salt evolved from pillows, ridges, and massifs to leaning domes and steep-sided stocks.

  20. Structural and stratigraphic evolution of the East Georges Bank Basin, offshore Nova Scotia, Canada

    SciTech Connect

    Carswell, A.B. ); Koning, T. ); Hibbs, D.C. )

    1990-05-01

    The East Georges Bank Basin is located offshore Nova Scotia on the southeastern Canadian continental shelf. The basin covers 2.5 million ac and is one of the last undrilled basins in North America. The geological interpretation is almost entirely based on 16,000 km of seismic data over the basin. Pertinent well control is limited to 10 wells on the US portion of the Georges Bank (West Georges Bank Basin) and two wells on the Scotian shelf. Seismic-stratigraphic analysis of this data has led to a structural and stratigraphic model for the basin. The basin formed during the Triassic when the landmass of Pange began separating along rift zones. A prominent Paleozoic basement high, the Yarmouth Arch separated the East Georges Bank Basin from the West Georges Bank Basin and had a dominant influence on sedimentation until the Middle Jurassic. Early synrift sequences consist of lacustrine clastics and shales. Marine incursions began in the late Triassic resulting in massive salt deposits that reflect the restricted extent of the basin and the arid Triassic and Early Jurassic climate. Further continental separation during the Early Jurassic resulted in deposition of carbonates and evaporites followed by Middle Jurassic continental shelf carbonates and deltaic sands. During the Middle Jurassic, major growth faulting and halokinesis was initiated by progradation of the deltaic sands. Post Middle Jurassic continental spreading in combination with changing climatic conditions resulted in a steady decline of carbonate sedimentation and dominance of clastic deposition throughout the remaining history of the basin.

  1. Structural and stratigraphic evolution of late Cretaceous convergent margins of southern Alaska and California

    SciTech Connect

    Nilsen, T.H.

    1988-02-01

    The most prominent and well-preserved remnants of the convergent margins are present in southern Alaska and California. The southern Alaska convergent margin appears to have developed in response to northward-directed subduction of the Kula plate and the California margin in response to eastward-directed subduction of the Farallon plate. The chief elements of the southern Alaska convergent margin, on the basis of paleomagnetic data, appear to have subsequently migrated northward and rotated in the post-Cretaceous. The chief elements of the California margin have been disrupted by Neogene strike-slip displacements on the San Andreas fault system and accretion of younger terranes to the west. In both southern Alaska and California, the forearc-basin deposits are well preserved and produce major amounts of gas. The principal reservoirs in Alaska are Tertiary nonmarine deposits and in California are Late Cretaceous and Tertiary deep marine and deltaic deposits. The accretionary wedge in southern Alaska forms a remarkably well-preserved assemblage of trench and trench-slope deposits that extend for about 2000 km along the Gulf of Alaska, flanked oceanward by younger accreted terranes. The accretionary wedge in California consists of a great variety of older and younger terranes, including some fragments of ocean crust that originated in southern latitudes. Comparative structural and stratigraphic analyses of the two Late Cretaceous margins reveals the complexity of tectonic, depositional, and stratigraphic patterns associated with subduction of very large oceanic plates at the margins of very large continental plates.

  2. Stratigraphic and structural evolution of the Selenga Delta Accommodation Zone, Lake Baikal Rift, Siberia

    USGS Publications Warehouse

    Scholz, C.A.; Hutchinson, D.R.

    2000-01-01

    Seismic reflection profiles from the Lake Baikal Rift reveal extensive details about the sediment thickness, structural geometry and history of extensional deformation and syn-rift sedimentation in this classic continental rift. The Selenga River is the largest single source of terrigenous input into Lake Baikal, and its large delta sits astride the major accommodation zone between the Central and South basins of the lake. Incorporating one of the world's largest lacustrine deltas, this depositional system is a classic example of the influence of rift basin structural segmentation on a major continental drainage. More than 3700 km of deep basin-scale multi-channel seismic reflection (MCS) data were acquired during the 1989 Russian and the 1992 Russian–American field programs. The seismic data image most of the sedimentary section, including pre-rift basement in several localities. The MCS data reveal that the broad bathymetric saddle between these two major half-graben basins is underlain by a complex of severely deformed basement blocks, and is not simply a consequence of long-term deltaic deposition. Maximum sediment thickness is estimated to be more than 9 km in some areas around the Selenga Delta. Detailed stratigraphic analyses of the Selenga area MCS data suggest that modes of deposition have shifted markedly during the history of the delta. The present mode of gravity- and mass-flow sedimentation that dominates the northern and southern parts of the modern delta, as well as the pronounced bathymetric relief in the area, are relatively recent developments in the history of the Lake Baikal Rift. Several episodes of major delta progradation, each extending far across the modern rift, can be documented in the MCS data. The stratigraphic framework defined by these prograding deltaic sequences can be used to constrain the structural as well as depositional evolution of this part of the Baikal Rift. An age model has been established for this stratigraphy, by

  3. Unconformity structures controlling stratigraphic reservoirs in the north-west margin of Junggar basin, North-west China

    NASA Astrophysics Data System (ADS)

    Wu, Kongyou; Paton, Douglas; Zha, Ming

    2013-03-01

    Tectonic movements formed several unconformities in the north-west margin of the Junggar basin. Based on data of outcrop, core, and samples, the unconformity is a structural body whose formation associates with weathering, leaching, and onlap. At the same time, the structural body may be divided into three layers, including upper layer, mid layer, and lower layer. The upper layer with good primary porosity serves as the hydrocarbon migration system, and also accumulates the hydrocarbon. The mid layer with compactness and ductility can play a role as cap rock, the strength of which increases with depth. The lower layer with good secondary porosity due to weathering and leaching can form the stratigraphic truncation traps. A typical stratigraphic reservoir lying in the unconformity between the Jurassic and Triassic in the north-west margin of the Junggar basin was meticulously analyzed in order to reveal the key controlling factors. The results showed that the hydrocarbon distribution in the stratigraphic onlap reservoirs was controlled by the onlap line, the hydrocarbon distribution in the stratigraphic truncation reservoirs was confined by the truncation line, and the mid layer acted as the key sealing rock. So a conclusion was drawn that "two lines (onlap line and truncation line) and a body (unconformity structural body)" control the formation and distribution of stratigraphic reservoirs.

  4. Automated Tape Laying Machine for Composite Structures.

    DTIC Science & Technology

    The invention comprises an automated tape laying machine, for laying tape on a composite structure. The tape laying machine has a tape laying head...neatly cut. The automated tape laying device utilizes narrow width tape to increase machine flexibility and reduce wastage.

  5. Structural and stratigraphic mapping from satellite imagery, Kalpin uplift, northwestern Tarim basin, northwest China

    SciTech Connect

    McKnight, C.L.; Carroll, A.R.; Chu, J.; Hendrix, M.S.; Graham, S.A.; Lyon, R.J.P. )

    1990-05-01

    The Kalpin uplift, located on the northwestern margin of the Tarim craton, northwest China, exposes a complete Paleozoic cratonal stratigraphic sequence. The lack of vegetative cover and the visible color contrasts between stratigraphic units afford an optimal situation for detailed geologic mapping from Landsat Multispectral Scanner imagery at a scale of 1:250,000. Field work in the eastern Kalpin uplift constrains the geologic interpretation of the satellite imagery. Exposed basement rock in the Kalpin uplift consists of deformed and metamorphosed upper Proterozoic strata cut by unmetamorphosed mafic dikes. The overlying sedimentary section was deposited primarily in shallow marine to nonmarine environments and includes Sinian (latest Proterozoic to early Cambrian) siliciclastics and carbonates; Cambrian and Ordovician carbonates; Silurian green shales; Devonian red beds; Carboniferous siliciclastics and carbonates; and Permian carbonates, siliciclastics, and subaerial basalt flows. Paleozoic strata are exposed in a series of low, parallel, curvilinear ranges located at the leading edges of low-angle, southeast-vergent thrust sheets. The regular thrust repetition of the entire Paleozoic section suggests the presence of a detachment horizon within the Cambrian section. These southeast-vergent thrust sheets override an older structural trend on the craton, the Bachu uplift, at right angles, folding as they do so. Strike-slip faults cutting the thrust sheets along the same trend as the Bachu uplift suggest the location of buried lateral ramps associated with the Bachu uplift. The young deformation in the Kalpin uplift is a response to compressive stresses produced by the northward movement of the Indian plate. Major faults in the Tian Shan mountain range to the north have been reactivated, resulting in southward-directed thrusting over the Tarim craton.

  6. Crestal unconformities as indicators of clastic stratigraphic traps: genetic relation of Berlin field and Elk City structure, deep Anadarko basin

    SciTech Connect

    Lyday, J.R.

    1988-02-01

    The Berlin fan-delta gas reservoir in the deep Anardarko basin was deposited during the late Atokan (Pennsylvanian) as a response to the initial uplift and erosion of the Elk City structure. During the late Atokan pulse of the episodic Pennsylvanian orogeny in the south-central US, abrupt epeirogenic uplift and brittle deformation created an interregional unconformity on positive areas around foreland and cratonic basins. The Elk City structure within the deep Anadarko basin originated as a distinct, subaerially exposed upthrust-block during the late Atokan tectonic event. A crestal unconformity developed on the emergent upthrust block concurrent with its uplift. Terrigenous, detrital Atoka dolomite, originally sourced from the Arbuckle dolomite (Cambrian-Ordovician) of the Amarillo-Wichita uplift, was eroded from the upthrust block and recycled northward as the Berlin fan-delta. Today, the Berlin recrystallized, recycled detrital dolomite fan-delta is a large 41 mi/sup 2/ overpressured gas reservoir with 242-362 bcf reserves at 15,000 ft. The Berlin field is genetically related to the late Atokan crestal unconformity of the Elk City structure, and is an example of the association of crestal unconformities and clastic stratigraphic traps. Such stratigraphic traps originated in marine environments proximal to active structures that have become subaerially exposed. With adequate seals and favorable structural position, detrital deposits recycled from local uplifts can form significant stratigraphic traps. Such stratigraphic traps can occur in compressional, extensional, and diapiric regions.

  7. Stratigraphic and metamorphic inversions in the central Menderes Massif: a new structural model

    NASA Astrophysics Data System (ADS)

    Okay, Aral I.

    2001-04-01

    The Menderes Massif is a large area of dominantly Tertiary metamorphic rocks in western Turkey. It is bordered in the west by the Cycladic Metamorphic Complex with Eocene high-pressure/low-temperature (HP/LT) metamorphism. In the Central Menderes the Aydın mountains are made up of a thrust stack of Eocene age. At the base of the thrust stack, greenschist-facies Paleozoic metasediments of the Menderes Massif form an inverted stratigraphic sequence. The Barrovian-type metamorphism is also inverted with garnet-bearing metapelites lying over the lower-grade biotite-bearing metapelites. The P-T conditions in the garnet zone are estimated as 530°C and 8 kbar. This schist sequence of the central Menderes Massif is interpreted as the inverted lower limb of a major southward closing recumbent fold, with the southern Menderes Massif representing a section from the near hinge of this fold. The Paleozoic metamorphic rocks of the central Menderes Massif are tectonically overlain by gneiss klippen possibly originating from the sheared and southward translated core of the Menderes fold. Lying also tectonically over the Paleozoic metamorphic rocks is a major thrust sheet belonging to the Cycladic metamorphic complex. It consists of garnet micaschist, Mesozoic marble, serpentinite and amphibolitised eclogite. Although it has a highly sheared internal structure, it probably represents an initially coherent sequence that has undergone HP/LT metamorphism during the Eocene. The Aydın mountains are dominated by contractional structures with subordinate extensional structures.

  8. Automated Characterization Of Vibrations Of A Structure

    NASA Technical Reports Server (NTRS)

    Bayard, David S.; Yam, Yeung; Mettler, Edward; Hadaegh, Fred Y.; Milman, Mark H.; Scheid, Robert E.

    1992-01-01

    Automated method of characterizing dynamical properties of large flexible structure yields estimates of modal parameters used by robust control system to stabilize structure and minimize undesired motions. Based on extraction of desired modal and control-design data from responses of structure to known vibrational excitations. Applicable to terrestrial structures where vibrations are important - aircraft, buildings, bridges, cranes, and drill strings.

  9. Triassic structural and stratigraphic evolution of the Central German North Sea sector

    NASA Astrophysics Data System (ADS)

    Wolf, Marco; Jähne-Klingberg, Fabian

    2017-04-01

    The subsurface of the Central German North Sea sector is characterized by a complex sequence of tectonic events that span from the Permo-Carboniferous initiation of the Southern Permian Basin to the present day. The Triassic period is one of the most prominent stratigraphic intervals in this area due to alternating phases of relatively tectonic quiescence and intense tectonic activity with the development of grabens, salt-tectonics movements, various regional and local erosional events and strong local and regional changes in subsidence over time. The heterogeneous geological history led to complex structural and lithological patterns. The presented results are part of a comprehensive investigation of the Central German North Sea sector. It was carried out within the scope of the project TUNB (www.bgr.bund.de). The main goal was to enhance the understanding of the Triassic geological development in the area of interest due to detailed seismic interpretation of several hundred 2D seismic lines and as well 3D seismic data sets. A seismostratigraphic concept was used to interpret most formations of the Triassic resulting in a detailed subdivision of the Triassic unit. Depth and thickness maps for every stratigraphic unit and geological cross sections provided new insights regarding an overall basin evolution as well as the timing and mechanisms of rifting and salt-tectonics. New results concerning the evolution of the Keuper in the German North Sea and especially the Triassic evolution of the Horn Graben, as one of the major Triassic rift-structures in the North Sea, will be highlighted. We will show aspects of strong tectonic subsidence in the Horn Graben in the Lower Triassic. In parts of the study area, halotectonic movements started in the Upper Triassic, earlier than previously proposed. Besides mapping of regional seismic reflectors, distinct sedimentary features like fluvial channel systems of the Stuttgart formation (Middle Keuper) or subrosion-like structures

  10. Implications of Stratigraphic and Structural Data from the Bitter Spring Region, Southern Nevada

    NASA Astrophysics Data System (ADS)

    Donatelle, A.; Goeden, J.; Hannon, M.; Hickson, T.; Holter, S.; Johnson, T.; Lamb, M.; Lindberg, J.

    2004-05-01

    Deposition of the Tertiary Horse Spring Formation (HSF) in southern Nevada has been used to infer varying styles of extensional and strike-slip basin formation. Beard (1996) proposes an initial large contiguous basin of Rainbow Gardens age (ca. 26-18 Ma) that is subsequently broken up into sub-basins during Thumb time (16-14 Ma). A key locality to test this hypothesis is near the southern end of East and West Longwell Ridges, on the Bitter Spring USGS 1:24000 quadrangle (BSQ). However, the stratigraphic framework in this area is poorly defined. The BSQ is located west of the Overton arm of Lake Mead near the junction of the Las Vegas Valley Shear Zone and the Lake Mead Fault System. By mapping a portion of the quadrangle at 1:5000 scale, measuring detailed sections, and collecting ash samples from key localities, we investigated the structural and sedimentary framework of the area and have begun to clarify the stratigraphic relationships between members of the HSF. Faults fall into three categories: one set strikes north and dips moderately to the west; another strikes east-northeast and dips shallowly to the northwest; and the last strikes north and dips to the east. Many of these faults show an oblique sense of movement and may be related to movement on the White Basin (WBF) and Rodgers Spring Faults (Bohannon, 1983). A distinctive resistant limestone caps gypsiferous and clastic units on both sides of the north-south trending WBF. To the west of the WBF, this limestone is mapped as the Bitter Ridge Limestone Member of the HSF, whereas to the east it is mapped as the Thumb Member by Beard (unpub) and as the Rainbow Gardens Member by Bohannon (1983). We suspect that these limestones may be correlative; geochemical and petrographic fingerprinting of numerous ashes from our sections should allow correlation of these units across the WBF. In addition, sections from the east side of the WBF spaced over 1.5 km show conglomerate at the base, overlain by a sequence of

  11. The geostatistical approach for structural and stratigraphic framework analysis of offshore NW Bonaparte Basin, Australia

    SciTech Connect

    Wahid, Ali Salim, Ahmed Mohamed Ahmed Yusoff, Wan Ismail Wan; Gaafar, Gamal Ragab

    2016-02-01

    Geostatistics or statistical approach is based on the studies of temporal and spatial trend, which depend upon spatial relationships to model known information of variable(s) at unsampled locations. The statistical technique known as kriging was used for petrophycial and facies analysis, which help to assume spatial relationship to model the geological continuity between the known data and the unknown to produce a single best guess of the unknown. Kriging is also known as optimal interpolation technique, which facilitate to generate best linear unbiased estimation of each horizon. The idea is to construct a numerical model of the lithofacies and rock properties that honor available data and further integrate with interpreting seismic sections, techtonostratigraphy chart with sea level curve (short term) and regional tectonics of the study area to find the structural and stratigraphic growth history of the NW Bonaparte Basin. By using kriging technique the models were built which help to estimate different parameters like horizons, facies, and porosities in the study area. The variograms were used to determine for identification of spatial relationship between data which help to find the depositional history of the North West (NW) Bonaparte Basin.

  12. ASTROS: A multidisciplinary automated structural design tool

    NASA Technical Reports Server (NTRS)

    Neill, D. J.

    1989-01-01

    ASTROS (Automated Structural Optimization System) is a finite-element-based multidisciplinary structural optimization procedure developed under Air Force sponsorship to perform automated preliminary structural design. The design task is the determination of the structural sizes that provide an optimal structure while satisfying numerous constraints from many disciplines. In addition to its automated design features, ASTROS provides a general transient and frequency response capability, as well as a special feature to perform a transient analysis of a vehicle subjected to a nuclear blast. The motivation for the development of a single multidisciplinary design tool is that such a tool can provide improved structural designs in less time than is currently needed. The role of such a tool is even more apparent as modern materials come into widespread use. Balancing conflicting requirements for the structure's strength and stiffness while exploiting the benefits of material anisotropy is perhaps an impossible task without assistance from an automated design tool. Finally, the use of a single tool can bring the design task into better focus among design team members, thereby improving their insight into the overall task.

  13. Stratigraphic and Structural Characteristics of the Santa Marta Impact Structure, Brazil

    NASA Astrophysics Data System (ADS)

    Oliveira, G. J. G.; Chamani, M.; Góes, A. M.; Crósta, A. P.; Vasconcelos, M. A. R.; Reimold, W. U.

    2016-08-01

    Santa Marta structure is a moderate-size complex impact structure formed in sedimentary targets, Brazil. We provide an overview of the stratigraphy and deformation patterns of the strata identified within the structure.

  14. The structural and stratigraphic evolution of the La Rioja basin, Argentina

    NASA Astrophysics Data System (ADS)

    Fisher, Nathan D.; Jordan, Teresa E.; Brown, Larry

    2002-04-01

    The La Rioja sedimentary basin underlies the Llanos de La Rioja valley in the Sierras Pampeanas region of western Argentina. The Sierras Pampeanas is a region of young reverse-fault-bounded ranges of crystalline basement separated by broad valleys. Repsol-YPF allowed use of 280 km of 2D seismic lines registered in the western La Rioja basin, which were processed and interpreted for structural and stratigraphic relationships. Lacking wells within the seismic grid, we relied on refraction data, nearby geological studies, and seismic stratigraphy to constrain the interpretation. The findings indicate a substantial thickness (up to 800 m) of Paleozoic strata thinning to the east and directly covering the crystalline basement. The predominate unit is Cenozoic fill, which dominates the upper 1-3 s of the seismic data and ranges in thickness from 3 km below the city of La Rioja, near the western basin margin, to approximately 1.5 km at the east end of the seismic grid, 60 km east of La Rioja. Between the Paleozoic and Cenozoic strata are two units, one regionally distributed and the other very localized. The regionally extensive unit is a thin horizon with high reflectivity that overlies the more localized unit. This local unit is interpreted as a narrow rift basin in the northern La Rioja basin that is likely of Cretaceous age. Deformation within the La Rioja basin is controlled predominantly by north-trending reverse faults with offsets ranging from 200 to 2000 m. Faults in the north half of the basin are not continuous with those in the south half, which suggests the existence of an east-trending transfer zone, aligned with the east-trending valley separating Sierra de Velasco into northern and southern blocks and aligned with the north end of Sierra Brava. The major north-trending faults were active during accumulation of the upper half of the Cenozoic strata.

  15. Automated structure solution with the PHENIX suite

    SciTech Connect

    Terwilliger, Thomas C; Zwart, Peter H; Afonine, Pavel V; Grosse - Kunstleve, Ralf W

    2008-01-01

    Significant time and effort are often required to solve and complete a macromolecular crystal structure. The development of automated computational methods for the analysis, solution, and completion of crystallographic structures has the potential to produce minimally biased models in a short time without the need for manual intervention. The PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution, and good quality data. This achievement has been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template- and pattern-based automated model-building (RESOLVE, TEXTAL), automated macromolecular refinement (phenix. refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that have been built and made available to the community. The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI.

  16. Automated Structure Solution with the PHENIX Suite

    SciTech Connect

    Zwart, Peter H.; Zwart, Peter H.; Afonine, Pavel; Grosse-Kunstleve, Ralf W.; Hung, Li-Wei; Ioerger, Tom R.; McCoy, A.J.; McKee, Eric; Moriarty, Nigel; Read, Randy J.; Sacchettini, James C.; Sauter, Nicholas K.; Storoni, L.C.; Terwilliger, Tomas C.; Adams, Paul D.

    2008-06-09

    Significant time and effort are often required to solve and complete a macromolecular crystal structure. The development of automated computational methods for the analysis, solution and completion of crystallographic structures has the potential to produce minimally biased models in a short time without the need for manual intervention. The PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution and good quality data. This achievement has been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template and pattern-based automated model-building (RESOLVE, TEXTAL), automated macromolecular refinement (phenix.refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that have been built and made available to the community. The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI.

  17. Automated modeling of RNA 3D structure.

    PubMed

    Rother, Kristian; Rother, Magdalena; Skiba, Pawel; Bujnicki, Janusz M

    2014-01-01

    This chapter gives an overview over the current methods for automated modeling of RNA structures, with emphasis on template-based methods. The currently used approaches to RNA modeling are presented with a side view on the protein world, where many similar ideas have been used. Two main programs for automated template-based modeling are presented: ModeRNA assembling structures from fragments and MacroMoleculeBuilder performing a simulation to satisfy spatial restraints. Both approaches have in common that they require an alignment of the target sequence to a known RNA structure that is used as a modeling template. As a way to find promising template structures and to align the target and template sequences, we propose a pipeline combining the ParAlign and Infernal programs on RNA family data from Rfam. We also briefly summarize template-free methods for RNA 3D structure prediction. Typically, RNA structures generated by automated modeling methods require local or global optimization. Thus, we also discuss methods that can be used for local or global refinement of RNA structures.

  18. The geology of Svalbard: structural, stratigraphic and geomorphic response to the formation of two passive margins

    NASA Astrophysics Data System (ADS)

    Osmundsen, P. T.; Braathen, A.; Maher, H.

    2012-04-01

    Svalbard is located at the junction of the North Atlantic and Arctic margins, preserves an onshore structural and stratigraphic record that spans from the Devonian to the Cenozoic and records several phases of extension characterized by different tectonic transport vectors. Contractional events such as the Devonian, so-called 'Svalbardian' fold phase and the formation of an Early Cenozoic fold and thrust belt have locally modified the evidence for extension and basin formation. However, several generations of extensional structures and associated, tectonically controlled basins are displayed in world-class exposures at different locations in the archipelago. At present, we focus on the following onshore features related to extension and margin formation: 1. Late-post orogenic extension: An extensional detachment and metamorphic core complex was recently identified by us in northwestern Spitsbergen, involving re-interpretation of tectonic contacts interpreted previously as thrusts. The undulating extensional detachment appears to have controlled 'Old Red' basin formation from the Early into the Late Devonian. The core complex evolved into a N-S trending anticline with flanks that eventually became the locus of strike-slip and normal faulting. Some of these faults were demonstrably reactivated, and we propose that the Devonian structural template became important in controlling the location of later rift structures that developed from the Carboniferous onwards. 2. Carboniferous rifting: Normal faulting controlled sedimentation in Carboniferous basins including an up to 2 km deep, coastal/marine half-graben with mixed siliclastic, carbonate and evaporite fill exposed in Central Spitsbergen. The Billefjorden Fault zone (BFZ) reactivates an older, N-S trending Devonian reverse fault, and coarse siliclastic debris was transported into the basin along relay ramps that developed between the normally reactivated strands of the BFZ. Monoclinal folds, interpreted previously

  19. Sequence stratigraphic-structural analysis of the East Midlands Carboniferous oil field, UK: Implications for fluvial reservoir models

    SciTech Connect

    Aitken, J.F.; Quirk, D.G.

    1996-12-31

    The integration of seismic, well log and core data from, the Scampton North and Welton oil fields, Lincolnshire, UK, has enabled the development of a sequence stratigraphic-structural model for late Namurian and early Westphalian fluvial reservoirs. The tectonic and sequence stratigraphic setting is remarkably similar to that in the Southern North Sea which extends more than 250 km to the east. Closer onshore well spacing, supplemented with coal exploration borehole data, provides an excellent analogue for new Carboniferous Southern North Sea developments and prospects. The reservoirs comprise medium-grained, low sinuosity fluvial aggradational packages within a coal-bearing, fluvio-deltaic depositional environment. Although major active faults occur within the Namurian, tectonic activity had ceased by the start of the Westphalian which has a tramline-like appearance on seismic. The reservoirs are poorly interconnected as a consequence of small-scale faults and extensive shale baffles, which have resulted in considerable production problems, accentuated by an initial poor reservoir correlation. Palynology has proven to be highly imprecise, consequently, the use of seismic picks as chronostratigraphic markers combined with the coal stratigraphy from British Coal boreholes and the application of sequence stratigraphic, concepts has enabled a more precise reservoir correlation to be made.

  20. Sequence stratigraphic-structural analysis of the East Midlands Carboniferous oil field, UK: Implications for fluvial reservoir models

    SciTech Connect

    Aitken, J.F.; Quirk, D.G. )

    1996-01-01

    The integration of seismic, well log and core data from, the Scampton North and Welton oil fields, Lincolnshire, UK, has enabled the development of a sequence stratigraphic-structural model for late Namurian and early Westphalian fluvial reservoirs. The tectonic and sequence stratigraphic setting is remarkably similar to that in the Southern North Sea which extends more than 250 km to the east. Closer onshore well spacing, supplemented with coal exploration borehole data, provides an excellent analogue for new Carboniferous Southern North Sea developments and prospects. The reservoirs comprise medium-grained, low sinuosity fluvial aggradational packages within a coal-bearing, fluvio-deltaic depositional environment. Although major active faults occur within the Namurian, tectonic activity had ceased by the start of the Westphalian which has a tramline-like appearance on seismic. The reservoirs are poorly interconnected as a consequence of small-scale faults and extensive shale baffles, which have resulted in considerable production problems, accentuated by an initial poor reservoir correlation. Palynology has proven to be highly imprecise, consequently, the use of seismic picks as chronostratigraphic markers combined with the coal stratigraphy from British Coal boreholes and the application of sequence stratigraphic, concepts has enabled a more precise reservoir correlation to be made.

  1. Stratigraphic traps 2

    SciTech Connect

    Not Available

    1991-01-01

    This volume contains studies of fields with traps that are mainly stratigraphic in nature. Structure plays a role in the traps of several fields, but overall, it is clear that the main trapping features with the group of fields in this volume are stratigraphic. The first six fields in this volume, Alabama Ferry, Rospo Mare, Walker Creek, Bindley, Lexington, and Newburg/South Westhope, have carbonate reservoirs. The latter two of these, Lexington and Newburg/South Westhope, also have sandstone reservoirs. The remaining fields, East Texas, East Clinton, Stockholm Southwest, Sorrento, Port Acres, and Lagoa Parda, have only sandstone reservoirs.

  2. Stratigraphic and structural framework of the western edge of Canada Basin, Arctic Ocean

    NASA Astrophysics Data System (ADS)

    Hutchinson, D. R.; Mosher, D. C.; Shimeld, J.; Chian, D.; Lebedeva-Ivanova, N. N.; Evangelatos, J.; Jackson, R.

    2012-12-01

    Seismic reflection and refraction data collected in joint two-icebreaker expeditions by the U.S. and Canada between 2008 and 2011 reveal how the western edge of the Canada Basin has evolved through rifting and post rifting history. Our observations suggest that the western margin of Canada Basin (along Northwind Ridge [NR} and the northern Chukchi Borderland [CB]) is a mix of highly stretched continental and transitional crust with unique attributes that reflect local influences of NR, CB, and Alpha Ridge with the extension that formed Canada Basin. The reflection character of basement and refraction velocities indicate that the regions adjacent to NR and north-northwest of CB are probably underlain by a high-velocity (7.2-7.5 km/s) layer that may be serpentinized mantle or a transitional, intruded lower continental crust. Between these two regions, north of CB, is an area underlain by highly stretched continental crust (lower crust with velocities less than 6.7 km/s). Dredge samples collected from near NR recovered basaltic rocks. The area north and northeast of CB also contains discontinuous, segmented, bright reflections at the base of the postrift Canada Basin sediments consistent with the kind of reflections seen in magmatically intruded regions. These bright reflections may indicate a postrift magmatic pulse associated with Alpha Ridge. On top of Northwind Ridge, the stratigraphic units above basement are truncated and eroded and tilt towards Canada basin. The relationship between these units and the deepest units in Canada Basin is speculative, but they are interpreted to represent prerift or synrift deposits that were faulted during the formation of NR. Similar truncated, eroded, and tilted deposits occur along the northern part of the CB and southern Alpha Ridge and can be traced both continuously and discontinuously into Canada Basin where they unconformably underlie the younger deposits that lap onto them. The postrift depositional patterns inferred from

  3. Stratigraphic and structural characterization of the OU-1 area at the former George Air Force Base, Adelanto, Southern California

    USGS Publications Warehouse

    Catchings, R.D.; Gandhok, G.; Goldman, M.R.

    2001-01-01

    The former George Air Force Base (GAFB), now known as the Southern California Logistics Airport (SCLA), is located in the town of Adelanto, approximately 100 km northeast of Los Angeles, California (Fig. 1). In this report, we present acquisition parameters, data, and interpretations of seismic images that were acquired in the OU-1 area of GAFB during July 1999 (Fig. 2). GAFB is scheduled for conversion to civilian use, however, during its years as an Air Force base, trichlorethylene (TCE) was apparently introduced into the subsurface as a result of spills during normal aircraft maintenance operations. To comply with congressional directives, TCE contaminant removal has been ongoing since the early-tomid 1990s. However, only a small percentage of the TCE believed to have been introduced into the subsurface has been recovered, due largely to difficulty in locating the TCE within the subsurface. Because TCE migrates within the subsurface by ground water movement, attempts to locate the TCE contaminants in the subsurface have employed an array of ground-water monitoring and extraction wells. These wells primarily sample within a shallow-depth (~40 m) aquifer system. Cores obtained from the monitoring and extraction wells indicate that the aquifer, which is composed of sand and gravel channels, is bounded by aquitards composed largely of clay and other fine-grained sediments. Based on well logs, the aquifer is about 3 to 5 m thick along the seismic profiles. A more thorough understanding of the lateral variations in the depth and thickness of the aquifer system may be a key to finding and removing the remaining TCE. However, due to its complex depositional and tectonic history, the structural and stratigraphic sequences are not easily characterized. An indication of the complex nature of the structure and stratigraphy is the appreciable variation in stratigraphic sequences observed in some monitoring wells that are only a few tens of meters apart. To better

  4. A preliminary synthesis of structural, stratigraphic, and magnetic data from part of the northwest Adirondacks, New York

    USGS Publications Warehouse

    Foose, M.P.; Brown, C. Ervin

    1976-01-01

    Synthesis of recent work in the NW Adirondacks, New York allows the development of a coherent geologic picture. Mapping of the Precambrian rock units enables the recognition of four major units which are, from bottom to top, 1) Granitic Gneiss (alaskite), 2) Lower Marble, 3) Major Gneiss, and 4) Upper Marble. Additionally, lenses of amphibolite and granite occur as intrusives within this succession. These rock units have been complexly deformed by three major folding episodes, and by two distinctly different styles of faulting. The result has been to produce large northeast-southwest trending dome and basin structures. Patterns of magnetic intensity closely parallel distribution of rock units and provide additional information for a structural and stratigraphic synthesis-.

  5. Carbohydrate structure: the rocky road to automation.

    PubMed

    Agirre, Jon; Davies, Gideon J; Wilson, Keith S; Cowtan, Kevin D

    2016-12-08

    With the introduction of intuitive graphical software, structural biologists who are not experts in crystallography are now able to build complete protein or nucleic acid models rapidly. In contrast, carbohydrates are in a wholly different situation: scant automation exists, with manual building attempts being sometimes toppled by incorrect dictionaries or refinement problems. Sugars are the most stereochemically complex family of biomolecules and, as pyranose rings, have clear conformational preferences. Despite this, all refinement programs may produce high-energy conformations at medium to low resolution, without any support from the electron density. This problem renders the affected structures unusable in glyco-chemical terms. Bringing structural glycobiology up to 'protein standards' will require a total overhaul of the methodology. Time is of the essence, as the community is steadily increasing the production rate of glycoproteins, and electron cryo-microscopy has just started to image them in precisely that resolution range where crystallographic methods falter most.

  6. Automated S/TEM metrology on advanced semiconductor gate structures

    NASA Astrophysics Data System (ADS)

    Strauss, M.; Arjavac, J.; Horspool, D. N.; Nakahara, K.; Deeb, C.; Hobbs, C.

    2012-03-01

    Alternate techniques for obatining metrology data from advanced semiconductor device structures may be required. Automated STEM-based dimensional metrology (CD-STEM) was developed for complex 3D geometries in read/write head metrology in teh hard disk drive industry. It has been widely adopted, and is the process of record for metrology. Fully automated S/TEM metrology on advanced semiconductor gate structures is viable, with good repeatability and robustness. Consistent automated throughput of 10 samples per hour was achieved. Automated sample preparation was developed with sufficient throughput and quality to support the automated CD-STEM.

  7. Hitting the MARC: Database Structure for Library Automation.

    ERIC Educational Resources Information Center

    Calame, Albert P.

    2000-01-01

    Outlines the basic database structure that should be in place in library automation systems. Suggests that any library automation system that includes a catalog should be using a database engine that uses the MARC record structure at its basic structure for record storage. Describes the elements of MARC 21 formats--the new standards for the…

  8. Seismic interpretation of the sedimentation systems, structural geology and stratigraphic of the Chicxulub crater, carbonate platform of Yucatan, Mexico.

    NASA Astrophysics Data System (ADS)

    Iza, Canales-Garcia; Jaime, Urrutia-Fucugauchi; Joaquin Eduardo, Aguayo-Camargo; Angel, Alatorre-Mendieta Miguel

    2016-04-01

    In order to describe the structural and stratigraphic features of the Chicxulub crater, was performed the present work of seismic interpretation, seismic attributes and generation of 3D surfaces. Load data it was performed in SEG-Y format, to display a total of 19 seismic reflection profiles were worked at domain time; the corresponding interpretation was carried out by separating five packages with textural differences, for this separation were used five horizons with seismic response representing the base of these packages, the correlation of horizons was made for all lines, creating composed lines so that all profiles were interpret together at intersections for form a grid. Multiple fault zones, were interpreted with the help of seismic attributes, like RMS amplitude, complex trace analysis, gradient of the trace and cosine phase. Was obtained the structural and stratigraphic interpretation , 3D models of the surfaces interpreted with which it is possible to observe the morphology of the base of the basin, it is controlled by the effect of the impact that formed the crater, has the features as a multi-ring crater. Shallower horizons shows that the topography of the base of the crater continues to affect the upper relief, which tends to be horizontal as it approaches the surface but is modeled by themselves sedimentary processes of the carbonate platform of Yucatán; packages below the base of the crater show the characteristics that own carbonated breccia, product the rupture of the material at impact, the material was deposited in a chaotic way, at this level we found the faults and fractures zone.

  9. Preliminary stratigraphic and structural architecture of Bhutan: Implications for the along strike architecture of the Himalayan system

    NASA Astrophysics Data System (ADS)

    McQuarrie, Nadine; Robinson, Delores; Long, Sean; Tobgay, Tobgay; Grujic, Djordje; Gehrels, George; Ducea, Mihai

    2008-07-01

    Preliminary mapping and stratigraphic correlation of Lesser Himalayan rock in eastern Bhutan using field characteristics, U-Pb detrital zircon dating, and ɛNd geochemistry define the first-order stratigraphic architecture of the Indian passive margin sequence in the eastern Himalaya. We use this new image of the lateral and vertical relationships of the original stratigraphy to determine the structural framework of the eastern Himalayan fold-thrust belt in Bhutan. We propose that Lesser Himalayan rock in Bhutan can be divided into lower Lesser Himalayan rocks with a Paleoproterozoic detrital zircon signal, and upper Lesser Himalayan rocks with detrital zircon signals of ˜ 1000-500 Ma. The ˜ 500 Ma detrital grains are from rocks in the frontal portions of the fold-thrust belt north of the Main Boundary thrust as well as directly in the footwall of the Main Central thrust in the hinterland. Our preliminary stratigraphic study coupled with mapping allows us to construct a composite balanced cross-section through the Kuru Chu valley in eastern Bhutan which provides the first image of the geometry and amount of shortening through Bhutan. The Main Frontal thrust tilts a 6 km of thick section of Neogene foreland basin deposits. These deposits are separated from folded and faulted upper Lesser Himalayan rocks by the Main Boundary thrust. North of the Main Boundary thrust, we propose two duplex systems. The southernmost duplex contains 9 repeated sections of upper Lesser Himalayan units, including the Permian Gondwana Sequence and the Cambrian (or younger) Baxa Group. The northernmost duplex is located in the footwall of the Main Central thrust, and is comprised of two repeated sections of the Proterozoic Shumar and Daling Formations. The southern boundary of this northern duplex is the Shumar thrust which acts as a roof thrust for the southern duplex system and may correlate to the Ramgarh thrust in Nepal and India. We propose that the development of the duplex systems

  10. New Geochronologic, Stratigraphic and Structural Data Constraining the Cretaceous Evolution of Southwestern Mexico

    NASA Astrophysics Data System (ADS)

    Martini, M.; Ferrari, L.; Cerca, M.; Valencia, V.

    2007-12-01

    The Mesozoic volcano-sedimentary successions of southwestern Mexico have been often interpreted to represent the record of a single or multi-arc system (Guerrero Terrane), built on oceanic crust far away from the continent, which was subsequently accreted to the continental margin of the North American plate in Late Cretaceous time after a prolonged period of W-directed subduction. An alternative model proposes that the Guerrero island arc was built partly on oceanic crust and partly on continental crust and later collided with the continent (Tardy et al., 1994). However, no solid data exist to support either a true accretionary process or the collision of two continental masses in southern Mexico during Laramide deformation. Furthermore, the occurrence of Paleozoic and Precambrian terrigenous sediments at various stratigraphic levels of the Cretaceous sedimentary succession of the southern Guerrero Terrane indicates that it formed relatively close to a continent. This is also supported by the Grenvillian inherited component recognized in zircons of the ~120 Ma Placeres del Oro pluton, which resulted from partial assimilation of either a lower crustal continental basement or of upper crustal detrital zircons recycled from Grenvillian basement. Models considering the accretion of intraoceanic insular arcs to nuclear Mexico during Late Cretaceous time cannot explain such continental influence and need to be revisited. We suggest that the Cretaceous volcano-sedimentary successions were deposited directly on the thinned continental margin of the North American plate, and were deformed in Late Cretaceous time to form a thrust-and- fold belt. The apparent litho-stratigrahic incompatibilities of the Mesozoic successions can be completely explained in terms of spatial and temporal variations of facies on a heterogeneous crust with a migrating continental arc, and its back-arc and fore-arc basins. The arc was related to eastward subduction of the Farallon oceanic plate. In

  11. Stratigraphic and structural reconstruction of an Upper Ordovician super-eruption (Catalan Pyrenees)

    NASA Astrophysics Data System (ADS)

    Marti, Joan; Casas, Josep Maria; Muñoz, Josep A.

    2017-04-01

    Pre-Variscan basement of the Pyrenees includes evidence of many magmatic episodes represented by different types of granitoids and volcanic rocks, which indicates the complex geodynamic history of this peri-Gondwana terrane during Palaeozoic. One of the most significative magmatic episodes is that of Upper Ordovician (Caradocian) age, which is represented by several granitic and granodioritic bodies and volcanic rocks mostly of pyroclastic nature. In the Catalan Pyrenees this magmatism is well represented in the Ribes de Freser and Nuria area, where the orthogneisses from the Nuria massif and the Ribes granophyre, both with a similar age of 457 Ma, seem to form a calc-alkaline plutonic suite covering terms from deeper to shallower levels. The presence of numerous pyroclastic deposits and lavas interbedded with Caradocian sediments and intruded by and immediately above the Ribes granophyre, suggests that this intrusive episode also generated significant volcanism. The area also hosts an important volume of rhyolitic ignimbrites and andesitic lavas strongly affected by Alpine tectonics and commonly showing tectonised contacts at the base and top of the sequences. These volcanic rocks were previously attributed to the Upper Carboniferous late-Variscan volcanism, extensively represented in the Pyrenees. However, new laser ablation U-Pb zircon geochronology from these rocks has revealed an Upper Ordovician age ( 455 Ma), similar to that of the plutonic rocks of the same area, thus suggesting a probable genetic relation between all them. The palinspatic reconstruction of the Alpine and Variscan tectonic units that affect this area has permitted to infer the geometry, facies distribution, original position, and thickness of these volcanic rocks previously attributed to the late-Variscan volcanism, and reveals how they are spatially (and stratigraphically) associated with the previously identified Late Ordovician volcanic rocks. In particular, the volcanic rocks cropping

  12. 3D Structural and Stratigraphic Architecture of the Northwest Santa Barbara Channel and Implications for Submarine Landslide Generation

    NASA Astrophysics Data System (ADS)

    Wright, A.; Kluesner, J. W.; Brothers, D. S.; Johnson, S. Y.

    2015-12-01

    Multiple submarine landslides have been previously documented on the north flank of the Santa Barbara Channel, and such failures are considered capable of generating local tsunamis. 2D seismic-reflection datasets provide a general view of regional framework geology, including faulting and folding associated with north-south compression. However, better understanding of the relationships between faults, folds, stratigraphic architecture, and submarine landslides can be obtained with 3D seismic datasets. In this study we use an industry 3D seismic-reflection volume that encompasses the slope and shelfbreak surrounding the Gaviota submarine landslide (3.8 km2) to investigate structural and stratigraphic controls on slope failure in this region. The depth-migrated seismic volume shows a network of stacked thrust faults, backthrusts, and splays that results in both broad and local zones of compression and folding along the slope and shelf. One localized zone of enhanced folding associated with small-offset thrust faults is located directly beneath the Gaviota landslide headwall, while another zone is located directly below an imaged seafloor fissure. In addition, 3D seismic attribute analysis provides insight into the shallow sedimentary section of the failed and non-failed sedimentary packages. Calculation of RMS amplitude and dominant frequency within a windowed region below the seafloor horizon delineates an apparent zone of gas-charged strata that onlaps onto older folded sediments. The up-dip limit of these gas-charged sediments aligns with the location of a seafloor fissure that extends westward from the Gaviota landslide headwall. We propose that the combination of deformation and fluid charging acted to pre-condition and trigger the failure of the Gaviota landslide, and as a result, the presence of these conditions along the fissure adjacent to the Gaviota landslide suggests this area should be considered landslide prone.

  13. Structural and stratigraphic controls on the origin and tectonic history of a subducted continental margin, Oman

    NASA Astrophysics Data System (ADS)

    Warren, C. J.; Miller, J. McL.

    2007-03-01

    Eclogites and blueschists exposed in Saih Hatat, Oman, record the subduction and exhumation of continental crustal material beneath the Cretaceous Semail Ophiolite during ophiolite obduction. The eclogite-bearing lower plate, originally part of Oman's distal continental margin, is exposed in two tectonic windows through the less metamorphosed upper plate by a previously mapped low angle, high strain, décollement structure. A major tectonic break, currently poorly exposed, records the juxtaposition of the highest pressure eclogites and garnet blueschists against lower pressure epidote-blueschists. The subsequent exhumation of the entire lower plate to mid crustal levels is marked by a pervasive shearing event associated with a regional greenschist facies overprint. The décollement truncates structures and the metamorphic field gradient in the lower plate, but does not significantly truncate structures or stratigraphy in the upper plate. It is not responsible for the exhumation of the high pressure rocks to mid-crustal levels. Most of the displacement across this structure was accommodated during continuing convergence after the subduction system had ceased to be active, and post ophiolite emplacement onto the platform carbonate sequences. A revised tectonic model is presented which accounts for the structural, geochronological and metamorphic observations.

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

    SciTech Connect

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

    1986-04-01

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

  15. Structural-stratigraphic setting of South Freshwater Bayou Prospect, Vermilion Parish, Louisiana

    SciTech Connect

    Cavanagh, T.; Pilger, R.H. Jr.; Bebout, D.G.; Bachman, A.L.

    1981-01-01

    The primary reservoir targets in South Freshwater Bayou Prospect are sands whose deposition appears to have been structurally controlled. The growth of a deep domal feature localized deepwater sand deposition on its flanks, thereby producing a significant thickness of subsequently geopressured sandstone. The area is, therefore, not only prospective in its own right, but provides an exploration model for other geopressured-geothermal prospects.

  16. Structural and stratigraphic compartmentalization of the Terry Sandstone and effects on reservoir fluid distributions: Latham Bar Trend, Denver Basin: Colorado

    SciTech Connect

    Al-Raisi, M.H.; Slatt, R.M.; Decker, M.K.

    1996-01-01

    The Latham Bar Trend, located in the Denver Basin of Colorado, is an elongate sandstone which extends in a northwest direction for more than 6 mi and is up to 1-2 mi wide. It is now under infill drilling on 40-acre spacing, with more than 65 wells producing from the Upper Cretaceous Terry Sandstone. Detailed analysis of four cores and 210 wells suggests that the Terry Sandstone within the Lantham Bar Trend was deposited in an open marine environment. Reservoir quality, particularly permeability, is primarily facies controlled, and secondarily controlled by diagenetic products. Estimated ultimate recovery (EUR) values in wells are related to thickness of this facies. Structural analysis indicates the Trend is dissected by a series of northeast-trending, northwest-dipping faults with vertical displacements of 30-100 ft. (9-30 m). The faults are interpreted to be sealing, separating the Terry Sandstone into isolated fault blocks, on the basis of the following criteria: (1) normalized GOR values exhibit a non-systematic areal distribution across the trend, but show systematic up-structure increases in GOR within individual fault blocks; (2) initial API gravity values from different wells also are non-systematically distributed areally across the Trend, but show similar groupings within fault blocks; (3) EUR values within each fault block exhibit a positive correlation with thickness of cross-bedded sandstone facies; (4) individual wells with specific normalized GOR values occur at lower structural elevations than wells in adjacent fault blocks with lower GORs, giving rise to structural reversal of fluid distributions. Recognition of the facies control on reservoir quality, reservoir facies thickness, sealing capacity of normal faults, and resultant compartmentalization can help explain complex stratigraphic and areas distribution patterns of gas and oil in these and other strata in the Denver Basin and to maximize reservoir producibility and exploration success.

  17. Arctic ice shelves and ice islands: Origin, growth and disintegration, physical characteristics, structural-stratigraphic variability, and dynamics

    SciTech Connect

    Jeffries, M.O. )

    1992-08-01

    Ice shelves are thick, floating ice masses most often associated with Antarctica where they are seaward extensions of the grounded Antarctic ice sheet and sources of many icebergs. However, there are also ice shelves in the Arctic, primarily located along the north coast of Ellesmere Island in the Canadian High Arctic. The only ice shelves in North America and the most extensive in the north polar region, the Ellesmere ice shelves originate from glaciers and from sea ice and are the source of ice islands, the tabular icebergs of the Arctic Ocean. The present state of knowledge and understanding of these ice features is summarized in this paper. It includes historical background to the discovery and early study of ice shelves and ice islands, including the use of ice islands as floating laboratories for polar geophysical research. Growth mechanisms and age, the former extent and the twentieth century disintegration of the Ellesmere ice shelves, and the processes and mechanisms of ice island calving are summarized. Surface features, thickness, thermal regime, and the size, shape, and numbers of ice islands are discussed. The structural-stratigraphic variability of ice islands and ice shelves and the complex nature of their growth and development are described. Large-scale and small-scale dynamics of ice islands are described, and the results of modeling their drift and recurrence intervals are presented. The conclusion identifies some unanswered questions and future research opportunities and needs. 97 refs., 18 figs.

  18. Stratigraphic and structural relations of Lower Triassic rocks within the frontal fold-and-thrust zone of southwestern Montana

    SciTech Connect

    Paull, R.K.; Paull, R.A. )

    1991-06-01

    New sections of Lower Triassic rocks were measured within the frontal fold-and-thrust zone of southwestern Montana at Garfield Canyon, Horse Prairie Creek, Kennison Spring, and Birch Creek to clarify stratigraphic and structural relations. Triassic rocks disconformably overlie Upper Permian units and unconformably underlie younger rocks. From oldest to youngest, they include the Dinwoody, Woodside, and Thaynes formations. The Dinwoody consists of shale, siltstone, and limestone; thickness varies from 152 to 273 m. Red beds of the Woodside thin northward to zero in the northern Tendoy Mountains. The Thaynes is comprised of limestone, siltstone, and sandstone; thickness varies from 244 m in the south, zero in the central area, to 51 m in the north. North of the Woodside termination, recognition of the Thaynes depends upon recovery of Smithian conodonts. Conodonts provide correlation and biofacies information for this study. From Birch Creek northward, conodonts are basinal, consistent with lithofacies data. This area is within the McCartney Mountain salient, a depositional basin which may have existed on the craton margin prior to thrusting. However, there is no evidence to support basinal conditions in the Blacktail Mountain salient to the south. Although thermal alteration values for most conodonts are within the range of oil and condensate production, those from Birch Creek north exceed the stability regime for hydrocarbons.

  19. Structural and stratigraphic evolution of Aleutian convergent-margin basins - Ridge crest to trench floor

    SciTech Connect

    Scholl, D.W.; Ryan, H.F.; Geist, E.L.; Vallier, T.L.

    1988-01-01

    The Aleutian Ridge lies along nearly 2,000 km of the north Pacific's obliquely converging plate boundary with North America. Since middle Eocene time, convergent-margin basins have repeatedly formed here, typically as summit basins along the ridge crest, and as forecarc basins on the landward trench slope. Thick (1-4 km) sequences of terrigenous, hemipelagic, and biogenic debris have accumulated in these depressions, which are mostly intra-arc structures floored by arc-basement rocks. Summit and forearc basins formed as a consequence of plate-boundary coupling and the application of compressional and right-lateral shear stresses to the arc massif. Basins typically evolved along shear zones in response to transtensional processes, and as trailing-edge grabens behind rotating blocks of arc massif. In the late Cenozoic, high rates of trench sedimentation led to the growth of an accretionary complex that underthrust forearc basement. Wedging and improved plate coupling elevated and laterally shifted blocks of outer forearc rocks, creating much of the structural framework of the regionally extensive Aleutian Terrace forearc basin. Changes in plate-boundary conditions that affected the ridge's volcanic activity and regional elevation importantly influenced basinal sedimentation. Changes of greatest significant were a major shift in convergence direction and rate about 42 Ma (reduced volcanism), ridge underthrusting by increasingly younger ocean crust in Oligocena and Miocene time (arc elevation), and the combination of more orthogonal underthrusting and the subduction of a dead spreading center 5-120 Ma (arc subsidence).

  20. Petrographic, stratigraphic, and structural study of the Smackover gray sand (Jurassic) in north Louisiana

    SciTech Connect

    Miciotto, S.A.

    1980-01-01

    The gas-producing gray sand, a dark gray to black, very fine-grained sand, occurs as 3 sand tongues in the lower member of the Smackover Formation in the subsurface of Bossier, Webster, Claiborne, and Lincoln parishes, Louisiana. A Flaser-bedded silty shale facies indicates deposition on a mid-tidal flat environment. Smackover deposition during the Jurassic in the study area was located on the gently dipping slope between a broad coastal shelf to the north and a basin to the south. The gray sand was deposited over the Norphlet formation and Louann salt before flowage and swelling of the Louann salt began. Uplift and swelling of the Louann salt later in the Jurassic created growing anticlines; sediment slumped off the structural highs of the growing salt anticlines into basinal muds and silts. The Smackover gray sand continues to challenge exploration geologists because of the lateral pinch out of its sand tongues. 11 references.

  1. Structural and stratigraphic evolution of Aleutian convergent-margin basins - ridge crest to trench floor

    SciTech Connect

    Scholl, D.W.; Ryan, H.F.; Geist, E.L.; Vallier, T.L.; Stevenson, A.J.; Childs, J.R. )

    1988-02-01

    The Aleutian Ridge lies along nearly 2000 km of the north Pacific's obliquely converging plate boundary with North America. Since middle Eocene time, convergent-margin basins have repeatedly formed here, typically as summit basins along the ridge crest, and as forearc basins on the landward trench slope. Summit and forearc basins formed as a consequence of plate-boundary coupling and the application of compressional and right-lateral shear stresses to the arc massif. Basins typically evolved along shear zones in response to transtensional processes, and as trailing-edge grabens behind rotating blocks of arc massif. In the late Cenozoic, high rates of trench sedimentation led to the growth of an accretionary complex that underthrust forearc basement. Wedging and improved plate coupling elevated and laterally shifted blocks of outer forearc rocks, creating much of the structural framework of the regionally extensive Aleutian Terrace forearc basin. Changes in plate-boundary conditions that affected the ridge's volcanic activity and regional elevation importantly influenced basinal sedimentation. Changes of greatest significance were a major shift in convergence direction and rate about 42 Ma (reduced volcanism), ridge underthrusting by increasingly younger ocean crust in Oligocene and Miocene time (arc elevation), and the combination of more orthogonal underthrusting and the subduction of a dead spreading center 5-10 Ma (arc subsidence).

  2. Stratigraphic and structural relationships of Strawn Group, Brown, Coleman, and Runnels Counties, Texas

    SciTech Connect

    Ware, G.D. )

    1987-02-01

    The Strawn Group (Atokan-Missourian) is exposed in two approximately triangular areas in north-central Texas: the Brazos River valley and the Colorado River valley. The exposures in the Brazos River valley are relatively well understood and are represented by cycles of fluvial-deltaic and transgressive shallow marine facies. These exposures have been traced into the subsurface, and grade laterally into a mostly carbonate shelf succession. The Strawn Group in the Colorado River valley has not been extensively studied, but recent work is increasing their knowledge of this significant area. In the Colorado River valley, the Strawn Group is subdivided into two lithogenetic units which accumulated in at least two depositional settings. The lower Strawn Group constitutes basin-fill sediments, and represents outer shelf, slope, and submarine-fan depositional environments. The upper Strawn, although exhibiting significant differences, is essentially correlatable to the Strawn Group known in the Brazos River valley and westward into the subsurface. Subsurface mapping westward from the Colorado River valley demonstrates the general applicability of published cyclic interpretations based on surface and subsurface work in north-central Texas. However, in the Colorado River valley and westward into the subsurface, mapping reveals a system of faults presumed to be related to the horst and graben structural development in the Llano uplift area. In addition, the Concho arch, a feature closely related to the Llano uplift, was a positive area which resisted subsidence and acted as a buttress to terrigenous clastic deposition. It thus became a core for a persistent algal buildup.

  3. Structural and stratigraphic analysis of the Dinaride thrust belt; A frontier exploration province in central-Southern Europe

    SciTech Connect

    Tasker, D.R.; Weir, G.M.; Dale, R.C. )

    1993-09-01

    The Dinarides are a 200-300-km-wide southwest vergent fold and thrust belt extending along the eastern margin of the Adriatic Sea. The complex and varied structural and stratigraphic relationships can be used to define three major tectonic units: the internal, central, and external Dinarides. In the Internal Dinarides, platform sequences deposited in the Early and Middle Triassic underwent rapid subsidence and drowning in the Late Triassic and Early Jurassic along with rifting and subsequent formation of oceanic crust. Melange and flysch were deposited during the late Jurassic through Cretaceous as the developing thrust belt encroached upon the northeastern margin of the Dinaride carbonate platform. The Dinaride carbonate platform forms the cores of the central and external Dinarides and is composed primarily of Permian-Triassic clastics and evaporites overlain by Middle Triassic through early Eocene platform carbonates. The entire sequence is overlain by late Eocene and early Oligocene synorogenic flysch. In the central Dinarides, late Jurassic and Early Cretaceous unconformities suggest structural uplift prior to the onset of thrusting. Deformation involves Paleozoic basement and includes a major decollement in the Permian Triassic clastic and evaporite unit. Thrusting in the external Dinarides occurred in the late Eocene-early Oligocene and is restricted to Middle Triassic and younger units with major detachments forming near the base of the Ladinian and within a Late Jurassic-Early Cretaceous evaporite. Important oil source and seal lithofacies occur within intraplatform basins and lagoons in the Mesozoic sequences of the central and external Dinarides. Widespread dolomitized units within the Mesozoic carbonate sequence are potential reservoir zones. The presence of surface hydrocarbon seeps and of existing production on trend to the Dinarides in the thrust belt of Italy and Albania suggest the potential for hydrocarbon discoveries in this underexplored area.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  5. Stratigraphic and structural analysis of the Neogene sediments of the offshore portion of the Salina del Istmo Basin, southeastern Mexico

    NASA Astrophysics Data System (ADS)

    Gomez-Cabrera, Pedro Tomas

    2003-10-01

    Southeastern Mexico has been affected by regional and local tectonic events. Regional tectonic events are the Gulf of Mexico opening and the lateral movement of micro-plates on the Pacific margin. The local tectonic events are related to salt tectonics. Autochthonous Jurassic salt serves as the detachment level for the main compressional event in the late Miocene. Jurassic salt was allochthonously emplaced in the late Miocene, then partially displaced by a huge quantity of terrigenous sediments during the Plio-Pleistocene. This research is a study of the main geological processes that have influenced the structural and stratigraphic evolution of the Neogene sediments in the offshore portion of the Salina del Istmo basin known as the Marbella area. Owing to data availability, the project was divided into regional and local studies. The regional study is based on 2D multi-channel seismic reflection data, and the local study is based on a 3D seismic streamer survey. Structural analysis in the regional study permits the recognition of four buried fold belts (Agua Dulce, Catemaco, Marbella, and Marbella Norte) trending roughly NE. These fold belts are the result of tectonic convergence in the pacific margin during late Miocene. The Agua Dulce and Marbella Norte fold belts are separated by an enormous salt withdrawal basin called the Pescadores basin. The Pescadores basin is bounded on the north by a spectacular stepped, counter-regional structure. Beyond the Pescadores basin, a salt mini-basin area is recognized in the upper continental slope. Another important structural element is the Sal Somera canopy in the southern part of the study area. Sedimentation-rate analysis, based on isochore mapping in the local study area, indicates that from SB-2.4 to SB-2.6 Ma, deposition rate peaked with a maximum of 7.5 mm/yr. Regional and local structural restorations show that, in general, the maximum allochthonous salt mobilization was during the Plio-Pleistocene because of the

  6. Evaluating subsurface structures and stratigraphic units using 2D electrical and magnetic data at the area north Greater Cairo, Egypt

    NASA Astrophysics Data System (ADS)

    Sultan, S. A.; Santos, F. A. M.

    2008-02-01

    2D dipole-dipole resistivity data and ground magnetic survey are used in combination with available data from boreholes and surface geology to detect subsurface structures and stratigraphic units and to study the ability of the site area (located at north Grater Cairo) for a building construction. Five 1-km length dipole-dipole profiles were measured using electrode spacing of 5 m. The data from these profiles, which were carried out parallel (125 m apart) and in E-W direction, have been inverted using a 2D regularization algorithm. The geoelectrical models obtained from inversion of the field data allowed the characterization of different geological units such as mud, alluvium, sandy clay and sand and sandstone deposits. Two hundred and twenty seven stations of ground magnetic data have been measured in a grid of 50 m × 50 m using two automatic proton precession magnetometers with an accuracy of 1 nT. The results showed that the depth of the basaltic basement varies between 24 and 122 m and it is affected by several fault elements trending NW-SE and crossing the southwestern part of the study area. These faults seem to control the distribution of the sedimentary cover. Fifteen boreholes drilled in the area with depths ranging from 50 to 202 m have been used to define the thickness of the different lithological units and the depth of the top of the basaltic sheet. The results of the boreholes logging indicate that the depth of basaltic sheet ranges from 23.7 m, in the western part of the study area, to 122 m in the central part.

  7. 3D Structural and Stratigraphic Architecture of the Northwest Santa Barbara Basin: Implications for Slope Stability and Submarine Landslide Occurrence

    NASA Astrophysics Data System (ADS)

    Wright, A.; Brothers, D. S.; Kluesner, J.; Johnson, S. Y.

    2016-12-01

    Multiple submarine landslides have been documented on the north flank of the Santa Barbara Basin and such failures are considered capable of generating local tsunami hazards to the Santa Barbara region. Past 2D seismic reflection data has provided a general view of the regional framework geology resulting from north-south compression, but fails to identify along-strike variations of faults and folds. This study uses industry 3D seismic reflection data encompassing the slope surrounding the 3.8 km2-Gaviota submarine landslide to investigate structural and stratigraphic controls of slope failure in this region. The 3D depth-migrated volume shows a complex network of faults that result in both broad and local zones of compression, folding, and uplift along the slope. One localized zone of enhanced anticlinal folding and uplift associated with small-scale thrust faults is located directly beneath the Gaviota slide, while another is beneath a seafloor fissure west of the slide inferred to represent incipient failure. New high-resolution 2D transects constrain the character of shallow deformation above the locally uplifted blocks. 3D isopach maps indicate the seafloor fissures trend along a key threshold of thickness between the seafloor and a shallow horizon; the fissures are also coincide with an apparent zone of shallow, gas-charged strata that onlap the steeply dipping flanks of local anticlinal deformation. Because the seafloor gradient near the Gaviota slide is significantly lower than the internal friction angle for fine-grained marine sediments, we propose that a combination of active deformation, sediment compaction, and gas charging acted to precondition the slope of the Gaviota landslide for failure by reducing the shear strength. Similar factors occur beneath intact sections of the slope adjacent to the slide, which should be considered prone to future landsliding.

  8. Pricing Structures for Automated Library Consortia.

    ERIC Educational Resources Information Center

    Machovec, George S.

    1993-01-01

    Discusses the development of successful pricing algorithms for cooperative library automation projects. Highlights include desirable characteristics of pricing measures, including simplicity and the ability to allow for system growth; problems with transaction-based systems; and a review of the pricing strategies of seven library consortia.…

  9. Structural and stratigraphic framework and spatial distribution of permeability of the Atlantic coastal plain, North Carolina to New York

    USGS Publications Warehouse

    Brown, Philip Monroe; Miller, James A.; Swain, Frederick Morrill

    1972-01-01

    This report describes and interprets the results of a detailed subsurface mapping program undertaken in that part of the Atlantic Coastal Plain which extends from the South Carolina and North Carolina border through Long Island, N.Y. Data obtained from more than 2,200 wells are analyzed. Seventeen chronostratigraphic units are mapped in the subsurface. They range in age from Jurassic(?) to post-Miocene. The purpose of the mapping program was to determine the external and internal geometry of mappable chronostratigraphic units and to derive and construct a permeability-distribution network for each unit based upon contrasts in the textures and compositions of its contained sediments. The report contains a structure map and a combined isopach, lithofacies, and permeability-distribution map for each of the chronostratigraphic units delineated in the subsurface. In addition, it contains a map of the top of the basement surface. These maps, together with 36 stratigraphic cross sections, present a three-dimensional view of the regional subsurface hydrogeology. They provide focal points of reference for a discussion of regional tectonics, structure, stratigraphy, and permeability distribution. Taken together and in chronologic sequence, the maps constitute a detailed sedimentary model, the first such model to be constructed for the middle Atlantic Coastal Plain. The chronostratigraphic units mapped record a structural history dominated by lateral and vertical movement along a system of intersecting hinge zones. Taphrogeny, related to transcurrent faulting, is the dominant type of deformation that controlled the geometry of the sedimentary model. Twelve of the seventeen chronostratigraphic units mapped have depositional alinements and thickening trends that are independent of the present-day configuration of the underlying basement surface. These 12 units, classified as genetically unrooted units, are assigned to a first-order tectonic stage. A structural model is proposed

  10. High Resolution Stratigraphic Mapping in Complex Terrain: A Comparison of Traditional Remote Sensing Techniques with Unmanned Aerial Vehicle - Structure from Motion Photogrammetry

    NASA Astrophysics Data System (ADS)

    Nesbit, P. R.; Hugenholtz, C.; Durkin, P.; Hubbard, S. M.; Kucharczyk, M.; Barchyn, T.

    2016-12-01

    Remote sensing and digital mapping have started to revolutionize geologic mapping in recent years as a result of their realized potential to provide high resolution 3D models of outcrops to assist with interpretation, visualization, and obtaining accurate measurements of inaccessible areas. However, in stratigraphic mapping applications in complex terrain, it is difficult to acquire information with sufficient detail at a wide spatial coverage with conventional techniques. We demonstrate the potential of a UAV and Structure from Motion (SfM) photogrammetric approach for improving 3D stratigraphic mapping applications within a complex badland topography. Our case study is performed in Dinosaur Provincial Park (Alberta, Canada), mapping late Cretaceous fluvial meander belt deposits of the Dinosaur Park formation amidst a succession of steeply sloping hills and abundant drainages - creating a challenge for stratigraphic mapping. The UAV-SfM dataset (2 cm spatial resolution) is compared directly with a combined satellite and aerial LiDAR dataset (30 cm spatial resolution) to reveal advantages and limitations of each dataset before presenting a unique workflow that utilizes the dense point cloud from the UAV-SfM dataset for analysis. The UAV-SfM dense point cloud minimizes distortion, preserves 3D structure, and records an RGB attribute - adding potential value in future studies. The proposed UAV-SfM workflow allows for high spatial resolution remote sensing of stratigraphy in complex topographic environments. This extended capability can add value to field observations and has the potential to be integrated with subsurface petroleum models.

  11. Cenozoic Structural and Stratigraphic Evolution of the Ulukışla and Sivas Basins (Central and Eastern Turkey)

    NASA Astrophysics Data System (ADS)

    Gürer, Derya; Darin, Michael H.; van Hinsbergen, Douwe J. J.; Umhoefer, Paul J.

    2017-04-01

    Because subduction is a destructive process, the surface record of subduction-dominated systems is naturally incomplete. Sedimentary basins may hold the most complete record of processes related to subduction, accretion, collision, and ocean closure, and thus provide key information for understanding the kinematic evolution of orogens. In central and eastern Anatolia, the Late Cretaceous-Paleogene stratigraphic record of the Ulukışla and Sivas basins supports the hypothesis that these once formed a contiguous basin. Importantly, their age and geographic positions relative to their very similar basement units and ahead of the Arabian indenter provide a critical record of pre-, syn- and post-collisional processes in the Anatolian Orogen. The Ulukışla-Sivas basin was dissected and translated along the major left-lateral Ecemiş fault zone. Since then, the basins on either side of the fault evolved independently, with considerably more plate convergence accommodated to the east in the Sivas region (eastern Anatolia) than in the Ulukışla region (central Anatolia). This led to the deformation of marine sediments and underlying ophiolites and structural growth of the Sivas Fold-and-Thrust Belt (SSFTB) since latest Eocene time, which played a major role in marine basin isolation and disconnection, along with a regionally important transition to continental conditions with evaporite deposition starting in the early Oligocene. We use geologic mapping, fault kinematic analysis, paleomagnetism, apatite fission track (AFT) thermochronology, and 40Ar/39Ar geochronology to characterize the architecture, deformation style, and structural evolution of the region. In the Ulukışla basin, dominantly E-W trending normal faults became folded or inverted due to N-S contraction since the Lutetian (middle Eocene). This was accompanied by significant counter-clockwise rotations, and post-Lutetian burial of the Niǧde Massif along the transpressional Ecemiş fault zone. Since Miocene

  12. Structural and stratigraphic evolution of the central Mississippi Canyon area: Interaction of salt tectonics and slope processes in the formation of engineering and geologic hazards

    NASA Astrophysics Data System (ADS)

    Brand, John Richard

    Approximately 720 square miles of digital 3-dimensional seismic data covering the eastern Mississippi Canyon area, Gulf of Mexico, continental shelf was used to examine the structural and stratigraphic evolution of the geology in the study area. The analysis focused on salt tectonics and sequence stratigraphy to develop a geologic model for the study area and its potential impact on engineering and geologic hazards. Salt in the study area was found to be established structural end-members derived from shallow-emplaced salt sheets. The transition from regional to local salt tectonics was identified through structural deformation of the stratigraphic section on the seismic data and occurred no later than ˜450,000 years ago. From ˜450,000 years to present, slope depositional processes have become the dominant geologic process in the study area. Six stratigraphic sequences (I-VI) were identified in the study area and found to correlate with sequences previously defined for the Eastern Mississippi Fan. Condensed sections were the key to the correlation. The sequence stratigraphy for the Eastern Mississippi Fan can be extended ˜28 miles west, adding another ˜720 square miles to the interpreted Fan. A previously defined channel within the Eastern Fan was identified in the study area and extended the channel ˜28 miles west. Previous work on the Eastern Fan identified the source of the Fan to be the Mobile River; however, extending the channel west suggests the sediment source to be from the Mississippi River, not the Mobile River. Further evidence for this was found in ponded turbidites whose source has been previously established as the Mississippi River. Ages of the stratigraphic sequences were compared to changes in eustatic sea level. The formation stratigraphic sequences appear decoupled from sea level change with "pseudo-highstands" forming condensed sections during pronounced Pleistocene sea level lowstands. Miocene and Pleistocene depositional analogues

  13. On automation of the procedure for crystal structure model refinement

    SciTech Connect

    Dudka, A. P.

    2008-03-15

    The methods of automation of the procedure for crystal structure model refinement from experimental diffraction data, implemented in the ASTRA program package, are described. Such tools as statistical tests, parameter scanning, and data scanning reduce the time necessary for structural investigation. At strong correlations between parameters, especially when the data set is limited, parameter scanning has an advantage over the full-matrix refinement.

  14. The Serra da Cangalha impact structure, Brazil: Geological, stratigraphic and petrographic aspects of a recently confirmed impact structure

    NASA Astrophysics Data System (ADS)

    Vasconcelos, Marcos Alberto Rodrigues; Crósta, Alvaro P.; Reimold, Wolf Uwe; Góes, Ana Maria; Kenkmann, Thomas; Poelchau, Michael H.

    2013-08-01

    Serra da Cangalha is a complex impact structure with an apparent diameter of 13.7 km located in essentially undisturbed sedimentary rocks of the Parnaíba basin in northeastern Brazil. The stratigraphy of the crater region includes, from bottom to top, the Longá, Poti, Piauí and Pedra de Fogo formations of Devonian to Late Permian age. The age of the impact event is constrained to <250 Ma by stratigraphy - the youngest formation affected by the event is the ˜250 Ma Pedra de Fogo Formation. The structure comprises a ˜5.8 km wide central uplift involving the Piauí, Poti and Longá formations and a prominent ˜3 km wide collar of Poti Formation rocks. We divided Serra da Cangalha into four distinctive structural domains (i-iv), from the innermost zone outward. (i) The central domain, with an inner collar ˜1.5 km radius from the center, yielded all the samples with microscopic shock features identified so far. These include planar deformation features (PDF), feather features (FF), and planar fractures (PF) in quartz grains found in polymict breccias and shatter cones from the central depression. Furthermore, significant cementation with iron oxide is observed in the rocks of Serra da Cangalha, especially in the Poti Formation and in the polymict breccias, conferring to them a peculiar red color. Macroscopic deformation involves faulted, folded and subvertical strata within a ˜2.9 km radius from the center. (ii) The annular basin domain has limited outcrops; its most prominent features are two concentric annular ridges formed by chert breccias and fossilized wood-bearing folded strata of the Pedra de Fogo Formation. (iii) The crater rim and (iv) external domains comprise undisturbed strata of the Pedra de Fogo and Piauí formations with well-preserved sedimentary structures. Whilst the existing literature on Serra da Cangalha has focused on the structure morphology, general geology and some shock features, we present here a detailed description of the

  15. Automating the determination of 3D protein structure

    SciTech Connect

    Rayl, K.D.

    1993-12-31

    The creation of an automated method for determining 3D protein structure would be invaluable to the field of biology and presents an interesting challenge to computer science. Unfortunately, given the current level of protein knowledge, a completely automated solution method is not yet feasible, therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the first step toward designing a program to determine protein conformation automatically.

  16. The Phenix software for automated determination of macromolecular structures.

    PubMed

    Adams, Paul D; Afonine, Pavel V; Bunkóczi, Gábor; Chen, Vincent B; Echols, Nathaniel; Headd, Jeffrey J; Hung, Li-Wei; Jain, Swati; Kapral, Gary J; Grosse Kunstleve, Ralf W; McCoy, Airlie J; Moriarty, Nigel W; Oeffner, Robert D; Read, Randy J; Richardson, David C; Richardson, Jane S; Terwilliger, Thomas C; Zwart, Peter H

    2011-09-01

    X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutics for human disease. Significant time and effort are required to determine and optimize many macromolecular structures because of the need for manual interpretation of complex numerical data, often using many different software packages, and the repeated use of interactive three-dimensional graphics. The Phenix software package has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on automation. This has required the development of new algorithms that minimize or eliminate subjective input in favor of built-in expert-systems knowledge, the automation of procedures that are traditionally performed by hand, and the development of a computational framework that allows a tight integration between the algorithms. The application of automated methods is particularly appropriate in the field of structural proteomics, where high throughput is desired. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface.

  17. Automated sizing of large structures by mixed optimization methods

    NASA Technical Reports Server (NTRS)

    Sobieszczanski, J.; Loendorf, D.

    1973-01-01

    A procedure for automating the sizing of wing-fuselage airframes was developed and implemented in the form of an operational program. The program combines fully stressed design to determine an overall material distribution with mass-strength and mathematical programming methods to design structural details accounting for realistic design constraints. The practicality and efficiency of the procedure is demonstrated for transport aircraft configurations. The methodology is sufficiently general to be applicable to other large and complex structures.

  18. Microcomputer stratigraphic applications

    SciTech Connect

    Choyce, R.

    1984-04-01

    With the advent of large-capacity computer files, interactive languages for retrieval of large data bases, and low-cost effective microcomputers, the approach to stratigraphic analysis has been dramatically improved. In terms of immediate payoff, the computer assumes the role of retriever and data presenter, while the geologist concentrates on analysis of retrieved data. The biggest benefit of these new approaches is a measurable increase in productivity for the geologist. Through use of the computer, gathering and interpretive data from sample logs are greatly facilitated. With the computer, logs are encoded electronically for access by the geologist via a computer terminal, and analysis of the data is accomplished interactively. The process obviates the need for the time-consuming process of locating the appropriate logs, hanging them for analysis, and researching each log to locate appropriate intervals for correlation and interpretation. Recent studies indicate that through computerized approaches, time required for these steps is vastly diminished, and resulting productivity is 40-80% greater than with conventional manual methods. A by-product of this approach results from the data being created in a form that lends itself to graphic presentation upon demand by the geologist. This avoids the time-consuming delays inherent in interrelating with the computing department for mapping requests to ensure that the results of the analysis are as expected. With the computer, many kinds of maps become practical to produce from the terminal, including base maps, cross sections, and lithofacies, structures, and isopach maps.

  19. Seismically induced soft-sediment deformation structures in the Palaeogene deposits of the Liaodong Bay Depression in the Bohai Bay basin and their spatial stratigraphic distribution

    NASA Astrophysics Data System (ADS)

    Liu, Lei; Zhong, Yijiang; Chen, Hongde; Xu, Changgui; Wu, Kui

    2016-08-01

    Soft-sediment deformation structures (SSDS) have been identified from well cores in the Palaeogene deposits of the Liaodong Bay Depression in the Bohai Bay basin, China. These deposits formed as interbedded sand and mud at a delta front or on the slope toe of the prodelta. According to criteria proposed by previous research, we established that these SSDS were induced by earthquakes and that they can be divided into two groups: ductile deformation structures (plastic intrusions, ball-and-pillow structures, flame structures, boudinage structures, irregular convolute stratifications, and synsedimentary faults and folds) and brittle deformation structures (sand dykes and autoclastic breccias). Based on their level of deformation, size, and complexity, the SSDS were divided into three Groups, from weak to strong, to reflect the intensity of palaeo-earthquakes. With consideration of the palaeo-sedimentary environment, we proposed a model to account for the production and preservation of these SSDS. According to the classification adopted in this study and the spatial stratigraphic distribution of the SSDS, the tectonic activities of the Tan-Lu faults in the Bohai Bay basin were investigated. The A and B oilfields (assumed names) are located in the tectonically active zones of the west and east branches of these faults, respectively. The extension tectonic activities in the A oilfield region exhibit a sharply decreasing trend from E2s3 to E2s1, and increase again in E3d2; whereas the strike-slip tectonic activities in the B oilfield region exhibit an increasing trend from E2s3 to E2s1, and finally, reach a maximum to E3d3. The results of this study show that the method of analysis of the spatial stratigraphic distribution of SSDS is suitable for determining the evolution of tectonic activity and thus, it can provide a new perspective for basin analysis.

  20. Syndepositional tectonics recorded by soft-sediment deformation and liquefaction structures (continental Lower Permian sediments, Southern Alps, Northern Italy): Stratigraphic significance

    NASA Astrophysics Data System (ADS)

    Berra, F.; Felletti, F.

    2011-04-01

    The Lower Permian succession of the Central Southern Alps (Lombardy, Northern Italy) was deposited in fault-controlled continental basins, probably related to transtensional tectonics. We focussed our study on the stratigraphic record of the Lower Permian Orobic Basin, which consists of a 1000 m thick succession of prevailing continental clastics with intercalations of ignimbritic flows and tuffs (Pizzo del Diavolo Formation, PDV) resting on the underlying prevailing pyroclastic flows of the Cabianca Volcanite. The PDV consists of a lower part (composed of conglomerates passing laterally to sandstones and distally to silt and shales), a middle part (pelitic, with carbonates) and an upper part (alternating sandstone, silt and volcanic flows). Syndepositional tectonics during the deposition of the PDV is recorded by facies distribution, thickness changes and by the presence of deformation and liquefaction structures interpreted as seismites. Deformation is recorded by both ductile structures (ball-and-pillow, plastic intrusion, disturbed lamination, convolute stratification and slumps) and brittle structures (sand dykes and autoclastic breccias). Both the sedimentological features and the geodynamic setting of the depositional basin confidently support the interpretation of the described deformation features as related to seismic shocks. The most significant seismically-induced deformation is represented by a slumped horizon (about 4 m thick on average) which can be followed laterally for more than 5 km. The slumped bed consists of playa-lake deposits (alternating pelites and microbial carbonates, associated with mud cracks and vertebrate tracks). The lateral continuity and the evidence of deposition on a very low-angle surface along with the deformation/liquefaction of the sediments suggest that the slump was triggered by a high-magnitude earthquake. The stratigraphic distribution of the seismites allows us to identify time intervals of intense seismic activity

  1. Quaternary Evolution of Cinarcik Basin, Marmara Sea, Turkey from structural and stratigraphic interpretation of multiple resolutions of seismic reflection data

    NASA Astrophysics Data System (ADS)

    Kurt, H.; Sorlien, C. C.; Seeber, L.; Steckler, M. S.; Shillington, D. J.; Çifçi, G.; Demirbag, E.; Cormier, M.; Atgin, O.; Barin, B.; Dondurur, D.; Imren, C.; Gurcay, S.; Okay, S.

    2011-12-01

    Marmara Sea in western Turkey is an active subsiding marine basin forming along the North Anatolian Fault (NAF). The NAF is 1500 km-long and in northwest Turkey accommodates the current GPS-derived ~25 mm/yr westward motion of the Anatolian platelet relative to Asia. The Marmara Sea contains three subbasins with water depths reaching 1250 m, called from west to east the Tekirdag, Central and Cinarcik basins. These basins are separated by shallower topographic highs, the Western and Central highs. The NAF has two main branches and multiple strands within Marmara Sea and Cinarcik basin is a wedge-shaped active transtensional basin located along the northern branch of the NAF. We use exisiting deep-penetration, low-resolution migrated multichannel seismic reflection (MCS) data and our new migrated high-resolution MCS data for seismic stratigraphic interpretations in Cinarcik basin. This basin has a thick and not uniformly distributed sediment fill, with a maximum sediment thickness of 6 km or more (Carton et al., 2007). We used all seismic reflection data to correlate five stratigraphic horizons from the Imrali basin to the south, which contains stacked low-stand shelf-edge deltas. Our age model assigns these horizons to glacial maxima separated by 100 ka. The age of the deepest horizon is older than 500 ka using our stratigraphic-age model for Imrali basin (Sorlien et al., in review). We used a simple 3D velocity model based on stacking velocities and refraction velocities (Dessa et al., 2007). Gridded digital horizons were depth-converted and subtracted from each other to produce isochore maps (vertical thickness) between horizons including the sea floor. Volumes were calculated for each isochore grid and combined with isochores for the basin to the south. Assuming a constant rate of deposition in the two basins, the near constant interval volumes support the age model. The east ends of depocenters for each ~100 ka interval migrate westward with respect to the

  2. Automated structural classification of lipids by machine learning.

    PubMed

    Taylor, Ryan; Miller, Ryan H; Miller, Ryan D; Porter, Michael; Dalgleish, James; Prince, John T

    2015-03-01

    Modern lipidomics is largely dependent upon structural ontologies because of the great diversity exhibited in the lipidome, but no automated lipid classification exists to facilitate this partitioning. The size of the putative lipidome far exceeds the number currently classified, despite a decade of work. Automated classification would benefit ongoing classification efforts by decreasing the time needed and increasing the accuracy of classification while providing classifications for mass spectral identification algorithms. We introduce a tool that automates classification into the LIPID MAPS ontology of known lipids with >95% accuracy and novel lipids with 63% accuracy. The classification is based upon simple chemical characteristics and modern machine learning algorithms. The decision trees produced are intelligible and can be used to clarify implicit assumptions about the current LIPID MAPS classification scheme. These characteristics and decision trees are made available to facilitate alternative implementations. We also discovered many hundreds of lipids that are currently misclassified in the LIPID MAPS database, strongly underscoring the need for automated classification. Source code and chemical characteristic lists as SMARTS search strings are available under an open-source license at https://www.github.com/princelab/lipid_classifier. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  3. Computer automated structure evaluation of quinolone antibacterial agents.

    PubMed Central

    Klopman, G; Macina, O T; Levinson, M E; Rosenkranz, H S

    1987-01-01

    The Computer Automated Structure Evaluation (CASE) program was used to study a series of quinolone antibacterial agents for which experimental data pertaining to DNA gyrase inhibition as well as MICs against several strains of gram-positive and gram-negative bacteria are available. The result of the analysis was the automatic generation of molecular fragments relevant to the respective biological endpoints. The potential significance of these major activating-inactivating fragments to the biological activity is discussed. PMID:2829716

  4. Automated Localization of Multiple Pelvic Bone Structures on MRI.

    PubMed

    Onal, Sinan; Lai-Yuen, Susana; Bao, Paul; Weitzenfeld, Alfredo; Hart, Stuart

    2016-01-01

    In this paper, we present a fully automated localization method for multiple pelvic bone structures on magnetic resonance images (MRI). Pelvic bone structures are at present identified manually on MRI to locate reference points for measurement and evaluation of pelvic organ prolapse (POP). Given that this is a time-consuming and subjective procedure, there is a need to localize pelvic bone structures automatically. However, bone structures are not easily differentiable from soft tissue on MRI as their pixel intensities tend to be very similar. In this paper, we present a model that combines support vector machines and nonlinear regression capturing global and local information to automatically identify the bounding boxes of bone structures on MRI. The model identifies the location of the pelvic bone structures by establishing the association between their relative locations and using local information such as texture features. Results show that the proposed method is able to locate the bone structures of interest accurately (dice similarity index >0.75) in 87-91% of the images. This research aims to enable accurate, consistent, and fully automated localization of bone structures on MRI to facilitate and improve the diagnosis of health conditions such as female POP.

  5. Fully automated localization of multiple pelvic bone structures on MRI.

    PubMed

    Onal, Sinan; Lai-Yuen, Susana; Bao, Paul; Weitzenfeld, Alfredo; Hart, Stuart

    2014-01-01

    In this paper, we present a fully automated localization method for multiple pelvic bone structures on magnetic resonance images (MRI). Pelvic bone structures are currently identified manually on MRI to identify reference points for measurement and evaluation of pelvic organ prolapse (POP). Given that this is a time-consuming and subjective procedure, there is a need to localize pelvic bone structures without any user interaction. However, bone structures are not easily differentiable from soft tissue on MRI as their pixel intensities tend to be very similar. In this research, we present a model that automatically identifies the bounding boxes of the bone structures on MRI using support vector machines (SVM) based classification and non-linear regression model that captures global and local information. Based on the relative locations of pelvic bones and organs, and local information such as texture features, the model identifies the location of the pelvic bone structures by establishing the association between their locations. Results show that the proposed method is able to locate the bone structures of interest accurately. The pubic bone, sacral promontory, and coccyx were correctly detected (DSI > 0.75) in 92%, 90%, and 88% of the testing images. This research aims to enable accurate, consistent and fully automated identification of pelvic bone structures on MRI to facilitate and improve the diagnosis of female pelvic organ prolapse.

  6. Automated output-only dynamic identification of civil engineering structures

    NASA Astrophysics Data System (ADS)

    Rainieri, C.; Fabbrocino, G.

    2010-04-01

    Modal-based damage detection algorithms are well-known techniques for structural health assessment, but they are not commonly used due to the lack of automated modal identification and tracking procedures. Development of such procedures is not a trivial task since traditional modal identification requires extensive interaction from an expert user. Nevertheless, computational efforts have to be carefully considered. If fast on-line data processing is crucial for quickly varying in time systems (such as a rocket burning fuel), a number of vibration-based condition monitoring applications are performed at very different time scales, resulting in satisfactory time steps for on-line data analysis. Moreover, promising results in the field of automated modal identification have been recently achieved. In the present paper, a literature review on this topic is presented and recent developments concerning fully automated output-only modal identification procedures are described. Some case studies are also reported in order to validate the approach. They are characterized by different levels of complexity, in terms of mode coupling, dynamic interaction effects and level of vibration. Advantages and drawbacks of the proposed approach will be pointed out with reference to available experimental results. The final objective is the implementation of a fully automated system for vibration-based structural health monitoring of civil engineering structures and identification of adequate requirements about sensor number and layout, record duration and hardware characteristics able to ensure a reliable low-cost health assessment of constructions. Results of application of the proposed methodology to modal parameter estimation in operational conditions and during ground motions induced by the recent L'Aquila earthquake will be finally presented and discussed.

  7. The link between tectonics and sedimentation in the Pannonian basin: seismic analysis of structural and stratigraphic features and compaction effects

    NASA Astrophysics Data System (ADS)

    Balázs, Attila; Matenco, Liviu; Magyar, Imre; Sztanó, Orsolya; Horváth, Ferenc; Cloetingh, Sierd

    2017-04-01

    The architecture of sedimentary basins reflects the relationship between accommodation space and sediment supply, their rates and localization being variable during basin evolution. A novel kinematic and seismic sequence stratigraphic interpretation calibrated by wells allows the quantification of the link between the formation of half-grabens and coeval sedimentation in the Great Hungarian Plain part of the basin. While the lower order tectonic induced cycles characterize the main phases of extension in various sub-basins, the higher order cyclicity and associated unconformities define individual moments of fault (re-)activation. The combined kinematic and depositional model at the scale of the entire basin infers that the cumulated amounts of Early to Late Miocene extension were much higher than previously thought, reaching about 220-290 km. The post-rift phase of the basin is associated with the evolution of Lake Pannon: an initial underfilled, balance fill and a final stage of overfilled large lacustrine basin. Paleobathymetric calculations based on the decompacted thickness of the prograding shelf-margin slope clinoforms indicate water depth values typically a few 100s meters up to 1 kilometer between the bottomsets and topsets. Additional 0-75 meters of water column covered the shelf controlled by climatically driven lake level variations. Sedimentary transport routes were primarily determined by inherited and/or local active tectonics including the control of the Miocene shelf-margin progradation directions and affecting recent fluvial geometries as well. Sediments up to 6 km thick are affected by continuous differential vertical movements and compaction creating gentle fold geometries and differential compaction induced faults, playing a major role in hydrocarbon migration and trapping.

  8. Teaching with Stratigraphic Profiles

    ERIC Educational Resources Information Center

    Stefanich, Greg P.

    1974-01-01

    Presents two exercises modeled after the ice age puzzle described in the ESCP textbook, including formation of terminal moraines and kettle lakes and intersection of normal faults with gold-quartz veins. Indicates that the stratigraphic profiles are usable in teaching earth science, geography, general science, and topographic problems. (CC)

  9. Teaching with Stratigraphic Profiles

    ERIC Educational Resources Information Center

    Stefanich, Greg P.

    1974-01-01

    Presents two exercises modeled after the ice age puzzle described in the ESCP textbook, including formation of terminal moraines and kettle lakes and intersection of normal faults with gold-quartz veins. Indicates that the stratigraphic profiles are usable in teaching earth science, geography, general science, and topographic problems. (CC)

  10. PYMORPH: automated galaxy structural parameter estimation using PYTHON

    NASA Astrophysics Data System (ADS)

    Vikram, Vinu; Wadadekar, Yogesh; Kembhavi, Ajit K.; Vijayagovindan, G. V.

    2010-12-01

    We present a new software pipeline - PYMORPH- for automated estimation of structural parameters of galaxies. Both parametric fits through a two-dimensional bulge disc decomposition and structural parameter measurements like concentration, asymmetry etc. are supported. The pipeline is designed to be easy to use yet flexible; individual software modules can be replaced with ease. A find-and-fit mode is available so that all galaxies in an image can be measured with a simple command. A parallel version of the PYMORPH pipeline runs on computer clusters and a virtual observatory compatible web enabled interface is under development.

  11. Multidisciplinary approach for fault detection: Integration of PS-InSAR, geomorphological, stratigraphic and structural data in the Venafro intermontane basin (Central-Southern Apennines, Italy)

    NASA Astrophysics Data System (ADS)

    Amato, Vincenzo; Aucelli, Pietro P. C.; Bellucci Sessa, Eliana; Cesarano, Massimo; Incontri, Pietro; Pappone, Gerardo; Valente, Ettore; Vilardo, Giuseppe

    2017-04-01

    A multidisciplinary methodology, integrating stratigraphic, geomorphological and structural data, combined with GIS-aided analysis and PS-InSAR interferometric data, was applied to characterize the relationships between ground deformations and the stratigraphic and the morphostructural setting of the Venafro intermontane basin. This basin is a morphostructural depression related to NW-SE and NE-SW oriented high angle normal faults bordering and crossing it. In particular, a well-known active fault crossing the plain is the Aquae Juliae Fault, whose recent activity is evidenced by archeoseismological data. The approach applied here reveals new evidence of possible faulting, acting during the Lower to Upper Pleistocene, which has driven the morphotectonic and the environmental evolution of the basin. In particular, the tectonic setting emerging from this study highlights the influence of the NW-SE oriented extensional phase during the late Lower Pleistocene - early Middle Pleistocene, in the generation of NE-SW trending, SE dipping, high-angle faults and NW-SE trending, high-angle transtensive faults. This phase has been followed by a NE-SW extensional one, responsible for the formation of NW-SE trending, both NW and SE dipping, high-angle normal faults, and the reactivation of the oldest NE-SW oriented structures. These NW-SE trending normal faults include the Aquae Juliae Fault and a new one, unknown until now, crossing the plain between the Venafro village and the Colle Cupone Mt. (hereinafter named the Venafro-Colle Cupone Fault, VCCF). This fault has controlled deposition of the youngest sedimentary units (late Middle Pleistocene to late Upper Pleistocene) suggesting its recent activity and it is well constrained by PS-InSAR data, as testified by the increase of the subsidence rate in the hanging wall block.

  12. Automated quantification of lung structures from optical coherence tomography images

    PubMed Central

    Pagnozzi, Alex M.; Kirk, Rodney W.; Kennedy, Brendan F.; Sampson, David D.; McLaughlin, Robert A.

    2013-01-01

    Characterization of the size of lung structures can aid in the assessment of a range of respiratory diseases. In this paper, we present a fully automated segmentation and quantification algorithm for the delineation of large numbers of lung structures in optical coherence tomography images, and the characterization of their size using the stereological measure of median chord length. We demonstrate this algorithm on scans acquired with OCT needle probes in fresh, ex vivo tissues from two healthy animal models: pig and rat. Automatically computed estimates of lung structure size were validated against manual measures. In addition, we present 3D visualizations of the lung structures using the segmentation calculated for each data set. This method has the potential to provide an in vivo indicator of structural remodeling caused by a range of respiratory diseases, including chronic obstructive pulmonary disease and pulmonary fibrosis. PMID:24298402

  13. A telerobotic system for automated assembly of large space structures

    NASA Technical Reports Server (NTRS)

    Rhodes, Marvin D.; Will, Ralph W.; Wise, Marion A.

    1989-01-01

    Future space missions such as polar platforms and antennas are anticipated to require large truss structures as their primary support system. During the past several years considerable research has been conducted to develop hardware and construction techniques suitable for astronaut assembly of truss structures in space. A research program has recently been initiated to develop the technology and to demonstrate the potential for automated in-space assembly of large erectable structures. The initial effort will be focussed on automated assembly of a tetrahedral truss composed of 2-meter members. The facility is designed as a ground based system to permit evaluation of assembly concepts and was not designed for space qualification. The system is intended to be used as a tool from which more sophisticated procedures and operations can be developed. The facility description includes a truss structure, motionbases and a robot arm equipped with an end effector. Other considerations and requirements of the structural assembly describe computer control systems to monitor and control the operations of the assembly facility.

  14. Automated 3D structure composition for large RNAs.

    PubMed

    Popenda, Mariusz; Szachniuk, Marta; Antczak, Maciej; Purzycka, Katarzyna J; Lukasiak, Piotr; Bartol, Natalia; Blazewicz, Jacek; Adamiak, Ryszard W

    2012-08-01

    Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues.

  15. Automated 3D structure composition for large RNAs

    PubMed Central

    Popenda, Mariusz; Szachniuk, Marta; Antczak, Maciej; Purzycka, Katarzyna J.; Lukasiak, Piotr; Bartol, Natalia; Blazewicz, Jacek; Adamiak, Ryszard W.

    2012-01-01

    Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues. PMID:22539264

  16. An automated, integrated approach to Space Station structural modeling

    NASA Technical Reports Server (NTRS)

    Lindenmoyer, Alan J.; Habermeyer, John A.

    1989-01-01

    NASA and its contractors have developed an integrated, interdisciplinary CAD/analysis system designated IDEAS(double asterisk)2 in order to conduct evaluations of alternative Space Station concepts' performance over the projected course of the Station's evolution in orbit. Attention is presently given to the requirements associated with automated FEM-building methods applicable to Space Station system-level structural dynamic analysis, and the ways in which IDEAS(double asterisk)2 addresses these requirements. Advantage is taken of the interactive capabilities of the SUPERTAB FEM preprocessor system for Space Station model manipulation and modification.

  17. Towards automated crystallographic structure refinement with phenix.refine

    PubMed Central

    Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel; Headd, Jeffrey J.; Moriarty, Nigel W.; Mustyakimov, Marat; Terwilliger, Thomas C.; Urzhumtsev, Alexandre; Zwart, Peter H.; Adams, Paul D.

    2012-01-01

    phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods. PMID:22505256

  18. Towards automated crystallographic structure refinement with phenix.refine.

    PubMed

    Afonine, Pavel V; Grosse-Kunstleve, Ralf W; Echols, Nathaniel; Headd, Jeffrey J; Moriarty, Nigel W; Mustyakimov, Marat; Terwilliger, Thomas C; Urzhumtsev, Alexandre; Zwart, Peter H; Adams, Paul D

    2012-04-01

    phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.

  19. ModLoop: automated modeling of loops in protein structures.

    PubMed

    Fiser, András; Sali, Andrej

    2003-12-12

    ModLoop is a web server for automated modeling of loops in protein structures. The input is the atomic coordinates of the protein structure in the Protein Data Bank format, and the specification of the starting and ending residues of one or more segments to be modeled, containing no more than 20 residues in total. The output is the coordinates of the non-hydrogen atoms in the modeled segments. A user provides the input to the server via a simple web interface, and receives the output by e-mail. The server relies on the loop modeling routine in MODELLER that predicts the loop conformations by satisfaction of spatial restraints, without relying on a database of known protein structures. For a rapid response, ModLoop runs on a cluster of Linux PC computers. The server is freely accessible to academic users at http://salilab.org/modloop

  20. Stratigraphic scale the Lower Precambrian of Russia

    NASA Astrophysics Data System (ADS)

    Anisimova, Svetlana; Bogdanov, Yuri

    2017-04-01

    The quality of state geological maps depends on the quality of the combined serial legends, which are based on the adopted stratigraphic scheme of the General stratigraphic scale, regional and local stratigraphic schemes. The main task of the General stratigraphic scale is the temporal correlation of stratigraphic units of regional schemes and the age of their boundaries. For the Precambrian age determination is based on paleontological and geochronological methods. Currently, work is being carried out to update the stratigraphic framework of the formations of the upper Proterozoic (Riphean and Vendian). Relatively less studied is the stratigraphy of the lower Precambrian. To the bottom are Precambrian structurally-material complexes of Archean and lower Proterozoic rocks, crystalline basement of ancient platforms and also included in the fold belts. The solution to the problems of stratigraphy of the lower Precambrian is possible only by creating and improving regional stratigraphic schemes. Such work should be based on the study of stratotype sections and references of boundaries in the model regions of the lower Precambrian. The current General stratigraphic scale of the lower Precambrian of Russia (RGSS) consists of the Lower Archean (Sami) and the Upper Archean (Lopi) and lower Proterozoic (Karelian) Eonotam. Archaea is divided into two Eonotam in Russian General stratigraphic scale, in the International Chronostratigraphic Chart (ICC) - three units, designated as Eon. The age of the boundary between Eonotam and Eon the same (3200 million years). The same and the age of the boundary between the Archean and the Proterozoic. The RGSS of the Precambrian, based on the comprehensive study of typical sections and analysis of isotopic Dating of different methods. Stratotype reference sections of the districts of Karelia and the Kola Peninsula represent different types of sections, the time (geochronological) correlation which was the basis for the regional scheme

  1. Verification Test of Automated Robotic Assembly of Space Truss Structures

    NASA Technical Reports Server (NTRS)

    Rhodes, Marvin D.; Will, Ralph W.; Quach, Cuong C.

    1995-01-01

    A multidisciplinary program has been conducted at the Langley Research Center to develop operational procedures for supervised autonomous assembly of truss structures suitable for large-aperture antennas. The hardware and operations required to assemble a 102-member tetrahedral truss and attach 12 hexagonal panels were developed and evaluated. A brute-force automation approach was used to develop baseline assembly hardware and software techniques. However, as the system matured and operations were proven, upgrades were incorporated and assessed against the baseline test results. These upgrades included the use of distributed microprocessors to control dedicated end-effector operations, machine vision guidance for strut installation, and the use of an expert system-based executive-control program. This paper summarizes the developmental phases of the program, the results of several assembly tests, and a series of proposed enhancements. No problems that would preclude automated in-space assembly or truss structures have been encountered. The test system was developed at a breadboard level and continued development at an enhanced level is warranted.

  2. The automated strength-aeroelastic design of aerospace structures program

    NASA Technical Reports Server (NTRS)

    Johnson, E. H.; Venkayya, V. B.

    1984-01-01

    An ongoing program whose goal is to develop an automated procedure that can assist in the preliminary design of aircraft and space structures is described. The approach and capabilities that are to be included in the final procedures are descussed. By using proven engineering software as a basis for the project, a reliable and interdisciplinary procedure is developed. The use of a control language for module sequencing and execution permits efficient development of the procedure and gives the user significant flexibility in altering or enhancing the procedure. The data base system provides reliable and efficient access to the large amounts of interrelated data required in an enterprise of this sort. In addition, the data base allows interfacing with existing pre- and post-processors in an almost trivial manner. Altogether, the procedure promises to be of considerable utility to preliminary structural design teams.

  3. pmx: Automated protein structure and topology generation for alchemical perturbations.

    PubMed

    Gapsys, Vytautas; Michielssens, Servaas; Seeliger, Daniel; de Groot, Bert L

    2015-02-15

    Computational protein design requires methods to accurately estimate free energy changes in protein stability or binding upon an amino acid mutation. From the different approaches available, molecular dynamics-based alchemical free energy calculations are unique in their accuracy and solid theoretical basis. The challenge in using these methods lies in the need to generate hybrid structures and topologies representing two physical states of a system. A custom made hybrid topology may prove useful for a particular mutation of interest, however, a high throughput mutation analysis calls for a more general approach. In this work, we present an automated procedure to generate hybrid structures and topologies for the amino acid mutations in all commonly used force fields. The described software is compatible with the Gromacs simulation package. The mutation libraries are readily supported for five force fields, namely Amber99SB, Amber99SB*-ILDN, OPLS-AA/L, Charmm22*, and Charmm36.

  4. pmx: Automated protein structure and topology generation for alchemical perturbations

    PubMed Central

    Gapsys, Vytautas; Michielssens, Servaas; Seeliger, Daniel; de Groot, Bert L

    2015-01-01

    Computational protein design requires methods to accurately estimate free energy changes in protein stability or binding upon an amino acid mutation. From the different approaches available, molecular dynamics-based alchemical free energy calculations are unique in their accuracy and solid theoretical basis. The challenge in using these methods lies in the need to generate hybrid structures and topologies representing two physical states of a system. A custom made hybrid topology may prove useful for a particular mutation of interest, however, a high throughput mutation analysis calls for a more general approach. In this work, we present an automated procedure to generate hybrid structures and topologies for the amino acid mutations in all commonly used force fields. The described software is compatible with the Gromacs simulation package. The mutation libraries are readily supported for five force fields, namely Amber99SB, Amber99SB*-ILDN, OPLS-AA/L, Charmm22*, and Charmm36. PMID:25487359

  5. Automated Glioblastoma Segmentation Based on a Multiparametric Structured Unsupervised Classification

    PubMed Central

    Juan-Albarracín, Javier; Fuster-Garcia, Elies; Manjón, José V.; Robles, Montserrat; Aparici, F.; Martí-Bonmatí, L.; García-Gómez, Juan M.

    2015-01-01

    Automatic brain tumour segmentation has become a key component for the future of brain tumour treatment. Currently, most of brain tumour segmentation approaches arise from the supervised learning standpoint, which requires a labelled training dataset from which to infer the models of the classes. The performance of these models is directly determined by the size and quality of the training corpus, whose retrieval becomes a tedious and time-consuming task. On the other hand, unsupervised approaches avoid these limitations but often do not reach comparable results than the supervised methods. In this sense, we propose an automated unsupervised method for brain tumour segmentation based on anatomical Magnetic Resonance (MR) images. Four unsupervised classification algorithms, grouped by their structured or non-structured condition, were evaluated within our pipeline. Considering the non-structured algorithms, we evaluated K-means, Fuzzy K-means and Gaussian Mixture Model (GMM), whereas as structured classification algorithms we evaluated Gaussian Hidden Markov Random Field (GHMRF). An automated postprocess based on a statistical approach supported by tissue probability maps is proposed to automatically identify the tumour classes after the segmentations. We evaluated our brain tumour segmentation method with the public BRAin Tumor Segmentation (BRATS) 2013 Test and Leaderboard datasets. Our approach based on the GMM model improves the results obtained by most of the supervised methods evaluated with the Leaderboard set and reaches the second position in the ranking. Our variant based on the GHMRF achieves the first position in the Test ranking of the unsupervised approaches and the seventh position in the general Test ranking, which confirms the method as a viable alternative for brain tumour segmentation. PMID:25978453

  6. Automated glioblastoma segmentation based on a multiparametric structured unsupervised classification.

    PubMed

    Juan-Albarracín, Javier; Fuster-Garcia, Elies; Manjón, José V; Robles, Montserrat; Aparici, F; Martí-Bonmatí, L; García-Gómez, Juan M

    2015-01-01

    Automatic brain tumour segmentation has become a key component for the future of brain tumour treatment. Currently, most of brain tumour segmentation approaches arise from the supervised learning standpoint, which requires a labelled training dataset from which to infer the models of the classes. The performance of these models is directly determined by the size and quality of the training corpus, whose retrieval becomes a tedious and time-consuming task. On the other hand, unsupervised approaches avoid these limitations but often do not reach comparable results than the supervised methods. In this sense, we propose an automated unsupervised method for brain tumour segmentation based on anatomical Magnetic Resonance (MR) images. Four unsupervised classification algorithms, grouped by their structured or non-structured condition, were evaluated within our pipeline. Considering the non-structured algorithms, we evaluated K-means, Fuzzy K-means and Gaussian Mixture Model (GMM), whereas as structured classification algorithms we evaluated Gaussian Hidden Markov Random Field (GHMRF). An automated postprocess based on a statistical approach supported by tissue probability maps is proposed to automatically identify the tumour classes after the segmentations. We evaluated our brain tumour segmentation method with the public BRAin Tumor Segmentation (BRATS) 2013 Test and Leaderboard datasets. Our approach based on the GMM model improves the results obtained by most of the supervised methods evaluated with the Leaderboard set and reaches the second position in the ranking. Our variant based on the GHMRF achieves the first position in the Test ranking of the unsupervised approaches and the seventh position in the general Test ranking, which confirms the method as a viable alternative for brain tumour segmentation.

  7. Stratigraphic controls on lateral variations in the structural style of northeastern Brooks Range, Arctic National Wildlife Refuge, Alaska

    SciTech Connect

    Wallace, W.K.; Hanks, C.L.

    1988-01-01

    The structural style of the range-front region of the northeastern Brooks Range in Arctic National Wildlife Refuge (ANWR) is strongly controlled by (1) the existence of detachment horizons in both pre-Mississippian rocks and the unconformably overlying Mississippian to Lower Cretaceous cover sequence, and (2) lithology and structural competency of the pre-Mississippian rocks. These variables strongly influence lateral changes in structural style. The Brooks Range of northwestern ANWR is dominated by a series of narrow linear anticlinoria, whereas in northeastern ANWR the Brooks Range is characterized by only two broad and strongly arcuate anticlinoria. In both areas, the anticlinoria are controlled by the geometry of a duplex bounded by a floor thrust in pre-Mississippian rocks and a roof thrust in the Kayak Shale, near the base of the cover sequence. In the west, where the pre-Mississippian partially consists of structurally competent carbonates, each anticlinorium marks a single horse in the duplex. However, in the east, pre-Mississippian rocks are relatively incompetent and each anticlinorium is cored by multiple horses. In the west, shortening above the roof thrust is by detachment folding, except where the shale detachment horizon is depositionally absent. In contrast, in eastern ANWR shortening above the roof thrust is by major thrust duplication of the entire cover sequence, perhaps due to lithology and thickness changes within the detachment horizon.

  8. Stratigraphic controls on lateral variations in the structural style of northeastern Brooks range, Arctic National Wildlife Refuge, Alaska

    SciTech Connect

    Wallace, W.K.; Hanks, C.L.

    1988-02-01

    The structural style of the range-front region of the northeastern Brooks Range in Arctic National Wildlife Refuge (ANWR) is strongly controlled by (1) the existence of detachment horizons in both pre-Mississippian rocks and the unconformably overlying Mississippian to Lower Cretaceous cover sequence, and (2) lithology and structural competency of the pre-Mississippian rocks. These variables strongly influence lateral changes in structural style. The Brooks Range of northwestern ANWR is dominated by a series of narrow linear anticlinoria, whereas in northeastern ANWR the Brooks Range is characterized by only two broad and strongly arcuate anticlinoria. In both areas, the anticlinoria are controlled by the geometry of a duplex bounded by a floor thrust in pre-Mississippian rocks and a roof thrust in the Kayak Shale, near the base of the cover sequence. In the west, where the pre-Mississippian partially consists of structurally competent carbonates, each anticlinorium marks a single horse in the duplex. However, in the east, pre-Mississippian rocks are relatively incompetent and each anticlinorium is cored by multiple horses. In the west, shortening above the roof thrust is by detachment folding, except where the shale detachment horizon is depositionally absent. In contrast, in eastern ANWR shortening above the roof thrust is by major thrust duplication of the entire cover sequence, perhaps due to lithology and thickness changes within the detachment horizon. A Devonian batholith marks the boundary between the eastern and western structural provinces. The thrust-controlled range front of eastern ANWR extends north of the batholith, suggesting that the batholith itself may be underlain by a thrust fault.

  9. Automated optimum design of wing structures. Deterministic and probabilistic approaches

    NASA Technical Reports Server (NTRS)

    Rao, S. S.

    1982-01-01

    The automated optimum design of airplane wing structures subjected to multiple behavior constraints is described. The structural mass of the wing is considered the objective function. The maximum stress, wing tip deflection, root angle of attack, and flutter velocity during the pull up maneuver (static load), the natural frequencies of the wing structure, and the stresses induced in the wing structure due to landing and gust loads are suitably constrained. Both deterministic and probabilistic approaches are used for finding the stresses induced in the airplane wing structure due to landing and gust loads. A wing design is represented by a uniform beam with a cross section in the form of a hollow symmetric double wedge. The airfoil thickness and chord length are the design variables, and a graphical procedure is used to find the optimum solutions. A supersonic wing design is represented by finite elements. The thicknesses of the skin and the web and the cross sectional areas of the flanges are the design variables, and nonlinear programming techniques are used to find the optimum solution.

  10. Semi-Automated Discovery of Application Session Structure

    SciTech Connect

    Kannan, J.; Jung, J.; Paxson, V.; Koksal, C.

    2006-09-07

    While the problem of analyzing network traffic at the granularity of individual connections has seen considerable previous work and tool development, understanding traffic at a higher level---the structure of user-initiated sessions comprised of groups of related connections---remains much less explored. Some types of session structure, such as the coupling between an FTP control connection and the data connections it spawns, have prespecified forms, though the specifications do not guarantee how the forms appear in practice. Other types of sessions, such as a user reading email with a browser, only manifest empirically. Still other sessions might exist without us even knowing of their presence, such as a botnet zombie receiving instructions from its master and proceeding in turn to carry them out. We present algorithms rooted in the statistics of Poisson processes that can mine a large corpus of network connection logs to extract the apparent structure of application sessions embedded in the connections. Our methods are semi-automated in that we aim to present an analyst with high-quality information (expressed as regular expressions) reflecting different possible abstractions of an application's session structure. We develop and test our methods using traces from a large Internet site, finding diversity in the number of applications that manifest, their different session structures, and the presence of abnormal behavior. Our work has applications to traffic characterization and monitoring, source models for synthesizing network traffic, and anomaly detection.

  11. Stratigraphic and structural framework of ellesmerian and older sequences in Sadlerochit and Shublik Mountains, Arctic National Wildlife Refuge (ANWR), northeastern Alaska

    SciTech Connect

    Robinson, M.S.; Decker, J.; Clough, J.G.; Dillon, J.T.

    1988-01-01

    Detailed geological mapping (1:25,000 scale) and stratigraphic reconstructions in the Sadlerochit and Shublik Mountains of northeastern Alaska, immediately south of the ANWR coastal plain, indicate a compressive structural province dominated by major thrust-ramp-related anticlinal uplifts. The Katakturuk Dolomite, a Proterozoic sequence, has been subdivided into 15 lithostratigraphic units that can be traced the entire length of both the Sadlerochit and Shublik Mountains. Overlying the Katakturuk Dolomite in these ranges in the Middle Devonian to Cambrian or older Nanook Limestone. In the Early Mississippian a major erosional event produced the pre-Mississippian unconformity upon which a Mississippian through Triassic sequence was deposited: Kayak Shale; Lisburne Group carbonates; and Sadlerochit Group clastic rocks. In the northern Sadlerochit Mountains, basal units of the Mississippian Alapah Limestone lie on the pre-Mississippian unconformity with no intervening Kayak Shale. The basal Alapah contains lithologies derived from the rock units on which it rests, indicating that the contact between the Alapah and the underlying units is depositional.

  12. Stratigraphic and structural framework of Ellesmerian and older sequences in Sadlerochit and Shublik Mountains, Arctic National Wildlife Refuge (ANWR), northeastern Alaska

    SciTech Connect

    Robinson, M.S.; Decker, J.; Clough, J.G.; Dillon, J.T.; Wallace, W.K.; Crowder, K.; Watts, K. )

    1988-02-01

    Detailed geological mapping (1:25,000 scale) and stratigraphic reconstructions in the Sadlerochit and Shublik Mountains of northeastern Alaska, immediately south of the ANWR coastal plain, indicate a compressive structural province dominated by major thrust-ramp-related anticlinal uplifts. The Katakturuk Dolomite, a Proterozoic sequence, has been subdivided into 15 lithostratigraphic units that can be traced the entire length of both the Sadlerochit and Shublik Mountains. Overlying the Katakturuk Dolomite in these ranges is the Middle Devonian to Cambrian or older Nanook Limestone. In the Early Mississippian a major erosional event produced the pre-Mississippian unconformity upon which a Mississippian through Triassic sequence was deposited: (A) Kayak Shale; (B) Lisburne Group carbonates; and (C) Sadlerochit Group clastic rocks. In the northern Sadlerochit Mountains, basal units of the Mississippian Alapah Limestone lie on the pre-Mississippian unconformity with no intervening Kayak Shale. The basal Alapah contains lithologies derived from the rocks units on which it rests, indicating that the contact between the Alapah and the underlying units is depositional. A regional decollement, localized along the pre-Mississippian unconformity in the Kayak Shale, is not a significant detachment surface north of the Shublik Mountains because the Kayak Shale is depositionally discontinuous and thin in the Sadlerochit Mountains.

  13. Latest Quaternary structural and stratigraphic controls on continental shelf morphology along a transpressive transform margin, Santa Barbara Channel, California

    NASA Astrophysics Data System (ADS)

    Johnson, S. Y.; Hartwell, S. R.; Sorlien, C. C.; Dartnell, P.; Ritchie, A.

    2016-12-01

    The Santa Barbara mainland continental shelf can be divided into three domains, (from SE to NW) bounded by the blind Oak Ridge and Pitas Point thrust fault systems. (1) South of and in the hanging wall of the blind, south-dipping Oak Ridge fault, the broad (as wide as 17 km), gently dipping Oxnard shelf has a convex-upward shape resulting from thick, deltaic sediment fill. (2) The 5- to 8-km-wide Ventura basin obliquely crosses the shelf and forms an asymmetric trough also filled by thick deltaic sediment. The basin lies between and in the footwalls of the Oak Ridge fault to the south and the blind, north-dipping Pitas Point fault system to the north. (3) The 4- to 7-km-wide central and western Santa Barbara shelf is located north of and in the hanging wall of the Pitas Point fault system. This fault system extends for about 105 km across the shelf and slope from Pitas Point to Point Conception. Numerous discontinuous folds and faults characterize the structurally complex hanging wall, and the concave-up shape of the shelf results from uplift, folding, limited sediment supply, marine erosion, and resulting lack of sediment cover. Two possible segment boundaries (the south strand of the Santa Ynez fault and a structural discontinuity a few km west of Coal Oil Point) coincide with significant shelfbreak submarine landslides. Ages of folded strata and the shelfbreak can be derived from correlation with sea-level curves, allowing estimates of uplift and deformation rates. Post-LGM slip rates on the offshore Oak Ridge fault are about 0.65 to 0.71 mm/yr. Slip rates on the Pitas Point fault system are a minimum of 2.1 to 2.4 mm/yr, and decrease to the west due largely to diminished hanging-wall faulting and folding. Given hanging-wall structural complexity, across-strike (north-south) deformation rates should not be extrapolated from the offshore to the onshore, and along-strike rates should only be extrapolated on the basis of detailed mapping.

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

    USGS Publications Warehouse

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

    1980-01-01

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

  15. An automated approach to network features of protein structure ensembles

    PubMed Central

    Bhattacharyya, Moitrayee; Bhat, Chanda R; Vishveshwara, Saraswathi

    2013-01-01

    Network theory applied to protein structures provides insights into numerous problems of biological relevance. The explosion in structural data available from PDB and simulations establishes a need to introduce a standalone-efficient program that assembles network concepts/parameters under one hood in an automated manner. Herein, we discuss the development/application of an exhaustive, user-friendly, standalone program package named PSN-Ensemble, which can handle structural ensembles generated through molecular dynamics (MD) simulation/NMR studies or from multiple X-ray structures. The novelty in network construction lies in the explicit consideration of side-chain interactions among amino acids. The program evaluates network parameters dealing with topological organization and long-range allosteric communication. The introduction of a flexible weighing scheme in terms of residue pairwise cross-correlation/interaction energy in PSN-Ensemble brings in dynamical/chemical knowledge into the network representation. Also, the results are mapped on a graphical display of the structure, allowing an easy access of network analysis to a general biological community. The potential of PSN-Ensemble toward examining structural ensemble is exemplified using MD trajectories of an ubiquitin-conjugating enzyme (UbcH5b). Furthermore, insights derived from network parameters evaluated using PSN-Ensemble for single-static structures of active/inactive states of β2-adrenergic receptor and the ternary tRNA complexes of tyrosyl tRNA synthetases (from organisms across kingdoms) are discussed. PSN-Ensemble is freely available from http://vishgraph.mbu.iisc.ernet.in/PSN-Ensemble/psn_index.html. PMID:23934896

  16. The subsurface structure and stratigraphic architecture of rift-related units in the Lishu Depression of the Songliao Basin, China

    NASA Astrophysics Data System (ADS)

    Wang, Hongyu; Fan, Tailiang; Wu, Yue

    2015-03-01

    from retrogradational, to progradational, to aggradational. Identification of sub-structural units and interpretation of their genetic relationships helps clarify basin evolution, and thus serves larger-scale continental basin analysis.

  17. Development of a machine vision system for automated structural assembly

    NASA Technical Reports Server (NTRS)

    Sydow, P. Daniel; Cooper, Eric G.

    1992-01-01

    Research is being conducted at the LaRC to develop a telerobotic assembly system designed to construct large space truss structures. This research program was initiated within the past several years, and a ground-based test-bed was developed to evaluate and expand the state of the art. Test-bed operations currently use predetermined ('taught') points for truss structural assembly. Total dependence on the use of taught points for joint receptacle capture and strut installation is neither robust nor reliable enough for space operations. Therefore, a machine vision sensor guidance system is being developed to locate and guide the robot to a passive target mounted on the truss joint receptacle. The vision system hardware includes a miniature video camera, passive targets mounted on the joint receptacles, target illumination hardware, and an image processing system. Discrimination of the target from background clutter is accomplished through standard digital processing techniques. Once the target is identified, a pose estimation algorithm is invoked to determine the location, in three-dimensional space, of the target relative to the robots end-effector. Preliminary test results of the vision system in the Automated Structural Assembly Laboratory with a range of lighting and background conditions indicate that it is fully capable of successfully identifying joint receptacle targets throughout the required operational range. Controlled optical bench test results indicate that the system can also provide the pose estimation accuracy to define the target position.

  18. Automated segmentation of tissue structures in optical coherence tomography data

    NASA Astrophysics Data System (ADS)

    Gasca, Fernando; Ramrath, Lukas; Huettmann, Gereon; Schweikard, Achim

    2009-05-01

    Segmentation of optical coherence tomography (OCT) images provides useful information, especially in medical imaging applications. Because OCT images are subject to speckle noise, the identification of structures is complicated. Addressing this issue, two methods for the automated segmentation of arbitrary structures in OCT images are proposed. The methods perform a seeded region growing, applying a model-based analysis of OCT A-scans for the seed's acquisition. The segmentation therefore avoids any user-intervention dependency. The first region-growing algorithm uses an adaptive neighborhood homogeneity criterion based on a model of an OCT intensity course in tissue and a model of speckle noise corruption. It can be applied to an unfiltered OCT image. The second performs region growing on a filtered OCT image applying the local median as a measure for homogeneity in the region. Performance is compared through the quantitative evaluation of artificial data, showing the capabilities of both in terms of structures detected and leakage. The proposed methods were tested on real OCT data in different scenarios and showed promising results for their application in OCT imaging.

  19. Automated segmentation of tissue structures in optical coherence tomography data.

    PubMed

    Gasca, Fernando; Ramrath, Lukas; Huettmann, Gereon; Schweikard, Achim

    2009-01-01

    Segmentation of optical coherence tomography (OCT) images provides useful information, especially in medical imaging applications. Because OCT images are subject to speckle noise, the identification of structures is complicated. Addressing this issue, two methods for the automated segmentation of arbitrary structures in OCT images are proposed. The methods perform a seeded region growing, applying a model-based analysis of OCT A-scans for the seed's acquisition. The segmentation therefore avoids any user-intervention dependency. The first region-growing algorithm uses an adaptive neighborhood homogeneity criterion based on a model of an OCT intensity course in tissue and a model of speckle noise corruption. It can be applied to an unfiltered OCT image. The second performs region growing on a filtered OCT image applying the local median as a measure for homogeneity in the region. Performance is compared through the quantitative evaluation of artificial data, showing the capabilities of both in terms of structures detected and leakage. The proposed methods were tested on real OCT data in different scenarios and showed promising results for their application in OCT imaging.

  20. Towards an automated analysis of bacterial peptidoglycan structure.

    PubMed

    Bern, Marshall; Beniston, Richard; Mesnage, Stéphane

    2017-01-01

    Peptidoglycan (PG) is an essential component of the bacterial cell envelope. This macromolecule consists of glycan chains alternating N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides containing nonstandard amino acids. Structural analysis of PG usually involves enzymatic digestion of glycan strands and separation of disaccharide peptides by reversed-phase HPLC followed by collection of individual peaks for MALDI-TOF and/or tandem mass spectrometry. Here, we report a novel strategy using shotgun proteomics techniques for a systematic and unbiased structural analysis of PG using high-resolution mass spectrometry and automated analysis of HCD and ETD fragmentation spectra with the Byonic software. Using the PG of the nosocomial pathogen Clostridium difficile as a proof of concept, we show that this high-throughput approach allows the identification of all PG monomers and dimers previously described, leaving only disambiguation of 3-3 and 4-3 cross-linking as a manual step. Our analysis confirms previous findings that C. difficile peptidoglycans include mainly deacetylated N-acetylglucosamine residues and 3-3 cross-links. The analysis also revealed a number of low abundance muropeptides with peptide sequences not previously reported. Graphical Abstract The bacterial cell envelope includes plasma membrane, peptidoglycan, and surface layer. Peptidoglycan is unique to bacteria and the target of the most important antibiotics; here it is analyzed by mass spectrometry.

  1. Automated identification of elemental ions in macromolecular crystal structures

    SciTech Connect

    Echols, Nathaniel Morshed, Nader; Afonine, Pavel V.; McCoy, Airlie J.; Read, Randy J.; Terwilliger, Thomas C.; Adams, Paul D.

    2014-04-01

    The solvent-picking procedure in phenix.refine has been extended and combined with Phaser anomalous substructure completion and analysis of coordination geometry to identify and place elemental ions. Many macromolecular model-building and refinement programs can automatically place solvent atoms in electron density at moderate-to-high resolution. This process frequently builds water molecules in place of elemental ions, the identification of which must be performed manually. The solvent-picking algorithms in phenix.refine have been extended to build common ions based on an analysis of the chemical environment as well as physical properties such as occupancy, B factor and anomalous scattering. The method is most effective for heavier elements such as calcium and zinc, for which a majority of sites can be placed with few false positives in a diverse test set of structures. At atomic resolution, it is observed that it can also be possible to identify tightly bound sodium and magnesium ions. A number of challenges that contribute to the difficulty of completely automating the process of structure completion are discussed.

  2. Structural and Stratigraphic Evidence for Active Deformation and Tsunami Hazard within the Sumatran Accretionary Wedge West of Siberut using MegaTera Seismic and Bathymetric data

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

    As part of the MegaTera (Mentawai Gap Tsunami Earthquake Risk Assessment) project, twenty marine seismic lines totalling 970 km in length were collected across the active Sumatran accretionary wedge southwest of the island of Siberut. In combination with 6000 km2 of detailed (30 meter resolution) swath bathymetry collected during the experiment, these data provide structural and stratigraphic controls on the recent deformation of the wedge. The studied region lies directly outboard of the only portion of the Sumatran megathrust that has not ruptured during the cascade of great earthquakes that followed the December 26, 2004 event, and is therefore a candidate for a tsunami-generating earthquake in the near future. We identify three along-strike structural domains within the frontal fold-and-thrust belt, defined by the dominant vergence of the frontal folds, and separated by diffuse transverse structures. The northern domain is characterized by landward-vergent thrust faults and a wedge surface slope of 4-5°. The central domain exhibits seaward-vergent faults and a frontal thrust that breaks the surface at the topographic front. Marine fans sourced from mass wasting of oversteepened limbs of seaward vergent folds have accumulated outboard of the central domain. The southern domain exhibits both fault landward and seaward vergences in the frontal region and seaward-vergent faults in the higher wedge. The boundary between the steep and rugged frontal wedge and the flat and smooth higher-elevation wedge is located 30-40 km from the deformation front. Geomorphic features and seismic images of deformed young sediments indicate the existence of an out-of-sequence megasplay fault. We conclude that 1) structural fault-and-fold models in all domains are consistent with a basal decollement level located near the base of the pelagic sequence, above the top of the oceanic crust 2) megathrust ruptures could propagate directly to the trench surface along the central and southern

  3. Automated web service composition supporting conditional branch structures

    NASA Astrophysics Data System (ADS)

    Wang, Pengwei; Ding, Zhijun; Jiang, Changjun; Zhou, Mengchu

    2014-01-01

    The creation of value-added services by automatic composition of existing ones is gaining a significant momentum as the potential silver bullet in service-oriented architecture. However, service composition faces two aspects of difficulties. First, users' needs present such characteristics as diversity, uncertainty and personalisation; second, the existing services run in a real-world environment that is highly complex and dynamically changing. These difficulties may cause the emergence of nondeterministic choices in the process of service composition, which has gone beyond what the existing automated service composition techniques can handle. According to most of the existing methods, the process model of composite service includes sequence constructs only. This article presents a method to introduce conditional branch structures into the process model of composite service when needed, in order to satisfy users' diverse and personalised needs and adapt to the dynamic changes of real-world environment. UML activity diagrams are used to represent dependencies in composite service. Two types of user preferences are considered in this article, which have been ignored by the previous work and a simple programming language style expression is adopted to describe them. Two different algorithms are presented to deal with different situations. A real-life case is provided to illustrate the proposed concepts and methods.

  4. 12 CFR Appendix D to Part 360 - Sweep/Automated Credit Account File Structure

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 5 2014-01-01 2014-01-01 false Sweep/Automated Credit Account File Structure D.... Character (25). 12. SW_Sub_Acct_Identifier Sweep/Automated Credit Sub-Account IdentifierIf available, the.... • AI = Deposit Held in an affiliated depository institution. • FF = Federal Funds. • CP =...

  5. 12 CFR Appendix D to Part 360 - Sweep/Automated Credit Account File Structure

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 12 Banks and Banking 5 2013-01-01 2013-01-01 false Sweep/Automated Credit Account File Structure D.... Character (25). 12. SW_Sub_Acct_Identifier Sweep/Automated Credit Sub-Account IdentifierIf available, the.... • AI = Deposit Held in an affiliated depository institution. • FF = Federal Funds. • CP =...

  6. 12 CFR Appendix D to Part 360 - Sweep/Automated Credit Account File Structure

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 12 Banks and Banking 5 2012-01-01 2012-01-01 false Sweep/Automated Credit Account File Structure D.... Character (25). 12. SW_Sub_Acct_Identifier Sweep/Automated Credit Sub-Account IdentifierIf available, the.... • AI = Deposit Held in an affiliated depository institution. • FF = Federal Funds. • CP =...

  7. 12 CFR Appendix D to Part 360 - Sweep/Automated Credit Account File Structure

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 4 2010-01-01 2010-01-01 false Sweep/Automated Credit Account File Structure D.... Character (25). 12. SW_Sub_Acct_Identifier Sweep/Automated Credit Sub-Account IdentifierIf available, the.... • AI = Deposit Held in an affiliated depository institution. • FF = Federal Funds. • CP =...

  8. 12 CFR Appendix D to Part 360 - Sweep/Automated Credit Account File Structure

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 4 2011-01-01 2011-01-01 false Sweep/Automated Credit Account File Structure D.... Character (25). 12. SW_Sub_Acct_Identifier Sweep/Automated Credit Sub-Account IdentifierIf available, the.... • AI = Deposit Held in an affiliated depository institution. • FF = Federal Funds. • CP =...

  9. Software design for automated assembly of truss structures

    NASA Technical Reports Server (NTRS)

    Herstrom, Catherine L.; Grantham, Carolyn; Allen, Cheryl L.; Doggett, William R.; Will, Ralph W.

    1992-01-01

    Concern over the limited intravehicular activity time has increased the interest in performing in-space assembly and construction operations with automated robotic systems. A technique being considered at LaRC is a supervised-autonomy approach, which can be monitored by an Earth-based supervisor that intervenes only when the automated system encounters a problem. A test-bed to support evaluation of the hardware and software requirements for supervised-autonomy assembly methods was developed. This report describes the design of the software system necessary to support the assembly process. The software is hierarchical and supports both automated assembly operations and supervisor error-recovery procedures, including the capability to pause and reverse any operation. The software design serves as a model for the development of software for more sophisticated automated systems and as a test-bed for evaluation of new concepts and hardware components.

  10. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.

    PubMed

    Haas, Brian J; Salzberg, Steven L; Zhu, Wei; Pertea, Mihaela; Allen, Jonathan E; Orvis, Joshua; White, Owen; Buell, C Robin; Wortman, Jennifer R

    2008-01-11

    EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

  11. Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

    SciTech Connect

    Haas, B J; Salzberg, S L; Zhu, W; Pertea, M; Allen, J E; Orvis, J; White, O; Buell, C R; Wortman, J R

    2007-12-10

    EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

  12. Automated construction of lightweight, simple, field-erected structures

    NASA Technical Reports Server (NTRS)

    Leonard, R. S.

    1980-01-01

    The feasibility of automation of construction processes which could result in mobile construction robots is examined. The construction of a large photovoltaic power plant with a peak power output of 100 MW is demonstrated. The reasons to automate the construction process, a conventional construction scenario as the reference for evaluation, and a list of potential cost benefits using robots are presented. The technical feasibility of using robots to construct SPS ground stations is addressed.

  13. Stratigraphic response across a structurally dynamic shelf: The latest guadalupian composite sequence at Walnut Canyon, New Mexico, U.S.A

    USGS Publications Warehouse

    Rush, J.; Kerans, C.

    2010-01-01

    The uppermost Yates and Tansill formations (Late Permian), as exposed along Walnut Canyon in Carlsbad Caverns National Park, New Mexico, USA, provide a unique opportunity to document the depositional architecture of a progradational, oversteepened, and mechanically failure-prone carbonate platform. Detailed facies mapping permitted critical assessment of depositional processes operating along this structurally dynamic platform margin. At the shelf crest, thick (12 m), vertically stacked fenestral-pisolite-tepee complexes indicate a stable shoreline. Early lithification of sediments and extensive cementation fostered rapid vertical accretion and allowed the shelf crest to easily adjust to base-level oscillations by stepping landward, stepping seaward, or aggrading. This production imbalance-in combination with syndepositional brittle failure and down-to-the-basin tilting(< 5??)-generated 22 m of depositional relief as measured from nearly horizontal (< 2??) shelf-crest toplap to an outer-shelf downlap surface (< 1??). Mechanical failure of Capitan-equivalent back-reef strata is constrained by stratigraphic architecture, fracture properties, and a highly refined fusulinid biostratigraphic framework. Where fractures tip out, down-to-the-basin rotation is often observed with concurrent seaward thickening of overlying beds, indicating that such fractures functioned as a syndepositional hinge. A facies disjunction and horizontally juxtaposed fusulinid zonation were documented across an 80?? seaward-dipping dilational fracture filled with polymict breccia. An overlying damage zone consisting of spar-cemented fractures nested within silt-filled fractures illustrates periodic reactivation. Field relationships indicate that the dilational fracture approximates a paleoescarpment that resulted from catastrophic failure of the Capitan platform margin. Younger strata onlapped the paleoescarpment and gradually filled the reentrant. This mechanically compromised paleoescarpment

  14. A new third-order sequence stratigraphic framework applied to the Triassic of the Paraná Basin, Rio Grande do Sul, Brazil, based on structural, stratigraphic and paleontological data

    NASA Astrophysics Data System (ADS)

    Horn, B. L. D.; Melo, T. M.; Schultz, C. L.; Philipp, R. P.; Kloss, H. P.; Goldberg, K.

    2014-11-01

    The Santacruzodon assemblage zone was originally defined as a vertebrate fossil assemblage composed basically of non-mammalian cynodonts found in Santa Cruz do Sul and Venâncio Aires municipalities in Southern Brazil. This assemblage zone was positioned at the top of the Sequence I, in the Triassic Santa Maria Supersequence, Paraná Basin. However, the Santacruzodon assemblage zone does not occur across the entire area of the Santa Maria Supersequence. Based on new paleontological, structural and sedimentological data, we propose the existence of a new third-order sequence (Santa Cruz Sequence) between Sequences I and II in the Santa Maria Supersequence. Satellite image analysis was used to identify regional, NW- and NE-oriented lineaments that limit the occurrence zone. Outcrop data allowed the identification of a regional, angular unconformity that bounds the new sequence. The faunal content allowed the correlation of the new Santa Cruz Sequence with Madagascar's Isalo II fauna, corresponding to the Ladinian (Middle Triassic). New names were suggested for the sequences in the Santa Maria Supersequence, since the Santa Cruz Sequence was deposited between the former Sequences I and II. This unit was deposited or preserved exclusively on the hanging wall of normal faults, being absent from the adjacent structural blocks.

  15. Towards fully automated structure-based function prediction in structural genomics: a case study.

    PubMed

    Watson, James D; Sanderson, Steve; Ezersky, Alexandra; Savchenko, Alexei; Edwards, Aled; Orengo, Christine; Joachimiak, Andrzej; Laskowski, Roman A; Thornton, Janet M

    2007-04-13

    As the global Structural Genomics projects have picked up pace, the number of structures annotated in the Protein Data Bank as hypothetical protein or unknown function has grown significantly. A major challenge now involves the development of computational methods to assign functions to these proteins accurately and automatically. As part of the Midwest Center for Structural Genomics (MCSG) we have developed a fully automated functional analysis server, ProFunc, which performs a battery of analyses on a submitted structure. The analyses combine a number of sequence-based and structure-based methods to identify functional clues. After the first stage of the Protein Structure Initiative (PSI), we review the success of the pipeline and the importance of structure-based function prediction. As a dataset, we have chosen all structures solved by the MCSG during the 5 years of the first PSI. Our analysis suggests that two of the structure-based methods are particularly successful and provide examples of local similarity that is difficult to identify using current sequence-based methods. No one method is successful in all cases, so, through the use of a number of complementary sequence and structural approaches, the ProFunc server increases the chances that at least one method will find a significant hit that can help elucidate function. Manual assessment of the results is a time-consuming process and subject to individual interpretation and human error. We present a method based on the Gene Ontology (GO) schema using GO-slims that can allow the automated assessment of hits with a success rate approaching that of expert manual assessment.

  16. Integration of seismic-reflection and well data to assess the potential impact of stratigraphic and structural features on sustainable water supply from the Floridan aquifer system, Broward County, Florida

    USGS Publications Warehouse

    Cunningham, Kevin J.

    2014-01-01

    The U.S. Geological Survey and Broward County water managers commenced a 3.5-year cooperative study in July 2012 to refine the geologic and hydrogeologic framework of the Floridan aquifer system (FAS) in Broward County. A lack of advanced stratigraphic knowledge of the physical system and structural geologic anomalies (faults and fractures originating from tectonics and karst-collapse structures) within the FAS pose a risk to the sustainable management of the resource. The principal objective of the study is to better define the regional stratigraphic and structural setting of the FAS in Broward County. The objective will be achieved through the acquisition, processing, and interpretation of new seismic-reflection data along several canals in Broward County. The interpretation includes integration of the new seismic-reflection data with existing seismic-reflection profiles along Hillsboro Canal in Broward County and within northeast Miami-Dade County, as well as with data from nearby FAS wellbores. The scope of the study includes mapping the geologic, hydrogeologic, and seismic-reflection framework of the FAS, and identifying stratigraphic and structural characteristics that could either facilitate or preclude the sustainable use of the FAS as an alternate water supply or a treated effluent repository. In addition, the investigation offers an opportunity to: (1) improve existing groundwater flow models, (2) enhance the understanding of the sensitivity of the groundwater system to well-field development and upconing of saline fluids, and (3) support site selection for future FAS projects, such as Class I wells that would inject treated effluent into the deep Boulder Zone.

  17. Concurrent combined verification: reducing false positives in automated NMR structure verification through the evaluation of multiple challenge control structures.

    PubMed

    Golotvin, Sergey S; Pol, Rostislav; Sasaki, Ryan R; Nikitina, Asya; Keyes, Philip

    2012-06-01

    Automated structure verification using (1)H NMR data or a combination of (1)H and heteronuclear single-quantum correlation (HSQC) data is gaining more interest as a routine application for qualitative evaluation of large compound libraries produced by synthetic chemistry. The goal of this automated software method is to identify a manageable subset of compounds and data that require human review. In practice, the automated method will flag structure and data combinations that exhibit some inconsistency (i.e. strange chemical shifts, conflicts in multiplicity, or overestimated and underestimated integration values) and validate those that appear consistent. One drawback of this approach is that no automated system can guarantee that all passing structures are indeed correct structures. The major reason for this is that approaches using only (1)H or even (1)H and HSQC spectra often do not provide sufficient information to properly distinguish between similar structures. Therefore, current implementations of automated structure verification systems allow, in principle, false positive results. Presented in this work is a method that greatly reduces the probability of an automated validation system passing incorrect structures (i.e. false positives). This novel method was applied to automatically validate 127 non-proprietary compounds from several commercial sources. Presented also is the impact of this approach on false positive and false negative results. Copyright © 2012 John Wiley & Sons, Ltd.

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

    USGS Publications Warehouse

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

    2002-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Buatois, Luis A.; Mángano, M. Gabriela; Alissa, Abdulrahman; Carr, Timothy R.

    2002-09-01

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

  20. STUDY OF ALUMINA CRYSTAL STRUCTURES (AUTOMATION OF THE VERNEUIL PROCESS).

    DTIC Science & Technology

    A careful analysis of the basic mechanisms of the Verneuil process led to a methodical study of the many parameters associated with it. Among these...powder feed rate. A completely automated Verneuil apparatus, incorporating this and other control systems, was designed and constructed to study crystal

  1. Instrumentation Automation for Concrete Structures: Report 2, Automation Hardware and Retrofitting Techniques, and Report 3, Available Data Collection and Reduction Software

    DTIC Science & Technology

    1987-06-01

    US-CE-CProperty ot the United States Government REPAIR, EVALUATION, MAINTENANCE, AND REHABILITATION RESEARCH PROGRAM TECHNICAL REPORT REMR-CS-5...INSTRUMENTATION AUTOMATION FOR CONCRETE STRUCTURES Report 2 AUTOMATION HARDWARE AND RETROFITTING TECHNIQUES by Aubrey Keeter, Byron Stonecypher...Vicksburg, Mississippi 39180-0631 The following two letters used as part of the number designating technical reports of research published under the Repair

  2. Exploring representations of protein structure for automated remote homology detection and mapping of protein structure space

    PubMed Central

    2014-01-01

    Background Due to rapid sequencing of genomes, there are now millions of deposited protein sequences with no known function. Fast sequence-based comparisons allow detecting close homologs for a protein of interest to transfer functional information from the homologs to the given protein. Sequence-based comparison cannot detect remote homologs, in which evolution has adjusted the sequence while largely preserving structure. Structure-based comparisons can detect remote homologs but most methods for doing so are too expensive to apply at a large scale over structural databases of proteins. Recently, fragment-based structural representations have been proposed that allow fast detection of remote homologs with reasonable accuracy. These representations have also been used to obtain linearly-reducible maps of protein structure space. It has been shown, as additionally supported from analysis in this paper that such maps preserve functional co-localization of the protein structure space. Methods Inspired by a recent application of the Latent Dirichlet Allocation (LDA) model for conducting structural comparisons of proteins, we propose higher-order LDA-obtained topic-based representations of protein structures to provide an alternative route for remote homology detection and organization of the protein structure space in few dimensions. Various techniques based on natural language processing are proposed and employed to aid the analysis of topics in the protein structure domain. Results We show that a topic-based representation is just as effective as a fragment-based one at automated detection of remote homologs and organization of protein structure space. We conduct a detailed analysis of the information content in the topic-based representation, showing that topics have semantic meaning. The fragment-based and topic-based representations are also shown to allow prediction of superfamily membership. Conclusions This work opens exciting venues in designing novel

  3. Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER

    PubMed Central

    Smart, Oliver S.; Womack, Thomas O.; Flensburg, Claus; Keller, Peter; Paciorek, Włodek; Sharff, Andrew; Vonrhein, Clemens; Bricogne, Gérard

    2012-01-01

    Maximum-likelihood X-ray macromolecular structure refinement in BUSTER has been extended with restraints facilitating the exploitation of structural similarity. The similarity can be between two or more chains within the structure being refined, thus favouring NCS, or to a distinct ‘target’ structure that remains fixed during refinement. The local structural similarity restraints (LSSR) approach considers all distances less than 5.5 Å between pairs of atoms in the chain to be restrained. For each, the difference from the distance between the corresponding atoms in the related chain is found. LSSR applies a restraint penalty on each difference. A functional form that reaches a plateau for large differences is used to avoid the restraints distorting parts of the structure that are not similar. Because LSSR are local, there is no need to separate out domains. Some restraint pruning is still necessary, but this has been automated. LSSR have been available to academic users of BUSTER since 2009 with the easy-to-use -autoncs and -­target target.pdb options. The use of LSSR is illustrated in the re-refinement of PDB entries 5rnt, where -target enables the correct ligand-binding structure to be found, and 1osg, where -autoncs contributes to the location of an additional copy of the cyclic peptide ligand. PMID:22505257

  4. Norwegian Offshore Stratigraphic Lexicon (NORLEX)

    NASA Astrophysics Data System (ADS)

    Gradstein, Felix M.; Hammer, Oyvind; Brunstad, Harald; Charnock, Mike; Hellem, Terje; Sigve Lervik, Kjell; Anthonissen, Erik

    2010-05-01

    The Norwegian Offshore Stratigraphic Lexicon (NORLEX) provides a relational stratigraphic database for the North Sea, Norwegian Sea, Barents Sea and Svalbard. Both regional lithostratigraphy and biostratigraphy are being substantially updated, following guidelines laid out in the International Stratigraphic Guide. The main body of information developed is available as a petroleum consortium (oracle-style) database, and the new lithostratigraphic definitions as a public domain (paper) document. NORLEX is presented as a browsing website via the internet at http://www.nhm.uio.no/norlex. Seismic cross-sections, core photographs, well logs, field outcrops, microfossil occurrences and other vital attributes are relationally cross-linked. In addition, there are menus for instantly finding updated formation and member tops or microfossil events in all wells, plus a map contouring routine for unit thicknesses and depths. Several new initiatives will expand data and user coverage: 1. Overhaul of Mesozoic stratigraphy, especially Triassic and Cretaceous, in the Barents Sea. 2. Coverage of East Greenland 3. Linkage to UK and Belgium and The Netherlands surface and subsurface stratigraphy 4. Creation of a Sequence Stratigraphic Framework for specific regions. 5. A national microfossil atlas to support zonations 6. Tight linkage to the basin datapacks in TimeScaleCreator Pro, as developed for Australia, New Zealand, Brasil, Gulf of Mexico, Canada and Russia. NORLEX may thus evolve to become STRATLEX, covering many basin regions.

  5. Automated frequency domain system identification of a large space structure

    NASA Technical Reports Server (NTRS)

    Yam, Y.; Bayard, D. S.; Hadaegh, F. Y.; Mettler, E.; Milman, M. H.

    1989-01-01

    This paper presents the development and experimental results of an automated on-orbit system identification method for large flexible spacecraft that yields estimated quantities to support on-line design and tuning of robust high performance control systems. The procedure consists of applying an input to the plant, obtaining an output, and then conducting nonparametric identification to yield the spectral estimate of the system transfer function. A parametric model is determined by curve fitting the spectral estimate to a rational transfer function. The identification method has been demonstrated experimentally on the Large Spacecraft Control Laboratory in JPL.

  6. Radioactive waste isolation in salt: peer review of the Texas Bureau of Economic Geology's report on the Petrographic, Stratigraphic, and Structural Evidence for Dissolution of Upper Permian Bedded Salt, Texas Panhandle

    SciTech Connect

    Fenster, D.F.; Anderson, R.Y.; Gonzales, S.; Baker, V.R.; Edgar, D.E.; Harrison, W.

    1984-08-01

    The following recommendations for improving the Texas Bureau of Economic Geology (TBEG) report entitled Petrographic, Stratigraphic, and Structural Evidence for Dissolution of Upper Permian Bedded Salt, Texas Panhandle have been abstracted from the body of this review report. The TBEG report should be resided to conform to one of the following alternatives: (1) If the report is intended to be a review or summary of previous work, it should contain more raw data, be edited to give equal treatment to all types of data, and include summary tables and additional figures. (2) If the report is intended to be a description and interpretation of petrographic evidence for salt dissolution, supported by collateral stratigraphic and structural evidence, the relevant indirect and direct data should become the focal point of the report. The following recommendations apply to one or both of the options listed above. (1) The text should differentiate more carefully between the data and inferences based on those data. (2) The authors should retain the qualifiers present in cited works. Statements in the report that are based on earlier papers are sometimes stronger than those in the papers themselves. (3) The next revision should present more complete data. (4) The authors should achieve a more balanced presentation of alternative hypotheses and interpretations. They could then discuss the relative merits of the alternative interpretations. (5) More attention should be given to clear exposition.

  7. Finite element based electrostatic-structural coupled analysis with automated mesh morphing

    SciTech Connect

    OWEN,STEVEN J.; ZHULIN,V.I.; OSTERGAARD,D.F.

    2000-02-29

    A co-simulation tool based on finite element principles has been developed to solve coupled electrostatic-structural problems. An automated mesh morphing algorithm has been employed to update the field mesh after structural deformation. The co-simulation tool has been successfully applied to the hysteric behavior of a MEMS switch.

  8. Guiding automated NMR structure determination using a global optimization metric, the NMR DP score

    PubMed Central

    Huang, Yuanpeng Janet; Mao, Binchen; Xu, Fei; Montelione, Gaetano

    2016-01-01

    ASDP is an automated NMR NOE assignment program. It uses a distinct bottom-up topology-constrained network anchoring approach for NOE interpretation, with 2D, 3D and/or 4D NOESY peak lists and resonance assignments as input, and generates unambiguous NOE constraints for iterative structure calculations. ASDP is designed to function interactively with various structure determination programs that use distance restraints to generate molecular models. In the CASD-NMR project, ASDP was tested and further developed using blinded NMR data, including resonance assignments, either raw or manually-curated (refined) NOESY peak list data, and in some cases 15N-1H residual dipolar coupling data. In these blinded tests, in which the reference structure was not available until after structures were generated, the fully-automated ASDP program performed very well on all targets using both the raw and refined NOESY peak list data. Improvements of ASDP relative to its predecessor program for automated NOESY peak assignments, AutoStructure, were driven by challenges provided by these CASD-NMR data. These algorithmic improvements include 1) using a global metric of structural accuracy, the Discriminating Power (DP) score, for guiding model selection during the iterative NOE interpretation process, and 2) identifying incorrect NOESY cross peak assignments caused by errors in the NMR resonance assignment list. These improvements provide a more robust automated NOESY analysis program, ASDP, with the unique capability of being utilized with alternative structure generation and refinement programs including CYANA, CNS, and/or Rosetta. PMID:26081575

  9. Aircraft wing structural design optimization based on automated finite element modelling and ground structure approach

    NASA Astrophysics Data System (ADS)

    Yang, Weizhu; Yue, Zhufeng; Li, Lei; Wang, Peiyan

    2016-01-01

    An optimization procedure combining an automated finite element modelling (AFEM) technique with a ground structure approach (GSA) is proposed for structural layout and sizing design of aircraft wings. The AFEM technique, based on CATIA VBA scripting and PCL programming, is used to generate models automatically considering the arrangement of inner systems. GSA is used for local structural topology optimization. The design procedure is applied to a high-aspect-ratio wing. The arrangement of the integral fuel tank, landing gear and control surfaces is considered. For the landing gear region, a non-conventional initial structural layout is adopted. The positions of components, the number of ribs and local topology in the wing box and landing gear region are optimized to obtain a minimum structural weight. Constraints include tank volume, strength, buckling and aeroelastic parameters. The results show that the combined approach leads to a greater weight saving, i.e. 26.5%, compared with three additional optimizations based on individual design approaches.

  10. Automated hexahedral meshing of anatomic structures using deformable registration.

    PubMed

    Grosland, Nicole M; Bafna, Ritesh; Magnotta, Vincent A

    2009-02-01

    This work introduces a novel method of automating the process of patient-specific finite element (FE) model development using a mapped mesh technique. The objective is to map a predefined mesh (template) of high quality directly onto a new bony surface (target) definition, thereby yielding a similar mesh with minimal user interaction. To bring the template mesh into correspondence with the target surface, a deformable registration technique based on the FE method has been adopted. The procedure has been made hierarchical allowing several levels of mesh refinement to be used, thus reducing the time required to achieve a solution. Our initial efforts have focused on the phalanx bones of the human hand. Mesh quality metrics, such as element volume and distortion were evaluated. Furthermore, the distance between the target surface and the final mapped mesh were measured. The results have satisfactorily proven the applicability of the proposed method.

  11. Texture analysis for automated classification of geologic structures

    USGS Publications Warehouse

    Shankar, V.; Rodriguez, J.J.; Gettings, M.E.

    2006-01-01

    Texture present in aeromagnetic anomaly images offers an abundance of useful geological information for discriminating between rock types, but current analysis of such images still relies on tedious, human interpretation. This study is believed to be the first effort to quantitatively assess the performance of texture-based digital image analysis for this geophysical exploration application. We computed several texture measures and determined the best subset using automated feature selection techniques. Pattern classification experiments measured the ability of various texture measures to automatically predict rock types. The classification accuracy was significantly better than a priori probability and prior weights-of-evidence results. The accuracy rates and choice of texture measures that minimize the error rate are reported. ?? 2006 IEEE.

  12. SOLVE and RESOLVE: automated structure solution, density modification and model building.

    PubMed

    Terwilliger, Thomas

    2004-01-01

    The software SOLVE and RESOLVE can carry out all the steps in macromolecular structure solution, from scaling and heavy-atom location through phasing, density modification and model-building in the MAD, SAD and MIR cases. SOLVE uses scoring scheme to convert the decision-making in macromolecular structure solution to an optimization problem. RESOLVE carries out the identification of NCS, density modification and automated model-building. The procedure is fully automated and can function at resolutions as low as 3 A.

  13. Development and verification testing of automation and robotics for assembly of space structures

    NASA Technical Reports Server (NTRS)

    Rhodes, Marvin D.; Will, Ralph W.; Quach, Cuong C.

    1993-01-01

    A program was initiated within the past several years to develop operational procedures for automated assembly of truss structures suitable for large-aperture antennas. The assembly operations require the use of a robotic manipulator and are based on the principle of supervised autonomy to minimize crew resources. A hardware testbed was established to support development and evaluation testing. A brute-force automation approach was used to develop the baseline assembly hardware and software techniques. As the system matured and an operation was proven, upgrades were incorprated and assessed against the baseline test results. This paper summarizes the developmental phases of the program, the results of several assembly tests, the current status, and a series of proposed developments for additional hardware and software control capability. No problems that would preclude automated in-space assembly of truss structures have been encountered. The current system was developed at a breadboard level and continued development at an enhanced level is warranted.

  14. Development and verification testing of automation and robotics for assembly of space structures

    NASA Technical Reports Server (NTRS)

    Rhodes, Marvin D.; Will, Ralph W.; Quach, Cuong C.

    1993-01-01

    A program was initiated within the past several years to develop operational procedures for automated assembly of truss structures suitable for large-aperture antennas. The assembly operations require the use of a robotic manipulator and are based on the principle of supervised autonomy to minimize crew resources. A hardware testbed was established to support development and evaluation testing. A brute-force automation approach was used to develop the baseline assembly hardware and software techniques. As the system matured and an operation was proven, upgrades were incorprated and assessed against the baseline test results. This paper summarizes the developmental phases of the program, the results of several assembly tests, the current status, and a series of proposed developments for additional hardware and software control capability. No problems that would preclude automated in-space assembly of truss structures have been encountered. The current system was developed at a breadboard level and continued development at an enhanced level is warranted.

  15. Blind testing of routine, fully automated determination of protein structures from NMR data

    PubMed Central

    Rosato, Antonio; Aramini, James M.; Arrowsmith, Cheryl; Bagaria, Anurag; Baker, David; Cavalli, Andrea; Doreleijers, Jurgen F.; Eletsky, Alexander; Giachetti, Andrea; Guerry, Paul; Gutmanas, Aleksandras; Güntert, Peter; He, Yunfen; Herrmann, Torsten; Huang, Yuanpeng J.; Jaravine, Victor; Jonker, Hendrik R.A.; Kennedy, Michael A.; Lange, Oliver F.; Liu, Gaohua; Malliavin, Thérèse E.; Mani, Rajeswari; Mao, Binchen; Montelione, Gaetano T.; Nilges, Michael; Rossi, Paolo; van der Schot, Gijs; Schwalbe, Harald; Szyperski, Thomas A.; Vendruscolo, Michele; Vernon, Robert; Vranken, Wim F.; de Vries, Sjoerd; Vuister, Geerten W.; Wu, Bin; Yang, Yunhuang; Bonvin, Alexandre M.J.J.

    2012-01-01

    SUMMARY The protocols currently used for protein structure determination by NMR depend on the determination of a large number of upper distance limits for proton-proton pairs. Typically, this task is performed manually by an experienced researcher rather than automatically by using a specific computer program. To assess whether it is indeed possible to generate in a fully automated manner NMR structures adequate for deposition in the Protein Data Bank, we gathered ten experimental datasets with unassigned NOESY peak lists for various proteins of unknown structure, computed structures for each of them using different, fully automatic programs, and compared the results to each other and to the manually solved reference structures that were not available at the time the data were provided. This constitutes a stringent “blind” assessment similar to the CASP and CAPRI initiatives. This study demonstrates the feasibility of routine, fully automated protein structure determination by NMR. PMID:22325772

  16. Automated Detection of Eruptive Structures for Solar Eruption Prediction

    NASA Astrophysics Data System (ADS)

    Georgoulis, Manolis K.

    2012-07-01

    The problem of data processing and assimilation for solar eruption prediction is, for contemporary solar physics, more pressing than the problem of data acquisition. Although critical solar data, such as the coronal magnetic field, are still not routinely available, space-based observatories deliver diverse, high-quality information at such a high rate that a manual or semi-manual processing becomes meaningless. We discuss automated data analysis methods and explain, using basic physics, why some of them are unlikely to advance eruption prediction. From this finding we also understand why solar eruption prediction is likely to remain inherently probabilistic. We discuss some promising eruption prediction measures and report on efforts to adapt them for use with high-resolution, high-cadence photospheric and coronal data delivered by the Solar Dynamics Observatory. Concluding, we touch on the problem of physical understanding and synthesis of different results: combining different measures inferred by different data sets is a yet-to-be-done exercise that, however, presents our best opportunity of realizing benefits in solar eruption prediction via a meaningful, targeted assimilation of solar data.

  17. An automated system for the study of ionospheric spatial structures

    NASA Astrophysics Data System (ADS)

    Belinskaya, I. V.; Boitman, O. N.; Vugmeister, B. O.; Vyborova, V. M.; Zakharov, V. N.; Laptev, V. A.; Mamchenko, M. S.; Potemkin, A. A.; Radionov, V. V.

    The system is designed for the study of the vertical distribution of electron density and the parameters of medium-scale ionospheric irregularities over the sounding site as well as the reconstruction of the spatial distribution of electron density within the range of up to 300 km from the sounding location. The system comprises an active central station as well as passive companion stations. The central station is equipped with the digital ionosonde ``Basis'', the measuring-and-computing complex IVK-2, and the receiver-recorder PRK-3M. The companion stations are equipped with receivers-recorders PRK-3. The automated comlex software system includes 14 subsystems. Data transfer between them is effected using magnetic disk data sets. The system is operated in both ionogram mode and Doppler shift and angle-of-arrival mode. Using data obtained in these two modes, the reconstruction of the spatial distribution of electron density in the region is carried out. Reconstruction is checked for accuracy using data from companion stations.

  18. Non-uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination

    PubMed Central

    Didenko, Tatiana; Proudfoot, Andrew; Dutta, Samit Kumar; Serrano, Pedro; Wüthrich, Kurt

    2015-01-01

    High-resolution structure determination of small proteins in solution is one of the big assets of NMR spectroscopy in structural biology. Improvements in efficiency of NMR structure determination by advances in NMR experiments and automation of data handling therefore attracts continued interest. Here, non-uniform sampling (NUS) of 3D heteronuclear-resolved [1H,1H]-NOESY data yielded two- to three-fold savings of instrument time for structure determinations of soluble proteins. With the 152-residue protein NP_372339.1 from Staphylococcus aureus and the 71-residue protein NP_346341.1 from Streptococcus pneumonia we show that high-quality structures can be obtained with NUS NMR data, which are equally well amenable to robust automated analysis as the corresponding uniformly sampled data. PMID:26227870

  19. Amazon Forest Structure from IKONOS Satellite Data and the Automated Characterization of Forest Canopy Properties

    Treesearch

    Michael Palace; Michael Keller; Gregory P. Asner; Stephen Hagen; Bobby . Braswell

    2008-01-01

    We developed an automated tree crown analysis algorithm using 1-m panchromatic IKONOS satellite images to examine forest canopy structure in the Brazilian Amazon. The algorithm was calibrated on the landscape level with tree geometry and forest stand data at the Fazenda Cauaxi (3.75◦ S, 48.37◦ W) in the eastern Amazon, and then compared with forest...

  20. Automated effective band structures for defective and mismatched supercells

    NASA Astrophysics Data System (ADS)

    Brommer, Peter; Quigley, David

    2014-12-01

    In plane-wave density functional theory codes, defects and incommensurate structures are usually represented in supercells. However, interpretation of E versus k band structures is most effective within the primitive cell, where comparison to ideal structures and spectroscopy experiments are most natural. Popescu and Zunger recently described a method to derive effective band structures (EBS) from supercell calculations in the context of random alloys. In this paper, we present bs_sc2pc, an implementation of this method in the CASTEP code, which generates an EBS using the structural data of the supercell and the underlying primitive cell with symmetry considerations handled automatically. We demonstrate the functionality of our implementation in three test cases illustrating the efficacy of this scheme for capturing the effect of vacancies, substitutions and lattice mismatch on effective primitive cell band structures.

  1. Automated effective band structures for defective and mismatched supercells.

    PubMed

    Brommer, Peter; Quigley, David

    2014-12-03

    In plane-wave density functional theory codes, defects and incommensurate structures are usually represented in supercells. However, interpretation of E versus k band structures is most effective within the primitive cell, where comparison to ideal structures and spectroscopy experiments are most natural. Popescu and Zunger recently described a method to derive effective band structures (EBS) from supercell calculations in the context of random alloys. In this paper, we present bs_sc2pc, an implementation of this method in the CASTEP code, which generates an EBS using the structural data of the supercell and the underlying primitive cell with symmetry considerations handled automatically. We demonstrate the functionality of our implementation in three test cases illustrating the efficacy of this scheme for capturing the effect of vacancies, substitutions and lattice mismatch on effective primitive cell band structures.

  2. Automated discovery of active motifs in multiple RNA secondary structures

    SciTech Connect

    Wang, J.T.L.; Chang, Chia-Yo; Shapiro, B.A.

    1996-12-31

    In this paper we present a method for discovering approximately common motifs (also known as active motifs) in multiple RNA secondary structures. The secondary structures can be represented as ordered trees (i.e., the order among siblings matters). Motifs in these trees are connected subgraphs that can differ in both substitutions and deletions/insertions. The proposed method consists of two steps: (1) find candidate motifs in a small sample of the secondary structures; (2) search all of the secondary structures to determine how frequently these motifs occur (within the allowed approximation) in the secondary structures. To reduce the running time, we develop two optimization heuristics based on sampling and pattern matching techniques. Experimental results obtained by running these algorithms on both generated data and RNA secondary structures show the good performance of the algorithms. To demonstrate the utility of our algorithms, we discuss their applications to conducting the phylogenetic study of RNA sequences obtained from GenBank.

  3. Automated Finite Element Modeling of Wing Structures for Shape Optimization

    NASA Technical Reports Server (NTRS)

    Harvey, Michael Stephen

    1993-01-01

    The displacement formulation of the finite element method is the most general and most widely used technique for structural analysis of airplane configurations. Modem structural synthesis techniques based on the finite element method have reached a certain maturity in recent years, and large airplane structures can now be optimized with respect to sizing type design variables for many load cases subject to a rich variety of constraints including stress, buckling, frequency, stiffness and aeroelastic constraints (Refs. 1-3). These structural synthesis capabilities use gradient based nonlinear programming techniques to search for improved designs. For these techniques to be practical a major improvement was required in computational cost of finite element analyses (needed repeatedly in the optimization process). Thus, associated with the progress in structural optimization, a new perspective of structural analysis has emerged, namely, structural analysis specialized for design optimization application, or.what is known as "design oriented structural analysis" (Ref. 4). This discipline includes approximation concepts and methods for obtaining behavior sensitivity information (Ref. 1), all needed to make the optimization of large structural systems (modeled by thousands of degrees of freedom and thousands of design variables) practical and cost effective.

  4. Automated Process Initialization of Laser Surface Structuring Processes by Inline Process Metrology

    NASA Astrophysics Data System (ADS)

    Schmitt, R.; Mallmann, G.; Winands, K.; Pothen, M.

    Laser micro machining as well as laser surface structuring are innovative manufacturing technologies with a wide range of machinable materials and a high level of flexibility. These techniques are characterized by different machine, workpiece and environmental parameters. The large amount of process dependencies lead however to a time consuming process initialization and a complex process control. Currently no automated solution exists to achieve material specific process parameters, nor does a sufficient inline process control exist to adapt processing parameters or strategies inline. Therefore a novel scanner based inline metrology solution and an automated process initialization strategy has been developed.

  5. Automated on-orbit frequency domain identification for large space structures

    NASA Technical Reports Server (NTRS)

    Bayard, D. S.; Hadaegh, F. Y.; Yam, Y.; Scheid, R. E.; Mettler, E.; Milman, M. H.

    1991-01-01

    Recent experiences in the field of flexible structure control in space have indicated a need for on-orbit system identification to support robust control redesign to avoid in-flight instabilities and maintain high spacecraft performance. This paper highlights an automated frequency domain system identification methodology recently developed to fulfill this need. The methodology is focused to support (1) the estimation of system quantities useful for robust control analysis and design; (2) experiment design tailored to performing system identification in a typically constrained on-orbit environment; and (3) the automation of operations to reduce 'human in the loop' requirements.

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

    NASA Astrophysics Data System (ADS)

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

    2017-07-01

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

  7. Automated Structure-Activity Relationship Mining: Connecting Chemical Structure to Biological Profiles.

    PubMed

    Wawer, Mathias J; Jaramillo, David E; Dančík, Vlado; Fass, Daniel M; Haggarty, Stephen J; Shamji, Alykhan F; Wagner, Bridget K; Schreiber, Stuart L; Clemons, Paul A

    2014-06-01

    Understanding the structure-activity relationships (SARs) of small molecules is important for developing probes and novel therapeutic agents in chemical biology and drug discovery. Increasingly, multiplexed small-molecule profiling assays allow simultaneous measurement of many biological response parameters for the same compound (e.g., expression levels for many genes or binding constants against many proteins). Although such methods promise to capture SARs with high granularity, few computational methods are available to support SAR analyses of high-dimensional compound activity profiles. Many of these methods are not generally applicable or reduce the activity space to scalar summary statistics before establishing SARs. In this article, we present a versatile computational method that automatically extracts interpretable SAR rules from high-dimensional profiling data. The rules connect chemical structural features of compounds to patterns in their biological activity profiles. We applied our method to data from novel cell-based gene-expression and imaging assays collected on more than 30,000 small molecules. Based on the rules identified for this data set, we prioritized groups of compounds for further study, including a novel set of putative histone deacetylase inhibitors. © 2014 Society for Laboratory Automation and Screening.

  8. MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes

    PubMed Central

    Stansfeld, Phillip J.; Goose, Joseph E.; Caffrey, Martin; Carpenter, Elisabeth P.; Parker, Joanne L.; Newstead, Simon; Sansom, Mark S.P.

    2015-01-01

    Summary There has been exponential growth in the number of membrane protein structures determined. Nevertheless, these structures are usually resolved in the absence of their lipid environment. Coarse-grained molecular dynamics (CGMD) simulations enable insertion of membrane proteins into explicit models of lipid bilayers. We have automated the CGMD methodology, enabling membrane protein structures to be identified upon their release into the PDB and embedded into a membrane. The simulations are analyzed for protein-lipid interactions, identifying lipid binding sites, and revealing local bilayer deformations plus molecular access pathways within the membrane. The coarse-grained models of membrane protein/bilayer complexes are transformed to atomistic resolution for further analysis and simulation. Using this automated simulation pipeline, we have analyzed a number of recently determined membrane protein structures to predict their locations within a membrane, their lipid/protein interactions, and the functional implications of an enhanced understanding of the local membrane environment of each protein. PMID:26073602

  9. Recent developments in automated structure elucidation of natural products.

    PubMed

    Steinbeck, Christoph

    2004-08-01

    Advancements in the field of Computer-Assisted Structure Elucidation (CASE) of Natural Products achieved in the past five years are discussed. This process starts with a dereplication procedure, supported by structure-spectrum databases. Both commercial and free products are available to support the procedure. A number of new programs,as well as advancements in existing ones, are presented. Finally, the option to validate the result by an independent procedure, a high quality ab initio quantum mechanical calculation, is discussed.

  10. Automated dynamic analytical model improvement for damped structures

    NASA Technical Reports Server (NTRS)

    Fuh, J. S.; Berman, A.

    1985-01-01

    A method is described to improve a linear nonproportionally damped analytical model of a structure. The procedure finds the smallest changes in the analytical model such that the improved model matches the measured modal parameters. Features of the method are: (1) ability to properly treat complex valued modal parameters of a damped system; (2) applicability to realistically large structural models; and (3) computationally efficiency without involving eigensolutions and inversion of a large matrix.

  11. Fully automated high-quality NMR structure determination of small (2)H-enriched proteins.

    PubMed

    Tang, Yuefeng; Schneider, William M; Shen, Yang; Raman, Srivatsan; Inouye, Masayori; Baker, David; Roth, Monica J; Montelione, Gaetano T

    2010-12-01

    Determination of high-quality small protein structures by nuclear magnetic resonance (NMR) methods generally requires acquisition and analysis of an extensive set of structural constraints. The process generally demands extensive backbone and sidechain resonance assignments, and weeks or even months of data collection and interpretation. Here we demonstrate rapid and high-quality protein NMR structure generation using CS-Rosetta with a perdeuterated protein sample made at a significantly reduced cost using new bacterial culture condensation methods. Our strategy provides the basis for a high-throughput approach for routine, rapid, high-quality structure determination of small proteins. As an example, we demonstrate the determination of a high-quality 3D structure of a small 8 kDa protein, E. coli cold shock protein A (CspA), using <4 days of data collection and fully automated data analysis methods together with CS-Rosetta. The resulting CspA structure is highly converged and in excellent agreement with the published crystal structure, with a backbone RMSD value of 0.5 Å, an all atom RMSD value of 1.2 Å to the crystal structure for well-defined regions, and RMSD value of 1.1 Å to crystal structure for core, non-solvent exposed sidechain atoms. Cross validation of the structure with (15)N- and (13)C-edited NOESY data obtained with a perdeuterated (15)N, (13)C-enriched (13)CH(3) methyl protonated CspA sample confirms that essentially all of these independently-interpreted NOE-based constraints are already satisfied in each of the 10 CS-Rosetta structures. By these criteria, the CS-Rosetta structure generated by fully automated analysis of data for a perdeuterated sample provides an accurate structure of CspA. This represents a general approach for rapid, automated structure determination of small proteins by NMR.

  12. RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data.

    PubMed

    Incarnato, Danny; Neri, Francesco; Anselmi, Francesca; Oliviero, Salvatore

    2016-02-01

    The rapidly increasing number of discovered non-coding RNAs makes the understanding of their structure a key feature toward a deeper comprehension of gene expression regulation. Various enzymatic- and chemically- based approaches have been recently developed to allow whole-genome studies of RNA secondary structures. Several methods have been recently presented that allow high-throughput RNA structure probing (CIRS-seq, Structure-seq, SHAPE-seq, PARS, etc.) and unbiased structural inference of residues within RNAs in their native conformation. We here present an analysis toolkit, named RNA Structure Framework (RSF), which allows fast and fully-automated analysis of high-throughput structure probing data, from data pre-processing to whole-transcriptome RNA structure inference. RSF is written in Perl and is freely available under the GPLv3 license from http://rsf.hugef-research.org. salvatore.oliviero@hugef-torino.org Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  13. From bacterial to human dihydrouridine synthase: automated structure determination

    SciTech Connect

    Whelan, Fiona Jenkins, Huw T.; Griffiths, Samuel C.; Byrne, Robert T.; Dodson, Eleanor J.; Antson, Alfred A.

    2015-06-30

    The crystal structure of a human dihydrouridine synthase, an enzyme associated with lung cancer, with 18% sequence identity to a T. maritima enzyme, has been determined at 1.9 Å resolution by molecular replacement after extensive molecular remodelling of the template. The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1–340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by phenix.mr-rosetta starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain–domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer.

  14. Reduced complexity structural modeling for automated airframe synthesis

    NASA Technical Reports Server (NTRS)

    Hajela, Prabhat

    1987-01-01

    A procedure is developed for the optimum sizing of wing structures based on representing the built-up finite element assembly of the structure by equivalent beam models. The reduced-order beam models are computationally less demanding in an optimum design environment which dictates repetitive analysis of several trial designs. The design procedure is implemented in a computer program requiring geometry and loading information to create the wing finite element model and its equivalent beam model, and providing a rapid estimate of the optimum weight obtained from a fully stressed design approach applied to the beam. The synthesis procedure is demonstrated for representative conventional-cantilever and joined wing configurations.

  15. Automated structural health monitoring based on adaptive kernel spectral clustering

    NASA Astrophysics Data System (ADS)

    Langone, Rocco; Reynders, Edwin; Mehrkanoon, Siamak; Suykens, Johan A. K.

    2017-06-01

    Structural health monitoring refers to the process of measuring damage-sensitive variables to assess the functionality of a structure. In principle, vibration data can capture the dynamics of the structure and reveal possible failures, but environmental and operational variability can mask this information. Thus, an effective outlier detection algorithm can be applied only after having performed data normalization (i.e. filtering) to eliminate external influences. Instead, in this article we propose a technique which unifies the data normalization and damage detection steps. The proposed algorithm, called adaptive kernel spectral clustering (AKSC), is initialized and calibrated in a phase when the structure is undamaged. The calibration process is crucial to ensure detection of early damage and minimize the number of false alarms. After the calibration, the method can automatically identify new regimes which may be associated with possible faults. These regimes are discovered by means of two complementary damage (i.e. outlier) indicators. The proposed strategy is validated with a simulated example and with real-life natural frequency data from the Z24 pre-stressed concrete bridge, which was progressively damaged at the end of a one-year monitoring period.

  16. Application of a hierarchical structure stochastic learning automation

    NASA Technical Reports Server (NTRS)

    Neville, R. G.; Chrystall, M. S.; Mars, P.

    1979-01-01

    A hierarchical structure automaton was developed using a two state stochastic learning automato (SLA) in a time shared model. Application of the hierarchical SLA to systems with multidimensional, multimodal performance criteria is described. Results of experiments performed with the hierarchical SLA using a performance index with a superimposed noise component of ? or - delta distributed uniformly over the surface are discussed.

  17. From bacterial to human dihydrouridine synthase: automated structure determination

    PubMed Central

    Whelan, Fiona; Jenkins, Huw T.; Griffiths, Samuel C.; Byrne, Robert T.; Dodson, Eleanor J.; Antson, Alfred A.

    2015-01-01

    The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1–340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by phenix.mr_rosetta starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain–domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer. PMID:26143927

  18. Three-dimensional visualization for evaluating automated, geomorphic pattern-recognition analyses of crustal structures

    NASA Astrophysics Data System (ADS)

    Foley, M. G.

    1991-02-01

    We are developing and applying a suite of automated remote geologic analysis (RGA) methods at Pacific Northwest Laboratory (PNL) for extracting structural and tectonic patterns from digital models of topography and other spatially registered geophysical data. In analyzing a map area, the geologist employs a variety of spatial representations (e.g., topographic maps; oblique, vertical and vertical stereographic aerial photographs; satellite-sensor images) in addition to actual field observations to provide a basis for recognizing features (patterns) diagnostic or suggestive of various geologic and geomorphic features. We intend that our automated analyses of digital models of elevation use the same photogeologic pattern-recognition methods as the geologist's; otherwise there is no direct basis for manually evaluating results of the automated analysis. Any system for automating geologic analysis should extend the geologist's pattern-recognition abilities and quantify them, rather than replace them. This requirement means that results of automated structural pattern-recognition analyses must be evaluated by geologists using the same method that would be employed in manual field checking: visual examination of the three-dimensional relationships among rocks, erosional patterns, and identifiable structures. Interactive computer-graphics in quantitative (i.e., spatially registered), simulated three-dimensional perspective and stereo are thus critical to the integration and interpretation of topography, imagery, point data, RGA-identified fracture/fault planes, stratigraphy, contoured geophysical data, nonplanar surfaces, boreholes, and three-dimensional zones (e.g., crush zones at fracture intersections). This graphical interaction presents the megabytes of digital geologic and geophysical data to the geologist in the same spatial format that field observations would take, permitting direct evaluation of RGA methods and results.

  19. Three-dimensional visualization for evaluating automated, geomorphic pattern-recognition analyses of crustal structures

    SciTech Connect

    Foley, M.G.

    1991-02-01

    We are developing and applying a suite of automated remote geologic analysis (RGA) methods at Pacific Northwest Laboratory (PNL) for extracting structural and tectonic patterns from digital models of topography and other spatially registered geophysical data. In analyzing a map area, the geologist employs a variety of spatial representations (e.g., topographic maps; oblique, vertical and vertical stereographic aerial photographs; satellite-sensor images) in addition to actual field observations to provide a basis for recognizing features (patterns) diagnostic or suggestive of various geologic and geomorphic features. We intend that our automated analyses of digital models of elevation use the same photogeologic pattern-recognition methods as the geologist's; otherwise there is no direct basis for manually evaluating results of the automated analysis. Any system for automating geologic analysis should extend the geologist's pattern-recognition abilities and quantify them, rather than replace them. This requirement means that results of automated structural pattern-recognition analyses must be evaluated by geologists using the same method that would be employed in manual field checking: visual examination of the three-dimensional relationships among rocks, erosional patterns, and identifiable structures. Interactive computer-graphics in quantitative (i.e., spatially registered), simulated three-dimensional perspective and stereo are thus critical to the integration and interpretation of topography, imagery, point data, RGA-identified fracture/fault planes, stratigraphy, contoured geophysical data, nonplanar surfaces, boreholes, and three-dimensional zones (e.g., crush zones at fracture intersections). This graphical interaction presents the megabytes of digital geologic and geophysical data to the geologist in the same spatial format that field observations would take, permitting direct evaluation of RGA methods and results. 5 refs., 2 figs.

  20. Automating the parallel processing of fluid and structural dynamics calculations

    NASA Technical Reports Server (NTRS)

    Arpasi, Dale J.; Cole, Gary L.

    1987-01-01

    The NASA Lewis Research Center is actively involved in the development of expert system technology to assist users in applying parallel processing to computational fluid and structural dynamic analysis. The goal of this effort is to eliminate the necessity for the physical scientist to become a computer scientist in order to effectively use the computer as a research tool. Programming and operating software utilities have previously been developed to solve systems of ordinary nonlinear differential equations on parallel scalar processors. Current efforts are aimed at extending these capabilties to systems of partial differential equations, that describe the complex behavior of fluids and structures within aerospace propulsion systems. This paper presents some important considerations in the redesign, in particular, the need for algorithms and software utilities that can automatically identify data flow patterns in the application program and partition and allocate calculations to the parallel processors. A library-oriented multiprocessing concept for integrating the hardware and software functions is described.

  1. Automating the parallel processing of fluid and structural dynamics calculations

    NASA Technical Reports Server (NTRS)

    Arpasi, Dale J.; Cole, Gary L.

    1987-01-01

    The NASA Lewis Research Center is actively involved in the development of expert system technology to assist users in applying parallel processing to computational fluid and structural dynamic analysis. The goal of this effort is to eliminate the necessity for the physical scientist to become a computer scientist in order to effectively use the computer as a research tool. Programming and operating software utilities have previously been developed to solve systems of ordinary nonlinear differential equations on parallel scalar processors. Current efforts are aimed at extending these capabilities to systems of partial differential equations, that describe the complex behavior of fluids and structures within aerospace propulsion systems. This paper presents some important considerations in the redesign, in particular, the need for algorithms and software utilities that can automatically identify data flow patterns in the application program and partition and allocate calculations to the parallel processors. A library-oriented multiprocessing concept for integrating the hardware and software functions is described.

  2. An automated procedure for covariation-based detection of RNA structure

    SciTech Connect

    Winker, S.; Overbeek, R.; Woese, C.R.; Olsen, G.J.; Pfluger, N.

    1989-12-01

    This paper summarizes our investigations into the computational detection of secondary and tertiary structure of ribosomal RNA. We have developed a new automated procedure that not only identifies potential bondings of secondary and tertiary structure, but also provides the covariation evidence that supports the proposed bondings, and any counter-evidence that can be detected in the known sequences. A small number of previously unknown bondings have been detected in individual RNA molecules (16S rRNA and 7S RNA) through the use of our automated procedure. Currently, we are systematically studying mitochondrial rRNA. Our goal is to detect tertiary structure within 16S rRNA and quaternary structure between 16S and 23S rRNA. Our ultimate hope is that automated covariation analysis will contribute significantly to a refined picture of ribosome structure. Our colleagues in biology have begun experiments to test certain hypotheses suggested by an examination of our program's output. These experiments involve sequencing key portions of the 23S ribosomal RNA for species in which the known 16S ribosomal RNA exhibits variation (from the dominant pattern) at the site of a proposed bonding. The hope is that the 23S ribosomal RNA of these species will exhibit corresponding complementary variation or generalized covariation. 24 refs.

  3. Automated Structural Optimization System (ASTROS). Volume 1. Theoretical Manual

    DTIC Science & Technology

    1988-12-01

    Analysis Problem Oriented Language). Such a control language, similar to the DMAP of NASTRAN or the typical query language of a data base management...aerospace environment is addressed by making the ASTROS procedure resemble that of NASTRAN in terms of user input and pre- and post-processor interfaces...While the ASTROS procedure does not contain many of the specialized capabilities available in NASTRAN , the basic structural analysis features have

  4. Stratigraphical characterization of the Anthropocene

    NASA Astrophysics Data System (ADS)

    Zalasiewicz, Jan

    2016-04-01

    The Anthropocene, currently under analysis as a potential addition to the Geological Time Scale, has been interpreted in a wide variety of ways since the term was first introduced into scientific debate by Paul Crutzen in 2000. If it is to become a formal geological time unit, it must be functional as both a geochronological unit (an 'abstract time' unit, for example, an Epoch) and a chronostratigraphical unit (the corresponding material 'time-rock' unit, a Series). The most compelling evidence collated to date by the Anthropocene Working Group comprises a range of stratigraphic proxies of physical (e.g. anthropogenic rock and mineral types), chemical (e.g. C, N isotopic changes, radionuclides, pesticides) and biological (species invasions, extinctions, assemblage changes) character; together these suggest that the most effective boundary may be placed around the mid-20th century. Formalisation will depend not just on the weight of stratigraphic evidence (already considerable) but also on perceived utility. As regards wider societal implications, the succession of phenomena associated with this concept strongly suggest that it will be associated with significant Earth system change for the foreseeable future, by contrast with the general stability of Holocene times.

  5. Automated motif extraction and classification in RNA tertiary structures

    PubMed Central

    Djelloul, Mahassine; Denise, Alain

    2008-01-01

    We used a novel graph-based approach to extract RNA tertiary motifs. We cataloged them all and clustered them using an innovative graph similarity measure. We applied our method to three widely studied structures: Haloarcula marismortui 50S (H.m 50S), Escherichia coli 50S (E. coli 50S), and Thermus thermophilus 16S (T.th 16S) RNAs. We identified 10 known motifs without any prior knowledge of their shapes or positions. We additionally identified four putative new motifs. PMID:18957493

  6. Bim Automation: Advanced Modeling Generative Process for Complex Structures

    NASA Astrophysics Data System (ADS)

    Banfi, F.; Fai, S.; Brumana, R.

    2017-08-01

    The new paradigm of the complexity of modern and historic structures, which are characterised by complex forms, morphological and typological variables, is one of the greatest challenges for building information modelling (BIM). Generation of complex parametric models needs new scientific knowledge concerning new digital technologies. These elements are helpful to store a vast quantity of information during the life cycle of buildings (LCB). The latest developments of parametric applications do not provide advanced tools, resulting in time-consuming work for the generation of models. This paper presents a method capable of processing and creating complex parametric Building Information Models (BIM) with Non-Uniform to NURBS) with multiple levels of details (Mixed and ReverseLoD) based on accurate 3D photogrammetric and laser scanning surveys. Complex 3D elements are converted into parametric BIM software and finite element applications (BIM to FEA) using specific exchange formats and new modelling tools. The proposed approach has been applied to different case studies: the BIM of modern structure for the courtyard of West Block on Parliament Hill in Ottawa (Ontario) and the BIM of Masegra Castel in Sondrio (Italy), encouraging the dissemination and interaction of scientific results without losing information during the generative process.

  7. Toolkit for automated and rapid discovery of structural variants.

    PubMed

    Soylev, Arda; Kockan, Can; Hormozdiari, Fereydoun; Alkan, Can

    2017-06-02

    Structural variations (SV) are broadly defined as genomic alterations that affect >50bp of DNA, which are shown to have significant effect on evolution and disease. The advent of high throughput sequencing (HTS) technologies and the ability to perform whole genome sequencing (WGS), makes it feasible to study these variants in depth. However, discovery of all forms of SV using WGS has proven to be challenging as the short reads produced by the predominant HTS platforms (<200bp for current technologies) and the fact that most genomes include large amounts of repeats make it very difficult to unambiguously map and accurately characterize such variants. Furthermore, existing tools for SV discovery are primarily developed for only a few of the SV types, which may have conflicting sequence signatures (i.e. read pairs, read depth, split reads) with other, untargeted SV classes. Here we are introduce a new framework, Tardis, which combines multiple read signatures into a single package to characterize most SV types simultaneously, while preventing such conflicts. Tardis also has a modular structure that makes it easy to extend for the discovery of additional forms of SV. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Automated analysis of Physarum network structure and dynamics

    NASA Astrophysics Data System (ADS)

    Fricker, Mark D.; Akita, Dai; Heaton, Luke LM; Jones, Nick; Obara, Boguslaw; Nakagaki, Toshiyuki

    2017-06-01

    We evaluate different ridge-enhancement and segmentation methods to automatically extract the network architecture from time-series of Physarum plasmodia withdrawing from an arena via a single exit. Whilst all methods gave reasonable results, judged by precision-recall analysis against a ground-truth skeleton, the mean phase angle (Feature Type) from intensity-independent, phase-congruency edge enhancement and watershed segmentation was the most robust to variation in threshold parameters. The resultant single pixel-wide segmented skeleton was converted to a graph representation as a set of weighted adjacency matrices containing the physical dimensions of each vein, and the inter-vein regions. We encapsulate the complete image processing and network analysis pipeline in a downloadable software package, and provide an extensive set of metrics that characterise the network structure, including hierarchical loop decomposition to analyse the nested structure of the developing network. In addition, the change in volume for each vein and intervening plasmodial sheet was used to predict the net flow across the network. The scaling relationships between predicted current, speed and shear force with vein radius were consistent with predictions from Murray’s law. This work was presented at PhysNet 2015.

  9. Automated determination of fibrillar structures by simultaneous model building and fiber diffraction refinement.

    PubMed

    Potrzebowski, Wojciech; André, Ingemar

    2015-07-01

    For highly oriented fibrillar molecules, three-dimensional structures can often be determined from X-ray fiber diffraction data. However, because of limited information content, structure determination and validation can be challenging. We demonstrate that automated structure determination of protein fibers can be achieved by guiding the building of macromolecular models with fiber diffraction data. We illustrate the power of our approach by determining the structures of six bacteriophage viruses de novo using fiber diffraction data alone and together with solid-state NMR data. Furthermore, we demonstrate the feasibility of molecular replacement from monomeric and fibrillar templates by solving the structure of a plant virus using homology modeling and protein-protein docking. The generated models explain the experimental data to the same degree as deposited reference structures but with improved structural quality. We also developed a cross-validation method for model selection. The results highlight the power of fiber diffraction data as structural constraints.

  10. Automated Quality Assessment of Structural Magnetic Resonance Brain Images Based on a Supervised Machine Learning Algorithm.

    PubMed

    Pizarro, Ricardo A; Cheng, Xi; Barnett, Alan; Lemaitre, Herve; Verchinski, Beth A; Goldman, Aaron L; Xiao, Ena; Luo, Qian; Berman, Karen F; Callicott, Joseph H; Weinberger, Daniel R; Mattay, Venkata S

    2016-01-01

    High-resolution three-dimensional magnetic resonance imaging (3D-MRI) is being increasingly used to delineate morphological changes underlying neuropsychiatric disorders. Unfortunately, artifacts frequently compromise the utility of 3D-MRI yielding irreproducible results, from both type I and type II errors. It is therefore critical to screen 3D-MRIs for artifacts before use. Currently, quality assessment involves slice-wise visual inspection of 3D-MRI volumes, a procedure that is both subjective and time consuming. Automating the quality rating of 3D-MRI could improve the efficiency and reproducibility of the procedure. The present study is one of the first efforts to apply a support vector machine (SVM) algorithm in the quality assessment of structural brain images, using global and region of interest (ROI) automated image quality features developed in-house. SVM is a supervised machine-learning algorithm that can predict the category of test datasets based on the knowledge acquired from a learning dataset. The performance (accuracy) of the automated SVM approach was assessed, by comparing the SVM-predicted quality labels to investigator-determined quality labels. The accuracy for classifying 1457 3D-MRI volumes from our database using the SVM approach is around 80%. These results are promising and illustrate the possibility of using SVM as an automated quality assessment tool for 3D-MRI.

  11. Automated Quality Assessment of Structural Magnetic Resonance Brain Images Based on a Supervised Machine Learning Algorithm

    PubMed Central

    Pizarro, Ricardo A.; Cheng, Xi; Barnett, Alan; Lemaitre, Herve; Verchinski, Beth A.; Goldman, Aaron L.; Xiao, Ena; Luo, Qian; Berman, Karen F.; Callicott, Joseph H.; Weinberger, Daniel R.; Mattay, Venkata S.

    2016-01-01

    High-resolution three-dimensional magnetic resonance imaging (3D-MRI) is being increasingly used to delineate morphological changes underlying neuropsychiatric disorders. Unfortunately, artifacts frequently compromise the utility of 3D-MRI yielding irreproducible results, from both type I and type II errors. It is therefore critical to screen 3D-MRIs for artifacts before use. Currently, quality assessment involves slice-wise visual inspection of 3D-MRI volumes, a procedure that is both subjective and time consuming. Automating the quality rating of 3D-MRI could improve the efficiency and reproducibility of the procedure. The present study is one of the first efforts to apply a support vector machine (SVM) algorithm in the quality assessment of structural brain images, using global and region of interest (ROI) automated image quality features developed in-house. SVM is a supervised machine-learning algorithm that can predict the category of test datasets based on the knowledge acquired from a learning dataset. The performance (accuracy) of the automated SVM approach was assessed, by comparing the SVM-predicted quality labels to investigator-determined quality labels. The accuracy for classifying 1457 3D-MRI volumes from our database using the SVM approach is around 80%. These results are promising and illustrate the possibility of using SVM as an automated quality assessment tool for 3D-MRI. PMID:28066227

  12. Knowledge structure representation and automated updates in intelligent information management systems

    NASA Technical Reports Server (NTRS)

    Corey, Stephen; Carnahan, Richard S., Jr.

    1990-01-01

    A continuing effort to apply rapid prototyping and Artificial Intelligence techniques to problems associated with projected Space Station-era information management systems is examined. In particular, timely updating of the various databases and knowledge structures within the proposed intelligent information management system (IIMS) is critical to support decision making processes. Because of the significantly large amounts of data entering the IIMS on a daily basis, information updates will need to be automatically performed with some systems requiring that data be incorporated and made available to users within a few hours. Meeting these demands depends first, on the design and implementation of information structures that are easily modified and expanded, and second, on the incorporation of intelligent automated update techniques that will allow meaningful information relationships to be established. Potential techniques are studied for developing such an automated update capability and IIMS update requirements are examined in light of results obtained from the IIMS prototyping effort.

  13. Automated model formulation for time-varying flexible structures

    NASA Technical Reports Server (NTRS)

    Glass, B. J.; Hanagud, S.

    1989-01-01

    Presented here is an identification technique that uses the sensor information to choose a new model out of a finite set of discrete model space, in order to follow the observed changes to the given time varying flexible structure. Boundary condition sets or other information on model variations are used to organize the set of possible models laterally into a search tree with levels of abstraction used to order the models vertically within branches. An object-oriented programming approach is used to represent the model set in the search tree. A modified A (asterisk) best first search algorithm finds the model where the model response best matches the current observations. Several extensions to this methodology are discussed. Methods of possible integration of rules with the current search algorithm are considered to give weight to interpreted trends that may be found in a series of observations. This capability might lead, for instance, to identifying a model that incorporates a progressive damage rather than with incorrect paramenters such as added mass. Another new direction is to consider the use of noisy time domain sensor feedback rather than frequency domain information in the search algorithm to improve the real-time capability of the developed procedure.

  14. Automated model formulation for time-varying flexible structures

    NASA Technical Reports Server (NTRS)

    Glass, B. J.; Hanagud, S.

    1989-01-01

    Presented here is an identification technique that uses the sensor information to choose a new model out of a finite set of discrete model space, in order to follow the observed changes to the given time varying flexible structure. Boundary condition sets or other information on model variations are used to organize the set of possible models laterally into a search tree with levels of abstraction used to order the models vertically within branches. An object-oriented programming approach is used to represent the model set in the search tree. A modified A (asterisk) best first search algorithm finds the model where the model response best matches the current observations. Several extensions to this methodology are discussed. Methods of possible integration of rules with the current search algorithm are considered to give weight to interpreted trends that may be found in a series of observations. This capability might lead, for instance, to identifying a model that incorporates a progressive damage rather than with incorrect paramenters such as added mass. Another new direction is to consider the use of noisy time domain sensor feedback rather than frequency domain information in the search algorithm to improve the real-time capability of the developed procedure.

  15. Revealing biological information using data structuring and automated learning.

    PubMed

    Mohorianu, Irina; Moulton, Vincent

    2010-11-01

    The intermediary steps between a biological hypothesis, concretized in the input data, and meaningful results, validated using biological experiments, commonly employ bioinformatics tools. Starting with storage of the data and ending with a statistical analysis of the significance of the results, every step in a bioinformatics analysis has been intensively studied and the resulting methods and models patented. This review summarizes the bioinformatics patents that have been developed mainly for the study of genes, and points out the universal applicability of bioinformatics methods to other related studies such as RNA interference. More specifically, we overview the steps undertaken in the majority of bioinformatics analyses, highlighting, for each, various approaches that have been developed to reveal details from different perspectives. First we consider data warehousing, the first task that has to be performed efficiently, optimizing the structure of the database, in order to facilitate both the subsequent steps and the retrieval of information. Next, we review data mining, which occupies the central part of most bioinformatics analyses, presenting patents concerning differential expression, unsupervised and supervised learning. Last, we discuss how networks of interactions of genes or other players in the cell may be created, which help draw biological conclusions and have been described in several patents.

  16. Structural/stratigraphic reconstruction of frontal [open quotes]Choctaw[close quotes] triangle zone within Oklahoma Atoka Trend - early controls (Prethrusting) on deposition of deep-water clastic reservoirs

    SciTech Connect

    Cox, D.; Foshee, R. )

    1993-09-01

    A structural and stratigraphic study in southwestern Oklahoma, encompassing approximately 30 townships in Atoka, Coal, and Pittsburg counties, was done using several hundred wells, surface geologic maps, and more than 400 mi of 1980 seismic data. Isopach maps of six Atokan sands covered various areas, all within a deep-water fan setting. Structural balancing, done on numerous geologic cross sections of six mi or less, allowed correlation of logs of the various reservoirs and structural details within the frontal [open quotes]Choctaw[close quotes] triangle zone. Two regional cross sections were made based, respectively. on 12 and 16 mi or recent high-fold common-depth-point seismic lines, with a minimum of one-well-per-mile control, diameter data, and surface geology. These cross sections were reconstructed by line balancing to illustrate the amount of thrusting in the section and the pre-Pennsylvanian normal faulting that subtly controlled the Atoka sands depositional framework. The thickest and most channelized sands are found downthrown to these earlier faults, with is past relationship now obscured by post-Atokan thrusting.

  17. North American Commission on Stratigraphic Nomenclature Note 66: records of Stratigraphic Commission, 2003-2013

    USGS Publications Warehouse

    Easton, Robert M.; Catuneanu, Octavian; Donovan, Art D.; Fluegeman, Richard H.; Hamblin, A.P.; Harper, Howard; Lasca, Norman P.; Morrow, Jared R.; Orndorff, Randall C.; Sadler, Peter; Scott, Robert W.; Tew, Berry H.

    2014-01-01

    Note 66 summarizes activities of the North American Commission on Stratigraphic Nomenclature (NACSN) from November 2003 to October 2013 and is condensed from the minutes of the NACSN’s 58th to 68th annual meetings1. The purposes of the Commission are to develop statements of stratigraphic principles,recommend procedures applicable to the classification and nomenclature of stratigraphic and related units, review problems in classifying and naming stratigraphic and related units, and formulate expressions of judgment on these matters.

  18. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data.

    PubMed

    Lee, Woonghee; Petit, Chad M; Cornilescu, Gabriel; Stark, Jaime L; Markley, John L

    2016-06-01

    We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27-98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models.

  19. Stratigraphic Signatures of Forearc Basin Formation Mechanisms

    NASA Astrophysics Data System (ADS)

    Mannu, U.; Ueda, K.; Gerya, T.; Willett, S.; Strasser, M.

    2014-12-01

    Forearc basins are loci of active sedimentation above the landward portion of accretionary prisms. Although these basins typically remain separated from the frontal prism by a forearc high, their evolution has a significant impact on the structure and deformation of the entire wedge. Formation of forearc basins has been proposed as a consequence of changes in wedge stability due to an increase of slab dip in subduction zones. Another hypothesis attributes this to higher hinterland sedimentation, which causes the rear of the wedge to stabilize and eventually develop a forearc basin. Basin stratigraphic architecture, revealed by high-resolution reflection seismic data and borehole data allows interpretation of structural development of the accretionary prism and associated basins with the goal of determining the underlying driving mechanism(s) of basin formation. In this study we supplement data interpretation with thermo-mechanical numerical models including high-resolution isochronal surface tracking to visualize the developing stratigraphy of basins that develop in subduction zone and wedge dynamic models. We use a dynamic 2D thermo mechanical model incorporating surface processes, strain weakening and sediment subduction. The model is a modification of I2VIS model, which is based on conservative, fully staggered finite differences and a non-diffusive marker- in-cell technique capable of modelling mantle convection. In the model different driving mechanisms for basin formation can be explored. Stratigraphic simulations obtained by isochronal surface tracking are compared to reflection pattern and stratigraphy of seismic and borehole data, respectively. Initial results from a model roughly representing the Nankai Trough Subduction Zone offshore Japan are compared to available seismic and Integrated Ocean Drilling (IODP) data. A calibrated model predicting forearc basin stratigraphy will be used to discern the underlying process of basins formation and wedge

  20. Stratigraphic signature of coastal transgressions

    SciTech Connect

    Boyd, R.; Penland, S.; Suter, J.R.

    1986-05-01

    Coastal transgression can produce a range of continental shelf sand bodies. Four categories of transgression can be recognized, each of which produces a characteristic shelf stratigraphy. 1)Rapid erosional transgression generates a discontinuous stratigraphy of overstepped coastal barriers separated by a thin transgressive veneer. 2)Slow erosional transgression generates a thin transgressive veneer overlying an unconformity. 3)Slow erosional transgression followed by stillstand generates a thin transgressive veneer terminated updip by a fully preserved coastal sequence. 4)During slow depositional transgression, a variable component of the coastal sequence is incorporated into the shelf stratigraphic record. These four categories are not distinct, but represent intervals of transgressive spectrum that is governed by sediment supply, regional gradient, relative sea level, and coastal oceanography. The preservation potential of transgressive stratigraphy is primarily governed by the translation path of the shoreface. A simple coastal stratigraphy may consist of a preexisting substrate, fine-grained back-barrier deposits, sandy barrier deposits, and a shelf mud. Horizontal translation of a deep shoreface incises an erosional unconformity into the preexisting substrate, which in turn if overlain by a sand lag veneer and a shelf mud. Horizontal and vertical translation of a shallower shoreface leaves the preexisting substrate intact, preserving 1)part of the back-barrier deposits, 2)all back-barrier deposits, or 3)all back-barrier deposits plus part of the barrier deposits, overlain by an erosional unconformity, a sandy lag veneer, and shelf mud. Abrupt horizontal and vertical shoreface translation cannot rework the entire shelf-retreat path of the coastal zone. Therefore, partly reworked segments of the coastal sequence are incorporated into the shelf stratigraphic record and in turn are overlain by a shelf mud.

  1. Automated protein motif generation in the structure-based protein function prediction tool ProMOL.

    PubMed

    Osipovitch, Mikhail; Lambrecht, Mitchell; Baker, Cameron; Madha, Shariq; Mills, Jeffrey L; Craig, Paul A; Bernstein, Herbert J

    2015-12-01

    ProMOL, a plugin for the PyMOL molecular graphics system, is a structure-based protein function prediction tool. ProMOL includes a set of routines for building motif templates that are used for screening query structures for enzyme active sites. Previously, each motif template was generated manually and required supervision in the optimization of parameters for sensitivity and selectivity. We developed an algorithm and workflow for the automation of motif building and testing routines in ProMOL. The algorithm uses a set of empirically derived parameters for optimization and requires little user intervention. The automated motif generation algorithm was first tested in a performance comparison with a set of manually generated motifs based on identical active sites from the same 112 PDB entries. The two sets of motifs were equally effective in identifying alignments with homologs and in rejecting alignments with unrelated structures. A second set of 296 active site motifs were generated automatically, based on Catalytic Site Atlas entries with literature citations, as an expansion of the library of existing manually generated motif templates. The new motif templates exhibited comparable performance to the existing ones in terms of hit rates against native structures, homologs with the same EC and Pfam designations, and randomly selected unrelated structures with a different EC designation at the first EC digit, as well as in terms of RMSD values obtained from local structural alignments of motifs and query structures. This research is supported by NIH grant GM078077.

  2. Automated refinement of macromolecular structures at low resolution using prior information

    PubMed Central

    Kovalevskiy, Oleg; Nicholls, Robert A.; Murshudov, Garib N.

    2016-01-01

    Since the ratio of the number of observations to adjustable parameters is small at low resolution, it is necessary to use complementary information for the analysis of such data. ProSMART is a program that can generate restraints for macromolecules using homologous structures, as well as generic restraints for the stabilization of secondary structures. These restraints are used by REFMAC5 to stabilize the refinement of an atomic model. However, the optimal refinement protocol varies from case to case, and it is not always obvious how to select appropriate homologous structure(s), or other sources of prior information, for restraint generation. After running extensive tests on a large data set of low-resolution models, the best-performing refinement protocols and strategies for the selection of homologous structures have been identified. These strategies and protocols have been implemented in the Low-Resolution Structure Refinement (LORESTR) pipeline. The pipeline performs auto-detection of twinning and selects the optimal scaling method and solvent parameters. LORESTR can either use user-supplied homologous structures, or run an automated BLAST search and download homologues from the PDB. The pipeline executes multiple model-refinement instances using different parameters in order to find the best protocol. Tests show that the automated pipeline improves R factors, geometry and Ramachandran statistics for 94% of the low-resolution cases from the PDB included in the test set. PMID:27710936

  3. Automated refinement of macromolecular structures at low resolution using prior information.

    PubMed

    Kovalevskiy, Oleg; Nicholls, Robert A; Murshudov, Garib N

    2016-10-01

    Since the ratio of the number of observations to adjustable parameters is small at low resolution, it is necessary to use complementary information for the analysis of such data. ProSMART is a program that can generate restraints for macromolecules using homologous structures, as well as generic restraints for the stabilization of secondary structures. These restraints are used by REFMAC5 to stabilize the refinement of an atomic model. However, the optimal refinement protocol varies from case to case, and it is not always obvious how to select appropriate homologous structure(s), or other sources of prior information, for restraint generation. After running extensive tests on a large data set of low-resolution models, the best-performing refinement protocols and strategies for the selection of homologous structures have been identified. These strategies and protocols have been implemented in the Low-Resolution Structure Refinement (LORESTR) pipeline. The pipeline performs auto-detection of twinning and selects the optimal scaling method and solvent parameters. LORESTR can either use user-supplied homologous structures, or run an automated BLAST search and download homologues from the PDB. The pipeline executes multiple model-refinement instances using different parameters in order to find the best protocol. Tests show that the automated pipeline improves R factors, geometry and Ramachandran statistics for 94% of the low-resolution cases from the PDB included in the test set.

  4. I-TASSER: a unified platform for automated protein structure and function prediction.

    PubMed

    Roy, Ambrish; Kucukural, Alper; Zhang, Yang

    2010-04-01

    The iterative threading assembly refinement (I-TASSER) server is an integrated platform for automated protein structure and function prediction based on the sequence-to-structure-to-function paradigm. Starting from an amino acid sequence, I-TASSER first generates three-dimensional (3D) atomic models from multiple threading alignments and iterative structural assembly simulations. The function of the protein is then inferred by structurally matching the 3D models with other known proteins. The output from a typical server run contains full-length secondary and tertiary structure predictions, and functional annotations on ligand-binding sites, Enzyme Commission numbers and Gene Ontology terms. An estimate of accuracy of the predictions is provided based on the confidence score of the modeling. This protocol provides new insights and guidelines for designing of online server systems for the state-of-the-art protein structure and function predictions. The server is available at http://zhanglab.ccmb.med.umich.edu/I-TASSER.

  5. Towards automated detection of depression from brain structural magnetic resonance images.

    PubMed

    Kipli, Kuryati; Kouzani, Abbas Z; Williams, Lana J

    2013-05-01

    Depression is a major issue worldwide and is seen as a significant health problem. Stigma and patient denial, clinical experience, time limitations, and reliability of psychometrics are barriers to the clinical diagnoses of depression. Thus, the establishment of an automated system that could detect such abnormalities would assist medical experts in their decision-making process. This paper reviews existing methods for the automated detection of depression from brain structural magnetic resonance images (sMRI). Relevant sources were identified from various databases and online sites using a combination of keywords and terms including depression, major depressive disorder, detection, classification, and MRI databases. Reference lists of chosen articles were further reviewed for associated publications. The paper introduces a generic structure for representing and describing the methods developed for the detection of depression from sMRI of the brain. It consists of a number of components including acquisition and preprocessing, feature extraction, feature selection, and classification. Automated sMRI-based detection methods have the potential to provide an objective measure of depression, hence improving the confidence level in the diagnosis and prognosis of depression.

  6. An automated method for detecting architectural distortions on mammograms using direction analysis of linear structures.

    PubMed

    Matsubara, T; Ito, A; Tsunomori, A; Hara, T; Muramatsu, C; Endo, T; Fujita, H

    2015-08-01

    Architectural distortion is one of the most important findings when evaluating mammograms for breast cancer. Abnormal breast architecture is characterized by the presence of spicules, which are distorted mammary structures that are not accompanied by an increased density or mass. We have been developing an automated method for detecting spiculated architectural distortions by analyzing linear structures extracted by normal curvature. However, some structures that are possibly related to distorted areas are not extracted using this method. The purpose of this study was to develop a new automated method for direction analysis of linear structures to improve detection performance in mammography. The direction of linear structures in each region of interest (ROI) was first determined using a direction filter and a background filter that can define one of eight directions (0°, 22.5°, 45°, 67.5°, 90°, 112.5°, 135°, and 157.5°). The concentration and isotropic indexes were calculated using the determined direction of the linear structures in order to extract the candidate areas. Discriminant analysis was performed to eliminate false positives results. Our database consisted of 168 abnormal images containing 174 distorted areas and 580 normal images. The sensitivity of the new method was 81%. There were 2.6 and 4.2 false positives per image using the new and previous methods, respectively. These findings show that our new method is effective for detecting spiculated architectural distortions.

  7. Automated detection of structural alerts (chemical fragments) in (eco)toxicology

    PubMed Central

    Lepailleur, Alban; Poezevara, Guillaume; Bureau, Ronan

    2013-01-01

    This mini-review describes the evolution of different algorithms dedicated to the automated discovery of chemical fragments associated to (eco)toxicological endpoints. These structural alerts correspond to one of the most interesting approach of in silico toxicology due to their direct link with specific toxicological mechanisms. A number of expert systems are already available but, since the first work in this field which considered a binomial distribution of chemical fragments between two datasets, new data miners were developed and applied with success in chemoinformatics. The frequency of a chemical fragment in a dataset is often at the core of the process for the definition of its toxicological relevance. However, recent progresses in data mining provide new insights into the automated discovery of new rules. Particularly, this review highlights the notion of Emerging Patterns that can capture contrasts between classes of data. PMID:24688706

  8. Automated fine structure image analysis method for discrimination of diabetic retinopathy stage using conjunctival microvasculature images

    PubMed Central

    Khansari, Maziyar M; O’Neill, William; Penn, Richard; Chau, Felix; Blair, Norman P; Shahidi, Mahnaz

    2016-01-01

    The conjunctiva is a densely vascularized mucus membrane covering the sclera of the eye with a unique advantage of accessibility for direct visualization and non-invasive imaging. The purpose of this study is to apply an automated quantitative method for discrimination of different stages of diabetic retinopathy (DR) using conjunctival microvasculature images. Fine structural analysis of conjunctival microvasculature images was performed by ordinary least square regression and Fisher linear discriminant analysis. Conjunctival images between groups of non-diabetic and diabetic subjects at different stages of DR were discriminated. The automated method’s discriminate rates were higher than those determined by human observers. The method allowed sensitive and rapid discrimination by assessment of conjunctival microvasculature images and can be potentially useful for DR screening and monitoring. PMID:27446692

  9. The immobilization of enzymes on nylon structures and their use in automated analysis

    PubMed Central

    Inman, D. J.; Hornby, W. E.

    1972-01-01

    1. Glucose oxidase (EC 1.1.3.4) and urease (EC 3.5.1.5) were covalently attached through glutaraldehyde to low-molecular-weight nylon powder. 2. Immobilized derivatives of glucose oxidase and urease were prepared by cross-linking the respective enzymes within the matrix of a nylon membrane. 3. An improved process is described for the immobilization of glucose oxidase and urease on the inside surface of partially hydrolysed nylon tube. 4. Automated analytical procedures are described for the determination of glucose with each of the three immobilized glucose oxidase derivatives and for the determination of urea with each of the three immobilized urease derivatives. 5. The efficiencies of the three immobilized enzyme structures as reagents for the automated determination of their substrates were compared. PMID:4643309

  10. Automation of three-dimensional structured mesh generation for turbomachinery blade passages

    NASA Technical Reports Server (NTRS)

    Ascoli, Edward P.; Prueger, George H.

    1995-01-01

    Hybrid tools have been developed which greatly reduce the time required to generate three-dimensional structured CFD meshes for turbomachinery blade passages. RAGGS, an existing Rockwell proprietary, general purpose mesh generation and visualization system, provides the starting point and framework for tool development. Utilities which manipulate and interface with RAGGS tools have been developed to (1) facilitate blade geometry inputs from point or CAD representations, (2) automate auxiliary surface creation, and (3) streamline and automate edge, surface, and subsequent volume mesh generation from minimal inputs. The emphasis of this approach has been to maintain all the functionality of the general purpose mesh generator while simultaneously eliminating the bulk of the repetitive and tediuos manual steps in the mesh generation process. Using this approach, mesh generation cycle times have been reduced from the order of days down to the order of hours.

  11. A two-level structure for advanced space power system automation

    NASA Technical Reports Server (NTRS)

    Loparo, Kenneth A.; Chankong, Vira

    1990-01-01

    The tasks to be carried out during the three-year project period are: (1) performing extensive simulation using existing mathematical models to build a specific knowledge base of the operating characteristics of space power systems; (2) carrying out the necessary basic research on hierarchical control structures, real-time quantitative algorithms, and decision-theoretic procedures; (3) developing a two-level automation scheme for fault detection and diagnosis, maintenance and restoration scheduling, and load management; and (4) testing and demonstration. The outlines of the proposed system structure that served as a master plan for this project, work accomplished, concluding remarks, and ideas for future work are also addressed.

  12. A two-level structure for advanced space power system automation

    NASA Astrophysics Data System (ADS)

    Loparo, Kenneth A.; Chankong, Vira

    1990-05-01

    The tasks to be carried out during the three-year project period are: (1) performing extensive simulation using existing mathematical models to build a specific knowledge base of the operating characteristics of space power systems; (2) carrying out the necessary basic research on hierarchical control structures, real-time quantitative algorithms, and decision-theoretic procedures; (3) developing a two-level automation scheme for fault detection and diagnosis, maintenance and restoration scheduling, and load management; and (4) testing and demonstration. The outlines of the proposed system structure that served as a master plan for this project, work accomplished, concluding remarks, and ideas for future work are also addressed.

  13. Sinkholes and caves related to evaporite dissolution in a stratigraphically and structurally complex setting, Fluvia Valley, eastern Spanish Pyrenees. Geological, geomorphological and environmental implications

    NASA Astrophysics Data System (ADS)

    Gutiérrez, Francisco; Fabregat, Ivan; Roqué, Carles; Carbonel, Domingo; Guerrero, Jesús; García-Hermoso, Fernando; Zarroca, Mario; Linares, Rogelio

    2016-08-01

    Evaporite karst and sinkhole development is analysed in a geologically complex area of NE Spain, including four evaporite units with different characteristics and affected by compressional and extensional tectonic structures. The exposed paleosinkholes, including remarkable Early Pleistocene paleontological sites, provide valuable information on the subsidence mechanisms and reveal the significant role played by interstratal karstification in the area. These gravitational deformation structures, including hectometre-scale bending folds and oversteepened normal faults, strongly suggest that the present-day compressional regime inferred in previous studies may be largely based on the analysis of non-tectonic structures. Two gypsum caves ca. 1 km long show that passages with restricted cross-sectional area may produce large breccia pipes and sinkholes thanks to the removal of breakdown boulders by high-competence episodic floods. Moreover, the upward progression of cave ceilings by paragenesis and condensation dissolution contributes to increase the probability of sinkhole occurrence. An inventory of 135 sinkholes together with their geological and geomorphological context has been developed. This data base has been used to infer several properties of the sinkholes with practical implications: a magnitude and frequency scaling relationship, spatial distribution patterns, dominant controlling factors and risk implications.

  14. Automated structure determination of proteins with the SAIL-FLYA NMR method.

    PubMed

    Takeda, Mitsuhiro; Ikeya, Teppei; Güntert, Peter; Kainosho, Masatsune

    2007-01-01

    The labeling of proteins with stable isotopes enhances the NMR method for the determination of 3D protein structures in solution. Stereo-array isotope labeling (SAIL) provides an optimal stereospecific and regiospecific pattern of stable isotopes that yields sharpened lines, spectral simplification without loss of information, and the ability to collect rapidly and evaluate fully automatically the structural restraints required to solve a high-quality solution structure for proteins up to twice as large as those that can be analyzed using conventional methods. Here, we describe a protocol for the preparation of SAIL proteins by cell-free methods, including the preparation of S30 extract and their automated structure analysis using the FLYA algorithm and the program CYANA. Once efficient cell-free expression of the unlabeled or uniformly labeled target protein has been achieved, the NMR sample preparation of a SAIL protein can be accomplished in 3 d. A fully automated FLYA structure calculation can be completed in 1 d on a powerful computer system.

  15. Integrating automated structured analysis and design with Ada programming support environments

    NASA Technical Reports Server (NTRS)

    Hecht, Alan; Simmons, Andy

    1986-01-01

    Ada Programming Support Environments (APSE) include many powerful tools that address the implementation of Ada code. These tools do not address the entire software development process. Structured analysis is a methodology that addresses the creation of complete and accurate system specifications. Structured design takes a specification and derives a plan to decompose the system subcomponents, and provides heuristics to optimize the software design to minimize errors and maintenance. It can also produce the creation of useable modules. Studies have shown that most software errors result from poor system specifications, and that these errors also become more expensive to fix as the development process continues. Structured analysis and design help to uncover error in the early stages of development. The APSE tools help to insure that the code produced is correct, and aid in finding obscure coding errors. However, they do not have the capability to detect errors in specifications or to detect poor designs. An automated system for structured analysis and design TEAMWORK, which can be integrated with an APSE to support software systems development from specification through implementation is described. These tools completement each other to help developers improve quality and productivity, as well as to reduce development and maintenance costs. Complete system documentation and reusable code also resultss from the use of these tools. Integrating an APSE with automated tools for structured analysis and design provide capabilities and advantages beyond those realized with any of these systems used by themselves.

  16. Interpretation of biostratigraphic data at a sequence stratigraphic scale

    SciTech Connect

    Goodman, D.K. ); Posamentier, H.W. )

    1993-02-01

    Recent advances in sequence stratigraphic concepts provide a framework within which biostratigraphic data can be used in conjunction with other stratigraphic tools in an integrated approach to stratigraphic analysis. Sequence stratigraphic concepts suggest that lithologic sections are composed of a succession of unconformity-bounded units or sequences. These sequences can, in turn, be subdivided into systems tracts bounded by flooding surfaces or maximum flooding surfaces. Three systems tracts comprise a sequence: the lowstand or shelf margin systems tract at the base, followed by the transgressive systems tract, and the highstand systems tract. On continental margins with a discrete shelf/slope break, deep-sea submarine fans, shelf-margin deltas, and incised-valley fills characterize the lowstand systems tract. On ramp-like continental margin, the lowstand systems tract is characterized by basinally-isolated lowstand shorelines with or without preserved incised-valley feeder systems. The transgressive systems tract has backstepping shorelines and estuarine fill of incised valley systems. The highstand systems tract is has forestepping depositional systems and widespread floodplain development. A large amount of the structure in the stratigraphic distribution of fossils can be attributed to sequence architecture. This structure can be statistically delineated in terms of a hierarchy that is independent of both fossil group and geological age. The definition of [open quotes]biological analogs[close quotes] of systems tracts reduces the complexity of paleontological census data to a set of (1) internal characteristics within genetic units and (2) boundary conditions at stratal discontinuities. Different taxon groups should display unique and repeatable patterns within different systems tracts and at stratal discontinuities within a basin, providing a new perspective of paleontological data across a spectrum of applications in sequence characterization and correlation.

  17. Automated Reconstruction of Historic Roof Structures from Point Clouds - Development and Examples

    NASA Astrophysics Data System (ADS)

    Pöchtrager, M.; Styhler-Aydın, G.; Döring-Williams, M.; Pfeifer, N.

    2017-08-01

    The analysis of historic roof constructions is an important task for planning the adaptive reuse of buildings or for maintenance and restoration issues. Current approaches to modeling roof constructions consist of several consecutive operations that need to be done manually or using semi-automatic routines. To increase efficiency and allow the focus to be on analysis rather than on data processing, a set of methods was developed for the fully automated analysis of the roof constructions, including integration of architectural and structural modeling. Terrestrial laser scanning permits high-detail surveying of large-scale structures within a short time. Whereas 3-D laser scan data consist of millions of single points on the object surface, we need a geometric description of structural elements in order to obtain a structural model consisting of beam axis and connections. Preliminary results showed that the developed methods work well for beams in flawless condition with a quadratic cross section and no bending. Deformations or damages such as cracks and cuts on the wooden beams can lead to incomplete representations in the model. Overall, a high degree of automation was achieved.

  18. Genius: a genetic algorithm for automated structure elucidation from 13C NMR spectra.

    PubMed

    Meiler, Jens; Will, Martin

    2002-03-06

    The automated structure elucidation of organic molecules from experimentally obtained properties is extended by an entirely new approach. A genetic algorithm is implemented that uses molecular constitution structures as individuals. With this approach, the structure of organic molecules can be optimized to meet experimental criteria, if in addition a fast and accurate method for the prediction of the used physical or chemical features is available. This is demonstrated using 13C NMR spectrum as readily obtainable information. By means of artificial neural networks a fast and accurate method for calculating the 13C NMR spectrum of the generated structures exists. The method is implemented and tested successfully for organic molecules with up to 18 non-hydrogen atoms.

  19. Application of TIMS data in stratigraphic analysis

    NASA Technical Reports Server (NTRS)

    Lang, H. R.

    1986-01-01

    An in-progress study demonstrates the utility of Thermal Infrared Multispectral Scanner (TIMS) data for unraveling the stratigraphic sequence of a western interior, North American foreland basin. The TIMS data can be used to determine the stratigraphic distribution of minerals that are diagnostic of specific depositional distribution. The thematic mapper (TM) and TIMS data were acquired in the Wind River/Bighorn area of central Wyoming in November 1982, and July 1983, respectively. Combined image processing, photogeologic, and spectral analysis methods were used to: map strata; construct stratigraphic columns; correlate data; and identify mineralogical facies.

  20. Small-scale, semi-automated purification of eukaryotic proteins for structure determination

    PubMed Central

    Frederick, Ronnie O.; Bergeman, Lai; Blommel, Paul G.; Bailey, Lucas J.; McCoy, Jason G.; Song, Jikui; Meske, Louise; Bingman, Craig A.; Riters, Megan; Dillon, Nicholas A.; Kunert, John; Yoon, Jung Whan; Lim, Ahyoung; Cassidy, Michael; Bunge, Jason; Aceti, David J.; Primm, John G.; Markley, John L.; Phillips, George N.

    2007-01-01

    A simple approach that allows cost-effective automated purification of recombinant proteins in levels sufficient for functional characterization or structural studies is described. Studies with four human stem cell proteins, an engineered version of green fluorescent protein, and other proteins are included. The method combines an expression vector (pVP62K) that provides in vivo cleavage of an initial fusion protein, a factorial designed auto-induction medium that improves the performance of small-scale production, and rapid, automated metal affinity purification of His8-tagged proteins. For initial small-scale production screening, single colony transformants were grown overnight in 0.4 ml of auto-induction medium, produced proteins were purified using the Promega Maxwell 16, and purification results were analyzed by Caliper LC90 capillary electrophoresis. The yield of purified [U-15N]-His8-Tcl-1 was 7.5 μg/ml of culture medium, of purified [U-15N]-His8-GFP was 68 μg/ml, and of purified selenomethione-labeled AIA–GFP (His8 removed by treatment with TEV protease) was 172 μg/ml. The yield information obtained from a successful automated purification from 0.4 ml was used to inform the decision to scale-up for a second meso-scale (10–50 ml) cell growth and automated purification. 1H–15N NMR HSQC spectra of His8-Tcl-1 and of His8-GFP prepared from 50 ml cultures showed excellent chemical shift dispersion, consistent with well folded states in solution suitable for structure determination. Moreover, AIA–GFP obtained by proteolytic removal of the His8 tag was subjected to crystallization screening, and yielded crystals under several conditions. Single crystals were subsequently produced and optimized by the hanging drop method. The structure was solved by molecular replacement at a resolution of 1.7 Å. This approach provides an efficient way to carry out several key target screening steps that are essential for successful operation of proteomics

  1. Automated design optimization of supersonic airplane wing structures under dynamic constraints

    NASA Technical Reports Server (NTRS)

    Fox, R. L.; Miura, H.; Rao, S. S.

    1972-01-01

    The problems of the preliminary and first level detail design of supersonic aircraft wings are stated as mathematical programs and solved using automated optimum design techniques. The problem is approached in two phases: the first is a simplified equivalent plate model in which the envelope, planform and structural parameters are varied to produce a design, the second is a finite element model with fixed configuration in which the material distribution is varied. Constraints include flutter, aeroelastically computed stresses and deflections, natural frequency and a variety of geometric limitations.

  2. Small-scale, semi-automated purification of eukaryotic proteins for structure determination.

    PubMed

    Frederick, Ronnie O; Bergeman, Lai; Blommel, Paul G; Bailey, Lucas J; McCoy, Jason G; Song, Jikui; Meske, Louise; Bingman, Craig A; Riters, Megan; Dillon, Nicholas A; Kunert, John; Yoon, Jung Whan; Lim, Ahyoung; Cassidy, Michael; Bunge, Jason; Aceti, David J; Primm, John G; Markley, John L; Phillips, George N; Fox, Brian G

    2007-12-01

    A simple approach that allows cost-effective automated purification of recombinant proteins in levels sufficient for functional characterization or structural studies is described. Studies with four human stem cell proteins, an engineered version of green fluorescent protein, and other proteins are included. The method combines an expression vector (pVP62K) that provides in vivo cleavage of an initial fusion protein, a factorial designed auto-induction medium that improves the performance of small-scale production, and rapid, automated metal affinity purification of His8-tagged proteins. For initial small-scale production screening, single colony transformants were grown overnight in 0.4 ml of auto-induction medium, produced proteins were purified using the Promega Maxwell 16, and purification results were analyzed by Caliper LC90 capillary electrophoresis. The yield of purified [U-15N]-His8-Tcl-1 was 7.5 microg/ml of culture medium, of purified [U-15N]-His8-GFP was 68 microg/ml, and of purified selenomethione-labeled AIA-GFP (His8 removed by treatment with TEV protease) was 172 microg/ml. The yield information obtained from a successful automated purification from 0.4 ml was used to inform the decision to scale-up for a second meso-scale (10-50 ml) cell growth and automated purification. 1H-15N NMR HSQC spectra of His8-Tcl-1 and of His8-GFP prepared from 50 ml cultures showed excellent chemical shift dispersion, consistent with well folded states in solution suitable for structure determination. Moreover, AIA-GFP obtained by proteolytic removal of the His8 tag was subjected to crystallization screening, and yielded crystals under several conditions. Single crystals were subsequently produced and optimized by the hanging drop method. The structure was solved by molecular replacement at a resolution of 1.7 A. This approach provides an efficient way to carry out several key target screening steps that are essential for successful operation of proteomics pipelines

  3. Automated design optimization of supersonic airplane wing structures under dynamic constraints.

    NASA Technical Reports Server (NTRS)

    Fox, R. L.; Miura, H.; Rao, S. S.

    1972-01-01

    The problems of the preliminary and first level detail design of supersonic aircraft wings are stated as mathematical programs and solved using automated optimum design techniques. The problem is approached in two phases: the first is a simplified equivalent plate model in which the envelope, plan form and structural parameters are varied to produce a design, the second is a finite element model with fixed configuration in which the material distribution is varied. Constraints include flutter, aeroelastically computed stresses and deflections, natural frequency and a variety of geometric limitations. The Phase I objective is a combination of weight and drag while Phase II is a weight minimization.

  4. Automated High Throughput Protein Crystallization Screening at Nanoliter Scale and Protein Structural Study on Lactate Dehydrogenase

    SciTech Connect

    Li, Fenglei

    2006-08-09

    The purposes of our research were: (1) To develop an economical, easy to use, automated, high throughput system for large scale protein crystallization screening. (2) To develop a new protein crystallization method with high screening efficiency, low protein consumption and complete compatibility with high throughput screening system. (3) To determine the structure of lactate dehydrogenase complexed with NADH by x-ray protein crystallography to study its inherent structural properties. Firstly, we demonstrated large scale protein crystallization screening can be performed in a high throughput manner with low cost, easy operation. The overall system integrates liquid dispensing, crystallization and detection and serves as a whole solution to protein crystallization screening. The system can dispense protein and multiple different precipitants in nanoliter scale and in parallel. A new detection scheme, native fluorescence, has been developed in this system to form a two-detector system with a visible light detector for detecting protein crystallization screening results. This detection scheme has capability of eliminating common false positives by distinguishing protein crystals from inorganic crystals in a high throughput and non-destructive manner. The entire system from liquid dispensing, crystallization to crystal detection is essentially parallel, high throughput and compatible with automation. The system was successfully demonstrated by lysozyme crystallization screening. Secondly, we developed a new crystallization method with high screening efficiency, low protein consumption and compatibility with automation and high throughput. In this crystallization method, a gas permeable membrane is employed to achieve the gentle evaporation required by protein crystallization. Protein consumption is significantly reduced to nanoliter scale for each condition and thus permits exploring more conditions in a phase diagram for given amount of protein. In addition

  5. Formation and evolution of the midlands of Venus: Geological features and structures, stratigraphic relationships and geologic history of the Fredegonde area (V-57)

    NASA Astrophysics Data System (ADS)

    Ivanov, Mikhail A.; Head, James W.

    2012-12-01

    The topographic midlands on Venus comprise about 80% of the surface and an understanding of their mode of formation is essential to unraveling the geologic and geodynamic history of the planet. We explore this question by undertaking a comprehensive geological mapping of the Fredegonde Quadrangle (V-57, 50-75°S, 60-120°E, 1:5M scale) that represents the transition zone from the midlands to the lowlands at the edge of Lada Terra. We report on the geologic units and structures and the sequence of events and, thus, the major stages in the evolution of this region of the midlands. At earlier stages of evolution of the long-wavelength topography, broad (hundreds of kilometers wide) and relatively low (1-1.5 km high) topographic ridges formed due to sequential development of deformation zones, first of contractional ridge belts (NW orientation) and then crosscut by extensional groove belts (NE orientation). Arcuate swarms of graben within groove belts often form the rims of coronae and represent their tectonic component. This suggests that groove belts and coronae within the quadrangle formed simultaneously. Intersections of these deformation zones caused separation of the topography of the region into a series of broad, shallow equidimensional basins many hundreds of kilometers across and currently hundreds of meters up to a kilometer deep. Thus, the principal topographic features within the quadrangle were established near the beginning of its observable geological record. The basins then remained sites of accumulation of successive volcanic plains units such as shield plains (psh) and the lower unit of regional plains (rp1). The flows of the younger plains, such as upper unit of regional plains (rp2) and lobate plains (pl), are less voluminous, and flow down the current topographic gradients. This implies that the major topographic pattern of the Fredegonde quadrangle has been stable since its establishment. Further evidence for this is that the vast volcanic plains

  6. Automating crystallographic structure solution and refinement of protein–ligand complexes

    SciTech Connect

    Echols, Nathaniel Moriarty, Nigel W. Klei, Herbert E.; Afonine, Pavel V.; Bunkóczi, Gábor; McCoy, Airlie J.; Oeffner, Robert D.; Read, Randy J.; Adams, Paul D.

    2014-01-01

    A software system for automated protein–ligand crystallography has been implemented in the Phenix suite. This significantly reduces the manual effort required in high-throughput crystallographic studies. High-throughput drug-discovery and mechanistic studies often require the determination of multiple related crystal structures that only differ in the bound ligands, point mutations in the protein sequence and minor conformational changes. If performed manually, solution and refinement requires extensive repetition of the same tasks for each structure. To accelerate this process and minimize manual effort, a pipeline encompassing all stages of ligand building and refinement, starting from integrated and scaled diffraction intensities, has been implemented in Phenix. The resulting system is able to successfully solve and refine large collections of structures in parallel without extensive user intervention prior to the final stages of model completion and validation.

  7. New tissue priors for improved automated classification of subcortical brain structures on MRI☆

    PubMed Central

    Lorio, S.; Fresard, S.; Adaszewski, S.; Kherif, F.; Chowdhury, R.; Frackowiak, R.S.; Ashburner, J.; Helms, G.; Weiskopf, N.; Lutti, A.; Draganski, B.

    2016-01-01

    Despite the constant improvement of algorithms for automated brain tissue classification, the accurate delineation of subcortical structures using magnetic resonance images (MRI) data remains challenging. The main difficulties arise from the low gray-white matter contrast of iron rich areas in T1-weighted (T1w) MRI data and from the lack of adequate priors for basal ganglia and thalamus. The most recent attempts to obtain such priors were based on cohorts with limited size that included subjects in a narrow age range, failing to account for age-related gray-white matter contrast changes. Aiming to improve the anatomical plausibility of automated brain tissue classification from T1w data, we have created new tissue probability maps for subcortical gray matter regions. Supported by atlas-derived spatial information, raters manually labeled subcortical structures in a cohort of healthy subjects using magnetization transfer saturation and R2* MRI maps, which feature optimal gray-white matter contrast in these areas. After assessment of inter-rater variability, the new tissue priors were tested on T1w data within the framework of voxel-based morphometry. The automated detection of gray matter in subcortical areas with our new probability maps was more anatomically plausible compared to the one derived with currently available priors. We provide evidence that the improved delineation compensates age-related bias in the segmentation of iron rich subcortical regions. The new tissue priors, allowing robust detection of basal ganglia and thalamus, have the potential to enhance the sensitivity of voxel-based morphometry in both healthy and diseased brains. PMID:26854557

  8. Forward Modeling of Stratigraphic Sequences at Continental Margins

    DTIC Science & Technology

    1998-09-30

    can now take into account along-strike variations in tectonic subsidence and the alterations to the sediment loading they cause. This was required...investigate the sequence architecture in rift basins. Initial experiments suggest that changes in sea level, rather than in sediment supply or tectonics are...patterns in extensional settings, AAPG Hedberg Conference, Integrated Structural and Sequence Stratigraphic Analysis in Rift Settings, Cairo, Egypt

  9. Automated measurement of CT noise in patient images with a novel structure coherence feature

    NASA Astrophysics Data System (ADS)

    Chun, Minsoo; Choi, Young Hun; Hyo Kim, Jong

    2015-12-01

    While the assessment of CT noise constitutes an important task for the optimization of scan protocols in clinical routine, the majority of noise measurements in practice still rely on manual operation, hence limiting their efficiency and reliability. This study presents an algorithm for the automated measurement of CT noise in patient images with a novel structure coherence feature. The proposed algorithm consists of a four-step procedure including subcutaneous fat tissue selection, the calculation of structure coherence feature, the determination of homogeneous ROIs, and the estimation of the average noise level. In an evaluation with 94 CT scans (16 517 images) of pediatric and adult patients along with the participation of two radiologists, ROIs were placed on a homogeneous fat region at 99.46% accuracy, and the agreement of the automated noise measurements with the radiologists’ reference noise measurements (PCC  =  0.86) was substantially higher than the within and between-rater agreements of noise measurements (PCCwithin  =  0.75, PCCbetween  =  0.70). In addition, the absolute noise level measurements matched closely the theoretical noise levels generated by a reduced-dose simulation technique. Our proposed algorithm has the potential to be used for examining the appropriateness of radiation dose and the image quality of CT protocols for research purposes as well as clinical routine.

  10. Automated measurement of lysosomal structure alterations in oocytes of mussels exposed to petroleum hydrocarbons.

    PubMed

    Cajaraville, M P; Marigómez, J A; Angulo, E

    1991-09-01

    The present study examines the structure of the lysosomal system of mature oocytes in mussels, Mytilus galloprovincialis, after a 21 day exposure to the water accommodated fraction (WAF) of two crude oils (types Ural and Maya) and of a commercial lubricant oil. The automated image analysis indicates that lysosomes, showing cytochemically demonstrable beta-glucuronidase activity, are smaller and much more numerous in oocytes of mussels treated with a 40% dose of Ural- and Lubricant-WAF when compared to controls. It is suggested that the structure of the lysosomal system of oocytes is different from that of somatic cells (i.e., digestive cells) and that budding or "fission" into smaller bodies occurs in oocyte lysosomes under certain petroleum hydrocarbon-exposure conditions. These changes in the lysosomal compartment appear to be associated to the process of gamete release or spawning.

  11. An expert system executive for automated assembly of large space truss structures

    NASA Technical Reports Server (NTRS)

    Allen, Cheryl L.

    1993-01-01

    Langley Research Center developed a unique test bed for investigating the practical problems associated with the assembly of large space truss structures using robotic manipulators. The test bed is the result of an interdisciplinary effort that encompasses the full spectrum of assembly problems - from the design of mechanisms to the development of software. The automated structures assembly test bed and its operation are described, the expert system executive and its development are detailed, and the planned system evolution is discussed. Emphasis is on the expert system implementation of the program executive. The executive program must direct and reliably perform complex assembly tasks with the flexibility to recover from realistic system errors. The employment of an expert system permits information that pertains to the operation of the system to be encapsulated concisely within a knowledge base. This consolidation substantially reduced code, increased flexibility, eased software upgrades, and realized a savings in software maintenance costs.

  12. Automated assembly of large space structures using an expert system executive

    NASA Technical Reports Server (NTRS)

    Allen, Cheryl L.

    1993-01-01

    NASA LaRC has developed a unique testbed for investigating the practical problems associated with the assembly of large space structures using robotic manipulators. The testbed is an interdisciplinary effort which considers the full spectrum of assembly problems from the design of mechanisms to the development of software. This paper will describe the automated structures assembly testbed and its operation, detail the expert system executive and its development, and discuss the planned system evolution. Emphasis will be placed on the expert system development of the program executive. The executive program must be capable of directing and reliably performing complex assembly tasks with the flexibility to recover from realistic system errors. By employing an expert system, information pertaining to the operation of the system was encapsulated concisely within a knowledge base. This lead to a substantial reduction in code, increased flexibility, eased software upgrades, and realized a savings in software maintenance costs.

  13. Some debatable problems of stratigraphic classification

    NASA Astrophysics Data System (ADS)

    Gladenkov, Yury

    2014-05-01

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

  14. Automating gene library synthesis by structure-based combinatorial protein engineering: examples from plant sesquiterpene synthases.

    PubMed

    Dokarry, Melissa; Laurendon, Caroline; O'Maille, Paul E

    2012-01-01

    Structure-based combinatorial protein engineering (SCOPE) is a homology-independent recombination method to create multiple crossover gene libraries by assembling defined combinations of structural elements ranging from single mutations to domains of protein structure. SCOPE was originally inspired by DNA shuffling, which mimics recombination during meiosis, where mutations from parental genes are "shuffled" to create novel combinations in the resulting progeny. DNA shuffling utilizes sequence identity between parental genes to mediate template-switching events (the annealing and extension of one parental gene fragment on another) in PCR reassembly reactions to generate crossovers and hence recombination between parental genes. In light of the conservation of protein structure and degeneracy of sequence, SCOPE was developed to enable the "shuffling" of distantly related genes with no requirement for sequence identity. The central principle involves the use of oligonucleotides to encode for crossover regions to choreograph template-switching events during PCR assembly of gene fragments to create chimeric genes. This approach was initially developed to create libraries of hybrid DNA polymerases from distantly related parents, and later developed to create a combinatorial mutant library of sesquiterpene synthases to explore the catalytic landscapes underlying the functional divergence of related enzymes. This chapter presents a simplified protocol of SCOPE that can be integrated with different mutagenesis techniques and is suitable for automation by liquid-handling robots. Two examples are presented to illustrate the application of SCOPE to create gene libraries using plant sesquiterpene synthases as the model system. In the first example, we outline how to create an active-site library as a series of complex mixtures of diverse mutants. In the second example, we outline how to create a focused library as an array of individual clones to distil minimal combinations of

  15. A method for fully automated measurement of neurological structures in MRI

    NASA Astrophysics Data System (ADS)

    Ashton, Edward A.; Riek, Jonathan K.; Molinelli, Larry; Berg, Michel J.; Parker, Kevin J.

    2003-05-01

    A method for fully automating the measurement of various neurological structures in MRI is presented. This technique uses an atlas-based trained maximum likelihood classifier. The classifier requires a map of prior probabilities, which is obtained by registering a large number of previously classified data sets to the atlas and calculating the resulting probability that each represented tissue type or structure will appear at each voxel in the data set. Classification is then carried out using the standard maximum likelihood discriminant function, assuming normal statistics. The results of this classification process can be used in three ways, depending on the type of structure that is being detected or measured. In the most straightforward case, measurement of a normal neural sub-structure such as the hippocampus, the results of the classifier provide a localization point for the initiation of a deformable template model, which is then optimized with respect to the original data. The detection and measurement of abnormal structures, such as white matter lesions in multiple sclerosis patients, requires a slightly different approach. Lesions are detected through the application of a spectral matched filter to areas identified by the classifier as white matter. Finally, detection of unknown abnormalities can be accomplished through anomaly detection.

  16. A script for automated 3-dimentional structure generation and conformer search from 2- dimentional chemical drawing.

    PubMed

    Ishikawa, Yoshinobu

    2013-01-01

    Building 3-dimensional (3D) molecules is the starting point in molecular modeling. Conformer search and identification of a global energy minimum structure are often performed computationally during spectral analysis of data from NMR, IR, and VCD or during rational drug design through ligand-based, structure-based, and QSAR approaches. I herein report a convenient script that allows for automated building of 3D structures and conformer searching from 2-dimensional (2D) drawing of chemical structures. With this Bash shell script, which runs on Mac OS X and the Linux platform, the tasks are consecutively and iteratively executed without a 3D molecule builder via the command line interface of the free (academic) software OpenBabel, Balloon, and MOPAC2012. A large number of 2D chemical drawing files can be processed simultaneously, and the script functions with stereoisomers. Semi-empirical quantum chemical calculation ensures reliable ranking of the generated conformers on the basis of energy. In addition to an energy-sorted list of file names of the conformers, their Gaussian input files are provided for ab initio and density functional theory calculations to predict rigorous electronic energies, structures, and properties. This script is freely available to all scientists.

  17. A Script for Automated 3-Dimentional Structure Generation and Conformer Search from 2- Dimentional Chemical Drawing

    PubMed Central

    Ishikawa, Yoshinobu

    2013-01-01

    Building 3-dimensional (3D) molecules is the starting point in molecular modeling. Conformer search and identification of a global energy minimum structure are often performed computationally during spectral analysis of data from NMR, IR, and VCD or during rational drug design through ligand-based, structure-based, and QSAR approaches. I herein report a convenient script that allows for automated building of 3D structures and conformer searching from 2-dimensional (2D) drawing of chemical structures. With this Bash shell script, which runs on Mac OS X and the Linux platform, the tasks are consecutively and iteratively executed without a 3D molecule builder via the command line interface of the free (academic) software OpenBabel, Balloon, and MOPAC2012. A large number of 2D chemical drawing files can be processed simultaneously, and the script functions with stereoisomers. Semi-empirical quantum chemical calculation ensures reliable ranking of the generated conformers on the basis of energy. In addition to an energy-sorted list of file names of the conformers, their Gaussian input files are provided for ab initio and density functional theory calculations to predict rigorous electronic energies, structures, and properties. This script is freely available to all scientists. PMID:24391363

  18. Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA.

    PubMed

    Mareuil, Fabien; Malliavin, Thérèse E; Nilges, Michael; Bardiaux, Benjamin

    2015-08-01

    In biological NMR, assignment of NOE cross-peaks and calculation of atomic conformations are critical steps in the determination of reliable high-resolution structures. ARIA is an automated approach that performs NOE assignment and structure calculation in a concomitant manner in an iterative procedure. The log-harmonic shape for distance restraint potential and the Bayesian weighting of distance restraints, recently introduced in ARIA, were shown to significantly improve the quality and the accuracy of determined structures. In this paper, we propose two modifications of the ARIA protocol: (1) the softening of the force field together with adapted hydrogen radii, which is meaningful in the context of the log-harmonic potential with Bayesian weighting, (2) a procedure that automatically adjusts the violation tolerance used in the selection of active restraints, based on the fitting of the structure to the input data sets. The new ARIA protocols were fine-tuned on a set of eight protein targets from the CASD-NMR initiative. As a result, the convergence problems previously observed for some targets was resolved and the obtained structures exhibited better quality. In addition, the new ARIA protocols were applied for the structure calculation of ten new CASD-NMR targets in a blind fashion, i.e. without knowing the actual solution. Even though optimisation of parameters and pre-filtering of unrefined NOE peak lists were necessary for half of the targets, ARIA consistently and reliably determined very precise and highly accurate structures for all cases. In the context of integrative structural biology, an increasing number of experimental methods are used that produce distance data for the determination of 3D structures of macromolecules, stressing the importance of methods that successfully make use of ambiguous and noisy distance data.

  19. Revision and update of the stratigraphic nomenclature of Netherlands

    SciTech Connect

    Van Adrichem Boogaert, A. ); Kouwe, W. )

    1993-09-01

    In 1991, the Geological Survey of the Netherlands started a project for revision and updating of the pre-Quaternary lithostratigraphy of Netherlands. This had not been done systematically since 1980. Main objective of the study are (1) to bring the lithostratigraphic ideas into agreement with new findings and increased knowledge of Dutch subsurface geology (lithostratigraphy was extended into the Lower Carboniferous and Devonian), (2) expansion and standardization of the definitions and descriptions of existing lithostratigraphic units, (3) application of modern concepts (e.g. sequence stratigraphy) in order to describe better the distribution of reservoir-prone sediments, and (4) to reach consensus on a number of stratigraphy-related subjects, such as a chronological time frame, application of biozonations, and the designation of the behavior of main structural elements through time. Eight working groups were formed, each working on a specific aspect or stratigraphic interval, under the supervision of a steering committee. Both working groups and steering committee were composed of persons from the Geological Survey, several leading oil companies and, in some cases, universities. Several working groups have completed their tasks, and updates of these stratigraphic intervals are available at the conference. Posters will display stratigraphic updates of lithostratigraphy for the Carboniferous, Zechstein, Lower Triassic, and Upper Jurassic-Lower Cretaceous.

  20. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta.

    PubMed

    Wang, Ray Yu-Ruei; Song, Yifan; Barad, Benjamin A; Cheng, Yifan; Fraser, James S; DiMaio, Frank

    2016-09-26

    Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions, accurately positioning individual atoms remains challenging and error-prone. Manually refining thousands of amino acids - typical in a macromolecular assembly - is tedious and time-consuming. We present an automated method that can improve the atomic details in models that are manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate that the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps.

  1. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

    PubMed Central

    Wang, Ray Yu-Ruei; Song, Yifan; Barad, Benjamin A; Cheng, Yifan; Fraser, James S; DiMaio, Frank

    2016-01-01

    Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3–4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions, accurately positioning individual atoms remains challenging and error-prone. Manually refining thousands of amino acids – typical in a macromolecular assembly – is tedious and time-consuming. We present an automated method that can improve the atomic details in models that are manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate that the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps. DOI: http://dx.doi.org/10.7554/eLife.17219.001 PMID:27669148

  2. Automated torso organ segmentation from 3D CT images using structured perceptron and dual decomposition

    NASA Astrophysics Data System (ADS)

    Nimura, Yukitaka; Hayashi, Yuichiro; Kitasaka, Takayuki; Mori, Kensaku

    2015-03-01

    This paper presents a method for torso organ segmentation from abdominal CT images using structured perceptron and dual decomposition. A lot of methods have been proposed to enable automated extraction of organ regions from volumetric medical images. However, it is necessary to adjust empirical parameters of them to obtain precise organ regions. This paper proposes an organ segmentation method using structured output learning. Our method utilizes a graphical model and binary features which represent the relationship between voxel intensities and organ labels. Also we optimize the weights of the graphical model by structured perceptron and estimate the best organ label for a given image by dynamic programming and dual decomposition. The experimental result revealed that the proposed method can extract organ regions automatically using structured output learning. The error of organ label estimation was 4.4%. The DICE coefficients of left lung, right lung, heart, liver, spleen, pancreas, left kidney, right kidney, and gallbladder were 0.91, 0.95, 0.77, 0.81, 0.74, 0.08, 0.83, 0.84, and 0.03, respectively.

  3. Modelling and interpreting biologically crusted dryland soil sub-surface structure using automated micropenetrometry

    NASA Astrophysics Data System (ADS)

    Hoon, Stephen R.; Felde, Vincent J. M. N. L.; Drahorad, Sylvie L.; Felix-Henningsen, Peter

    2015-04-01

    Soil penetrometers are used routinely to determine the shear strength of soils and deformable sediments both at the surface and throughout a depth profile in disciplines as diverse as soil science, agriculture, geoengineering and alpine avalanche-safety (e.g. Grunwald et al. 2001, Van Herwijnen et al. 2009). Generically, penetrometers comprise two principal components: An advancing probe, and a transducer; the latter to measure the pressure or force required to cause the probe to penetrate or advance through the soil or sediment. The force transducer employed to determine the pressure can range, for example, from a simple mechanical spring gauge to an automatically data-logged electronic transducer. Automated computer control of the penetrometer step size and probe advance rate enables precise measurements to be made down to a resolution of 10's of microns, (e.g. the automated electronic micropenetrometer (EMP) described by Drahorad 2012). Here we discuss the determination, modelling and interpretation of biologically crusted dryland soil sub-surface structures using automated micropenetrometry. We outline a model enabling the interpretation of depth dependent penetration resistance (PR) profiles and their spatial differentials using the model equations, σ {}(z) ={}σ c0{}+Σ 1n[σ n{}(z){}+anz + bnz2] and dσ /dz = Σ 1n[dσ n(z) /dz{} {}+{}Frn(z)] where σ c0 and σ n are the plastic deformation stresses for the surface and nth soil structure (e.g. soil crust, layer, horizon or void) respectively, and Frn(z)dz is the frictional work done per unit volume by sliding the penetrometer rod an incremental distance, dz, through the nth layer. Both σ n(z) and Frn(z) are related to soil structure. They determine the form of σ {}(z){} measured by the EMP transducer. The model enables pores (regions of zero deformation stress) to be distinguished from changes in layer structure or probe friction. We have applied this method to both artificial calibration soils in the

  4. Description and recognition of regular and distorted secondary structures in proteins using the automated protein structure analysis method.

    PubMed

    Ranganathan, Sushilee; Izotov, Dmitry; Kraka, Elfi; Cremer, Dieter

    2009-08-01

    The Automated Protein Structure Analysis (APSA) method, which describes the protein backbone as a smooth line in three-dimensional space and characterizes it by curvature kappa and torsion tau as a function of arc length s, was applied on 77 proteins to determine all secondary structural units via specific kappa(s) and tau(s) patterns. A total of 533 alpha-helices and 644 beta-strands were recognized by APSA, whereas DSSP gives 536 and 651 units, respectively. Kinks and distortions were quantified and the boundaries (entry and exit) of secondary structures were classified. Similarity between proteins can be easily quantified using APSA, as was demonstrated for the roll architecture of proteins ubiquitin and spinach ferridoxin. A twenty-by-twenty comparison of all alpha domains showed that the curvature-torsion patterns generated by APSA provide an accurate and meaningful similarity measurement for secondary, super secondary, and tertiary protein structure. APSA is shown to accurately reflect the conformation of the backbone effectively reducing three-dimensional structure information to two-dimensional representations that are easy to interpret and understand. 2008 Wiley-Liss, Inc.

  5. Managing expectations: assessment of chemistry databases generated by automated extraction of chemical structures from patents.

    PubMed

    Senger, Stefan; Bartek, Luca; Papadatos, George; Gaulton, Anna

    2015-12-01

    First public disclosure of new chemical entities often takes place in patents, which makes them an important source of information. However, with an ever increasing number of patent applications, manual processing and curation on such a large scale becomes even more challenging. An alternative approach better suited for this large corpus of documents is the automated extraction of chemical structures. A number of patent chemistry databases generated by using the latter approach are now available but little is known that can help to manage expectations when using them. This study aims to address this by comparing two such freely available sources, SureChEMBL and IBM SIIP (IBM Strategic Intellectual Property Insight Platform), with manually curated commercial databases. When looking at the percentage of chemical structures successfully extracted from a set of patents, using SciFinder as our reference, 59 and 51 % were also found in our comparison in SureChEMBL and IBM SIIP, respectively. When performing this comparison with compounds as starting point, i.e. establishing if for a list of compounds the databases provide the links between chemical structures and patents they appear in, we obtained similar results. SureChEMBL and IBM SIIP found 62 and 59 %, respectively, of the compound-patent pairs obtained from Reaxys. In our comparison of automatically generated vs. manually curated patent chemistry databases, the former successfully provided approximately 60 % of links between chemical structure and patents. It needs to be stressed that only a very limited number of patents and compound-patent pairs were used for our comparison. Nevertheless, our results will hopefully help to manage expectations of users of patent chemistry databases of this type and provide a useful framework for more studies like ours as well as guide future developments of the workflows used for the automated extraction of chemical structures from patents. The challenges we have encountered

  6. Some New Constraints On The Stratigraphic And Structural Setting Of The Soda Lake Geothermal Field, Churchill County, Nevada - McLACHLAN, Holly S. and FAULDS, James E., Nevada Bureau of Mines and Geology, University of Nevada, Reno, NV 89557

    NASA Astrophysics Data System (ADS)

    McLachlan, H. S.

    2012-12-01

    consist of a thick (>1500 m) package of fine-grained altered basalts and interbedded sedimentary rocks. Within this package, in the central portion of the well field, a ~300-500 m thick marker of laminated siltstones + coarse-grained, porphyritic plagioclase basalt has been identified in cuttings. Variations in thickness within the marker suggest older faults with significant throw were primarily northwest striking. Large local variations in the thickness of the 5.11 Ma trachytic basalt body support this interpretation and indicate NW-striking faulting likely continued through ~5 Ma B.P. However, all evidence indicates near-surface (<1000 m depth) faults at the Soda Lake geothermal field strike NNE, perpendicular to the contemporary extension direction. Structural interpretation is in progress for the Soda Lake geothermal field. In conjunction with recently obtained 3D seismic and microgravity surveys, stratigraphic information obtained from cuttings broadly constrains the structural setting. These data may permit determination of the specific structural host environment and should allow for assessment of how the prevailing faults at the site correlate with regional scale trends.

  7. Vibration based structural health monitoring of an arch bridge: From automated OMA to damage detection

    NASA Astrophysics Data System (ADS)

    Magalhães, F.; Cunha, A.; Caetano, E.

    2012-04-01

    In order to evaluate the usefulness of approaches based on modal parameters tracking for structural health monitoring of bridges, in September of 2007, a dynamic monitoring system was installed in a concrete arch bridge at the city of Porto, in Portugal. The implementation of algorithms to perform the continuous on-line identification of modal parameters based on structural responses to ambient excitation (automated Operational Modal Analysis) has permitted to create a very complete database with the time evolution of the bridge modal characteristics during more than 2 years. This paper describes the strategy that was followed to minimize the effects of environmental and operational factors on the bridge natural frequencies, enabling, in a subsequent stage, the identification of structural anomalies. Alternative static and dynamic regression models are tested and complemented by a Principal Components Analysis. Afterwards, the identification of damages is tried with control charts. At the end, it is demonstrated that the adopted processing methodology permits the detection of realistic damage scenarios, associated with frequency shifts around 0.2%, which were simulated with a numerical model.

  8. Automated mutual exclusion rules discovery for structured observational codes in echocardiography reporting

    PubMed Central

    Forsberg, Thomas A.; Sevenster, Merlijn; Bieganski, Szymon; Bhagat, Puran; Kanasseril, Melvin; Jia, Yugang; Spencer, Kirk T.

    2015-01-01

    Structured reporting in medicine has been argued to support and enhance machine-assisted processing and communication of pertinent information. Retrospective studies showed that structured echocardiography reports, constructed through point-and-click selection of finding codes (FCs), contain pair-wise contradictory FCs (e.g., “No tricuspid regurgitation” and “Severe regurgitation”) downgrading report quality and reliability thereof. In a prospective study, contradictions were detected automatically using an extensive rule set that encodes mutual exclusion patterns between FCs. Rules creation is a labor and knowledge-intensive task that could benefit from automation. We propose a machine-learning approach to discover mutual exclusion rules in a corpus of 101,211 structured echocardiography reports through semantic and statistical analysis. Ground truth is derived from the extensive prospectively evaluated rule set. On the unseen test set, F-measure (0.439) and above-chance level AUC (0.885) show that our approach can potentially support the manual rules creation process. Our methods discovered previously unknown rules per expert review. PMID:26958191

  9. Stratigraphic control of flow and transport characteristics.

    PubMed

    Edington, Dwaine; Poeter, Eileen

    2007-01-01

    Ground water flow and travel time are dependent on stratigraphic architecture, which is governed by competing processes that control the spatial and temporal distribution of accommodation and sediment supply. Accommodation is the amount of space in which sediment may accumulate as defined by the difference between the energy gradient and the topographic surface. The temporal and spatial distribution of accommodation is affected by processes that change the distribution of energy (e.g., sea level or subsidence). Fluvial stratigraphic units, generated by FLUVSIM (a stratigraphic simulator based on accommodation and sediment supply), with varying magnitudes and causes of accommodation, were incorporated into a hydraulic regime using MODFLOW (a ground water flow simulator), and particles were tracked using MODPATH (a particle-tracking algorithm). These experiments illustrate that the dominant type of accommodation process influences the degree of continuity of stratigraphic units and thus affects ground water flow and transport. When the hydraulic gradient is parallel to the axis of the fluvial system in the depositional environment, shorter travel times occur in low-total accommodation environments and longer travel times in high-total accommodation environments. Given the same total accommodation, travel times are longer when sea-level change is the dominant process than those in systems dominated by subsidence.

  10. Colorstratigraphy; A New Stratigraphic Correlation Technique

    NASA Astrophysics Data System (ADS)

    Nanayakkara, N. U.; Ranasinghage, P. N.; Priyantha, C.; Abillapitiya, T.

    2016-12-01

    Here we introduce a novel stratigraphic technique namely colorstratigraphy for correlating sedimentary sequences. Minihagalkanda is about 1 km long amphitheater like sedimentary terrain, situated at the southeastern coast of Sri Lanka. It has Miocene sedimentary sequences, separated in to 10-12 m high small hillocks by erosion, and bounded by about 30 m high escarpment. Sandstone, yellowish sandy clay, greenish silty clay sequences are capped by 4-5 m limestone bed in these hillocks but not at the boundary escarpment. Stratigraphic profiles at two hillocks and the boundary escarpment, separated each other by 200-300 m, were selected to test the new colorstartigraphic correlation technique. Color reflectance (DSR) was measured at four samples in each sequence at every profile and hence altogether 36 reflectance measurements were taken using Minolta 2500D hand-held color spectrophotometer. The first-derivative of the reflectance spectra (dR/dλ) defines the "spectral shape" of the sample. Therefore, DSR data (360-740 nm) measured at 10 nm resolution were used to calculate a center-weighted, first-derivative spectra for each reflectance sample consisting of 39 channels. Particle size of each sequence was measured at all 03 profiles using laser particle size analyzer to verify the stratigraphic correlation. Mean reflectance spectrum for each sequence at all 03 profiles were plotted on the same graph for comparison. Same was done for the grain size spectrums. Discriminant function analysis was performed separately for dsr data and grain size data using a number assigned to each sedimentary sequence as the grouping variable Color spectrums of sandstone, yellowish sandy clay, and greenish silty clay sequences at all three profiles perfectly match showing clear stratigraphic correlation among these three stratigraphic profiles. Matching grain size distribution curves of the three sequence at the three profiles verify the stratigraphic correlation. Perfect 100

  11. Automated metric characterization of urban structure using building decomposition from very high resolution imagery

    NASA Astrophysics Data System (ADS)

    Heinzel, Johannes; Kemper, Thomas

    2015-03-01

    Classification approaches for urban areas are mostly of qualitative and semantic nature. They produce interpreted classes similar to those from land cover and land use classifications. As a complement to those classes, quantitative measures directly derived from the image could lead to a metric characterization of the urban area. While these metrics lack of qualitative interpretation they are able to provide objective measure of the urban structures. Such quantitative measures are especially important in rapidly growing cities since, beside of the growth in area, they can provide structural information for specific areas and detect changes. Rustenburg, which serves as test area for the present study, is amongst the fastest growing cities in South Africa. It reveals a heterogeneous face of housing and building structures reflecting social and/or economic differences often linked to the spatial distribution of industrial and local mining sites. Up to date coverage with aerial photographs is provided by aerial surveys in regular intervals. Also recent satellite systems provide imagery with suitable resolution. Using such set of very high resolution images a fully automated algorithm has been developed which outputs metric classes by systematically combining important measures of building structure. The measurements are gained by decomposition of buildings directly from the imagery and by using methods from mathematical morphology. The decomposed building objects serve as basis for the computation of grid statistics. Finally a systematic combination of the single features leads to combined metrical classes. For the dominant urban structures verification results indicate an overall accuracy of at least 80% on the single feature level and 70% for the combined classes.

  12. Harmony field, Clarke County, Mississippi: a true stratigraphic trap

    SciTech Connect

    Lieber, R.B.; Carothers, M.C.

    1983-09-01

    Harmony field in Clarke County, Mississippi, has produced approximately 2 million bbl of oil since its discovery in 1968. Production has been from oolitic grainstones in the upper Jurasic Smackover Formation. The trappng mechanism at Harmony field is a complex stratigraphic trap. Porous oolitic grainstones pinch out updip into tight carbonates and anhydrite. Structure contour maps on top of the Smackover Formation indicate a low relief structural nose associated with the field. Additional structure maps contoured at the top of the Haynesville anhydrite, approximately 500 ft (150 m) above the top of the Smackover, reveal only regional southwesterly dip. An isopach map of the interval between the two structural markers shows a thinning of Haynesville section coincident with the field area. Evidence suggests, therefore, that the porous Smackover in Harmony field was deposited with depositional relief above the surrounding sediments. This relief had been completely masked by the time the Haynesville anhydrite was deposited. Stratigraphic and structural cross sections using the Haynesville anhydrite as datum indicate the Smackover in Harmony field consists of not one, but multiple, thin olitic zones which are productive in various portions of the field. These zones grade laterally as well as updip into nonporous anhydritic carbonates. The Smackover Formation is often considered to be a chronolithologic unit. In the Harmony field area it is a lithostratigraphic unit, i.e. a unit defined not by time but by a particular rock type, in this case a porous limestone.

  13. ABodyBuilder: Automated antibody structure prediction with data–driven accuracy estimation

    PubMed Central

    Leem, Jinwoo; Dunbar, James; Georges, Guy; Shi, Jiye; Deane, Charlotte M.

    2016-01-01

    ABSTRACT Computational modeling of antibody structures plays a critical role in therapeutic antibody design. Several antibody modeling pipelines exist, but no freely available methods currently model nanobodies, provide estimates of expected model accuracy, or highlight potential issues with the antibody's experimental development. Here, we describe our automated antibody modeling pipeline, ABodyBuilder, designed to overcome these issues. The algorithm itself follows the standard 4 steps of template selection, orientation prediction, complementarity-determining region (CDR) loop modeling, and side chain prediction. ABodyBuilder then annotates the ‘confidence’ of the model as a probability that a component of the antibody (e.g., CDRL3 loop) will be modeled within a root–mean square deviation threshold. It also flags structural motifs on the model that are known to cause issues during in vitro development. ABodyBuilder was tested on 4 separate datasets, including the 11 antibodies from the Antibody Modeling Assessment–II competition. ABodyBuilder builds models that are of similar quality to other methodologies, with sub–Angstrom predictions for the ‘canonical’ CDR loops. Its ability to model nanobodies, and rapidly generate models (∼30 seconds per model) widens its potential usage. ABodyBuilder can also help users in decision–making for the development of novel antibodies because it provides model confidence and potential sequence liabilities. ABodyBuilder is freely available at http://opig.stats.ox.ac.uk/webapps/abodybuilder. PMID:27392298

  14. [Automated morphometric evaluation of the chromatin structure of liver cell nuclei after vagotomy].

    PubMed

    Butusova, N N; Zhukotskiĭ, A V; Sherbo, I V; Gribkov, E N; Dubovaia, T K

    1989-05-01

    The morphometric analysis of the interphase chromatine structure of the hepatic cells nuclei was carried out on the automated TV installation for the quantitative analysis of images "IBAS-2" (by the OPTON firm, the FRG) according to 50 optical and geometric parameters during various periods (1.2 and 4 weeks) after the vagotomy operation. It is determined that upper-molecular organisation of chromatine undergoes the biggest changes one week after operation, and changes of granular component are more informative than changes of the nongranular component (with the difference 15-20%). It was also revealed that chromatine components differ in tinctorial properties, which are evidently dependent on physicochemical characteristics of the chromatine under various functional conditions of the cell. As a result of the correlation analysis the group of morphometric indices of chromatine structure was revealed, which are highly correlated with level of transcription activity of chromatine during various terms after denervation. The correlation quotient of these parameters is 0.85-0.97. The summing up: vagus denervation of the liver causes changes in the morphofunctional organisation of the chromatine.

  15. Automated laser-based barely visible impact damage detection in honeycomb sandwich composite structures

    SciTech Connect

    Girolamo, D. Yuan, F. G.; Girolamo, L.

    2015-03-31

    Nondestructive evaluation (NDE) for detection and quantification of damage in composite materials is fundamental in the assessment of the overall structural integrity of modern aerospace systems. Conventional NDE systems have been extensively used to detect the location and size of damages by propagating ultrasonic waves normal to the surface. However they usually require physical contact with the structure and are time consuming and labor intensive. An automated, contactless laser ultrasonic imaging system for barely visible impact damage (BVID) detection in advanced composite structures has been developed to overcome these limitations. Lamb waves are generated by a Q-switched Nd:YAG laser, raster scanned by a set of galvano-mirrors over the damaged area. The out-of-plane vibrations are measured through a laser Doppler Vibrometer (LDV) that is stationary at a point on the corner of the grid. The ultrasonic wave field of the scanned area is reconstructed in polar coordinates and analyzed for high resolution characterization of impact damage in the composite honeycomb panel. Two methodologies are used for ultrasonic wave-field analysis: scattered wave field analysis (SWA) and standing wave energy analysis (SWEA) in the frequency domain. The SWA is employed for processing the wave field and estimate spatially dependent wavenumber values, related to discontinuities in the structural domain. The SWEA algorithm extracts standing waves trapped within damaged areas and, by studying the spectrum of the standing wave field, returns high fidelity damage imaging. While the SWA can be used to locate the impact damage in the honeycomb panel, the SWEA produces damage images in good agreement with X-ray computed tomographic (X-ray CT) scans. The results obtained prove that the laser-based nondestructive system is an effective alternative to overcome limitations of conventional NDI technologies.

  16. E-novo: an automated workflow for efficient structure-based lead optimization.

    PubMed

    Pearce, Bradley C; Langley, David R; Kang, Jia; Huang, Hongwei; Kulkarni, Amit

    2009-07-01

    An automated E-Novo protocol designed as a structure-based lead optimization tool was prepared through Pipeline Pilot with existing CHARMm components in Discovery Studio. A scaffold core having 3D binding coordinates of interest is generated from a ligand-bound protein structural model. Ligands of interest are generated from the scaffold using an R-group fragmentation/enumeration tool within E-Novo, with their cores aligned. The ligand side chains are conformationally sampled and are subjected to core-constrained protein docking, using a modified CHARMm-based CDOCKER method to generate top poses along with CDOCKER energies. In the final stage of E-Novo, a physics-based binding energy scoring function ranks the top ligand CDOCKER poses using a more accurate Molecular Mechanics-Generalized Born with Surface Area method. Correlation of the calculated ligand binding energies with experimental binding affinities were used to validate protocol performance. Inhibitors of Src tyrosine kinase, CDK2 kinase, beta-secretase, factor Xa, HIV protease, and thrombin were used to test the protocol using published ligand crystal structure data within reasonably defined binding sites. In-house Respiratory Syncytial Virus inhibitor data were used as a more challenging test set using a hand-built binding model. Least squares fits for all data sets suggested reasonable validation of the protocol within the context of observed ligand binding poses. The E-Novo protocol provides a convenient all-in-one structure-based design process for rapid assessment and scoring of lead optimization libraries.

  17. SV-AUTOPILOT: optimized, automated construction of structural variation discovery and benchmarking pipelines.

    PubMed

    Leung, Wai Yi; Marschall, Tobias; Paudel, Yogesh; Falquet, Laurent; Mei, Hailiang; Schönhuth, Alexander; Maoz Moss, Tiffanie Yael

    2015-03-25

    Many tools exist to predict structural variants (SVs), utilizing a variety of algorithms. However, they have largely been developed and tested on human germline or somatic (e.g. cancer) variation. It seems appropriate to exploit this wealth of technology available for humans also for other species. Objectives of this work included: a) Creating an automated, standardized pipeline for SV prediction. b) Identifying the best tool(s) for SV prediction through benchmarking. c) Providing a statistically sound method for merging SV calls. The SV-AUTOPILOT meta-tool platform is an automated pipeline for standardization of SV prediction and SV tool development in paired-end next-generation sequencing (NGS) analysis. SV-AUTOPILOT comes in the form of a virtual machine, which includes all datasets, tools and algorithms presented here. The virtual machine easily allows one to add, replace and update genomes, SV callers and post-processing routines and therefore provides an easy, out-of-the-box environment for complex SV discovery tasks. SV-AUTOPILOT was used to make a direct comparison between 7 popular SV tools on the Arabidopsis thaliana genome using the Landsberg (Ler) ecotype as a standardized dataset. Recall and precision measurements suggest that Pindel and Clever were the most adaptable to this dataset across all size ranges while Delly performed well for SVs larger than 250 nucleotides. A novel, statistically-sound merging process, which can control the false discovery rate, reduced the false positive rate on the Arabidopsis benchmark dataset used here by >60%. SV-AUTOPILOT provides a meta-tool platform for future SV tool development and the benchmarking of tools on other genomes using a standardized pipeline. It optimizes detection of SVs in non-human genomes using statistically robust merging. The benchmarking in this study has demonstrated the power of 7 different SV tools for analyzing different size classes and types of structural variants. The optional merge

  18. Repair, Evaluation, Maintenance, and Rehabilitation Research Program. Instrumentation Automation for Concrete Structures. Report 2. Automation Hardware and Retrofitting Techniques.

    DTIC Science & Technology

    1987-06-01

    0.% AW = %’,"% i. Power requirements and recommendations: 115 VAC (90- 132V tolerance), 50/60 Hz, 168 watts. j-. Compatible equipment: RS-232-C and 8...structures, charge controllers, meters, alarms, and batteries. A n. Comments: None. .’ J 4 iM85 SOLR ELECTRIC CHARGING UNIT (PHOTO COURTESY OF ACO

  19. Application of AN Automated Wireless Structural Monitoring System for Long-Span Suspension Bridges

    NASA Astrophysics Data System (ADS)

    Kurata, M.; Lynch, J. P.; van der Linden, G. W.; Hipley, P.; Sheng, L.-H.

    2011-06-01

    This paper describes an automated wireless structural monitoring system installed at the New Carquinez Bridge (NCB). The designed system utilizes a dense network of wireless sensors installed in the bridge but remotely controlled by a hierarchically designed cyber-environment. The early efforts have included performance verification of a dense network of wireless sensors installed on the bridge and the establishment of a cellular gateway to the system for remote access from the internet. Acceleration of the main bridge span was the primary focus of the initial field deployment of the wireless monitoring system. An additional focus of the study is on ensuring wireless sensors can survive for long periods without human intervention. Toward this end, the life-expectancy of the wireless sensors has been enhanced by embedding efficient power management schemes in the sensors while integrating solar panels for power harvesting. The dynamic characteristics of the NCB under daily traffic and wind loads were extracted from the vibration response of the bridge deck and towers. These results have been compared to a high-fidelity finite element model of the bridge.

  20. Application of an automated wireless structural monitoring system for long-span suspension bridges

    SciTech Connect

    Kurata, M.; Lynch, J. P.; Linden, G. W. van der; Hipley, P.; Sheng, L.-H.

    2011-06-23

    This paper describes an automated wireless structural monitoring system installed at the New Carquinez Bridge (NCB). The designed system utilizes a dense network of wireless sensors installed in the bridge but remotely controlled by a hierarchically designed cyber-environment. The early efforts have included performance verification of a dense network of wireless sensors installed on the bridge and the establishment of a cellular gateway to the system for remote access from the internet. Acceleration of the main bridge span was the primary focus of the initial field deployment of the wireless monitoring system. An additional focus of the study is on ensuring wireless sensors can survive for long periods without human intervention. Toward this end, the life-expectancy of the wireless sensors has been enhanced by embedding efficient power management schemes in the sensors while integrating solar panels for power harvesting. The dynamic characteristics of the NCB under daily traffic and wind loads were extracted from the vibration response of the bridge deck and towers. These results have been compared to a high-fidelity finite element model of the bridge.

  1. Automated foveola localization in retinal 3D-OCT images using structural support vector machine prediction.

    PubMed

    Liu, Yu-Ying; Ishikawa, Hiroshi; Chen, Mei; Wollstein, Gadi; Schuman, Joel S; Rehg, James M

    2012-01-01

    We develop an automated method to determine the foveola location in macular 3D-OCT images in either healthy or pathological conditions. Structural Support Vector Machine (S-SVM) is trained to directly predict the location of the foveola, such that the score at the ground truth position is higher than that at any other position by a margin scaling with the associated localization loss. This S-SVM formulation directly minimizes the empirical risk of localization error, and makes efficient use of all available training data. It deals with the localization problem in a more principled way compared to the conventional binary classifier learning that uses zero-one loss and random sampling of negative examples. A total of 170 scans were collected for the experiment. Our method localized 95.1% of testing scans within the anatomical area of the foveola. Our experimental results show that the proposed method can effectively identify the location of the foveola, facilitating diagnosis around this important landmark.

  2. Combined computational metabolite prediction and automated structure-based analysis of mass spectrometric data.

    PubMed

    Stranz, David D; Miao, Shichang; Campbell, Scott; Maydwell, George; Ekins, Sean

    2008-01-01

    ABSTRACT As high-throughput technologies have developed in the pharmaceutical industry, the demand for identification of possible metabolites using predominantly liquid chromatographic/mass spectrometry-mass spectrometry/mass spectrometry (LC/MS-MS/MS) for a large number of molecules in drug discovery has also increased. In parallel, computational technologies have also been developed to generate predictions for metabolites alongside methods to predict MS spectra and score the quality of the match with experimental spectra. The goal of the current study was to generate metabolite predictions from molecular structure with a software product, MetaDrug. In vitro microsomal incubations were used to ultimately produce MS data that could be used to verify the predictions with Apex, which is a new software tool that can predict the molecular ion spectrum and a fragmentation spectrum, automating the detailed examination of both MS and MS/MS spectra. For the test molecule imipramine used to illustrate the combined in vitro/in silico process proposed, MetaDrug predicts 16 metabolites. Following rat microsomal incubations with imipramine and analysis of the MS(n) data using the Apex software, strong evidence was found for imipramine and five metabolites and weaker evidence for five additional metabolites. This study suggests a new approach to streamline MS data analysis using a combination of predictive computational approaches with software capable of comparing the predicted metabolite output with empirical data when looking at drug metabolites.

  3. Time Series Analysis Programs for Stratigraphic Data,

    DTIC Science & Technology

    1984-07-01

    species of planktonic foraminifers with changing relative abundances in the same core will show apparent offsets in the timing of events due to mixing...isotope carrier ( foraminifer species) as described in Hutson (1980). The user is asked for input file- names for isotopes, abundances and the mixing...complicated driver program that attempts to remove stratigraphic offset between two stable isotope signals from different foraminifer species in a single core

  4. Stratigraphic Architecture of Aeolian Dune Interactions

    NASA Astrophysics Data System (ADS)

    Brothers, S. C.; Kocurek, G.

    2015-12-01

    Dune interactions, which consist of collisions and detachments, are a known driver of changing dune morphology and provide the dynamics for field-scale patterning. Although interactions are ubiquitous in modern dune fields, the stratigraphic record of interactions has not been explored. This raises the possibility that an entire class of signature architectures of bounding surfaces and cross-strata has gone misidentified or unrecognized. A unique data set for the crescentic dunes of the White Sands Dune Field, New Mexico, allows for the coupling of dune interactions with their resultant stratigraphic architecture. Dune interactions are documented by a decadal time-series of aerial photos and LiDAR-derived digital elevation models. Plan-view cross-strata in interdune areas provide a record tying past dune positions and morphologies to the current dunes. Three-dimensional stratigraphic architecture is revealed by imaging of dune interiors with ground-penetrating radar. The architecture of a dune defect merging with a target dune downwind consists of lateral truncation of the target dune set by an interaction bounding surface. Defect cross-strata tangentially approach and downlap onto the surface. Downwind, the interaction surface curves, and defect and adjacent target dune sets merge into a continuous set. Predictable angular relationships reflect field-scale patterns of dune migration direction and approach angle of migrating defects. The discovery of interaction architectures emphasizes that although dunes appear as continuous forms on the surface, they consist of discrete segments, each with a distinct morphodynamic history. Bedform interactions result in the morphologic recombination of dune bodies, which is manifested stratigraphically within the sets of cross-strata.

  5. Stratigraphic framework of productive carbonate buildups

    SciTech Connect

    Greenlee, S.M.; Lehmann, P.J. )

    1990-05-01

    Hydrocarbon-productive carbonate buildups are found within a relatively narrow window of geologic time and stratigraphic settings. Because buildups are common exploration objectives in frontier and mature basins, an understanding of their stratigraphic occurrence permits them to be more accurately explored. Based on a worldwide survey, most production occurs in isolated periods of geologic time: Middle Silurian-Late Silurian, late Middle and Late Devonian, Late Pennsylvanian and Early Permian, Late Cretaceous, Paleocene, and Miocene. The authors results suggest that many factors of successful buildup plays are predictable on the basis of geohistory analysis and of basin-filling stratal patterns. Deposition of extensive source beds and thick buildups coincide with second-order eustatic rises. Other primary controls on the temporal distribution of buildups include reef-building organism type, mineralogy, and paleolatitude. Geohistory analysis indicates that periods immediately prior to or during the earliest portion of rapid increases of accommodation correspond to times of productive buildup growth. During this time, shelf margins step landward and buildups become progressively more areally restricted. Buildups eventually are unable to keep pace with high rates of accommodation increase and often are overlain by distal toes of clinoforms within regressive wedges deposited during subsequent periods with lower rates of accommodation increase. The result is a stratigraphic juxtaposition of mounded reservoir carbonate and deep-marine sealing shale. This basin-fill position accounts for over 70% of known buildup-reservoired hydrocarbons. Buildups deposited in overlying regressive wedges are often lower relief and prone to seal problems.

  6. The Chemical Validation and Standardization Platform (CVSP): large-scale automated validation of chemical structure datasets.

    PubMed

    Karapetyan, Karen; Batchelor, Colin; Sharpe, David; Tkachenko, Valery; Williams, Antony J

    2015-01-01

    There are presently hundreds of online databases hosting millions of chemical compounds and associated data. As a result of the number of cheminformatics software tools that can be used to produce the data, subtle differences between the various cheminformatics platforms, as well as the naivety of the software users, there are a myriad of issues that can exist with chemical structure representations online. In order to help facilitate validation and standardization of chemical structure datasets from various sources we have delivered a freely available internet-based platform to the community for the processing of chemical compound datasets. The chemical validation and standardization platform (CVSP) both validates and standardizes chemical structure representations according to sets of systematic rules. The chemical validation algorithms detect issues with submitted molecular representations using pre-defined or user-defined dictionary-based molecular patterns that are chemically suspicious or potentially requiring manual review. Each identified issue is assigned one of three levels of severity - Information, Warning, and Error - in order to conveniently inform the user of the need to browse and review subsets of their data. The validation process includes validation of atoms and bonds (e.g., making aware of query atoms and bonds), valences, and stereo. The standard form of submission of collections of data, the SDF file, allows the user to map the data fields to predefined CVSP fields for the purpose of cross-validating associated SMILES and InChIs with the connection tables contained within the SDF file. This platform has been applied to the analysis of a large number of data sets prepared for deposition to our ChemSpider database and in preparation of data for the Open PHACTS project. In this work we review the results of the automated validation of the DrugBank dataset, a popular drug and drug target database utilized by the community, and ChEMBL 17 data set

  7. Numeric stratigraphic modeling: Testing sequence Numeric stratigraphic modeling: Testing sequence stratigraphic concepts using high resolution geologic examples

    SciTech Connect

    Armentrout, J.M.; Smith-Rouch, L.S.; Bowman, S.A.

    1996-08-01

    Numeric simulations based on integrated data sets enhance our understanding of depositional geometry and facilitate quantification of depositional processes. Numeric values tested against well-constrained geologic data sets can then be used in iterations testing each variable, and in predicting lithofacies distributions under various depositional scenarios using the principles of sequence stratigraphic analysis. The stratigraphic modeling software provides a broad spectrum of techniques for modeling and testing elements of the petroleum system. Using well-constrained geologic examples, variations in depositional geometry and lithofacies distributions between different tectonic settings (passive vs. active margin) and climate regimes (hothouse vs. icehouse) can provide insight to potential source rock and reservoir rock distribution, maturation timing, migration pathways, and trap formation. Two data sets are used to illustrate such variations: both include a seismic reflection profile calibrated by multiple wells. The first is a Pennsylvanian mixed carbonate-siliciclastic system in the Paradox basin, and the second a Pliocene-Pleistocene siliciclastic system in the Gulf of Mexico. Numeric simulations result in geometry and facies distributions consistent with those interpreted using the integrated stratigraphic analysis of the calibrated seismic profiles. An exception occurs in the Gulf of Mexico study where the simulated sediment thickness from 3.8 to 1.6 Ma within an upper slope minibasin was less than that mapped using a regional seismic grid. Regional depositional patterns demonstrate that this extra thickness was probably sourced from out of the plane of the modeled transect, illustrating the necessity for three-dimensional constraints on two-dimensional modeling.

  8. Towards Automated Seismic Moment Tensor Inversion in Australia Using 3D Structural Model

    NASA Astrophysics Data System (ADS)

    Hingee, M.; Tkalcic, H.; Fichtner, A.; Sambridge, M.; Kennett, B. L.; Gorbatov, A.

    2009-12-01

    functions. Implementation of this 3D model will improve warning systems, and we present results that are an important step towards automated MT inversion in Australia. [1] Fichtner, A., Kennett, B.L.N., Igel, H., Bunge, H.-P., 2009. Full seismic waveform tomography for upper-mantle structure in the Australasian region using adjoint methods. Geophys. J. Int., in press.

  9. Using Automated Morphometry to Detect Associations Between ERP Latency and Structural Brain MRI in Normal Adults

    PubMed Central

    Cardenas, Valerie A.; Chao, Linda L.; Blumenfeld, Rob; Song, Enmin; Meyerhoff, Dieter J.; Weiner, Michael W.; Studholme, Colin

    2008-01-01

    Despite the clinical significance of event-related potential (ERP) latency abnormalities, little attention has focused on the anatomic substrate of latency variability. Volume conduction models do not identify the anatomy responsible for delayed neural transmission between neural sources. To explore the anatomic substrate of ERP latency variability in normal adults using automated measures derived from magnetic resonance imaging (MRI), ERPs were recorded in the visual three-stimulus oddball task in 59 healthy participants. Latencies of the P3a and P3b components were measured at the vertex. Measures of local anatomic size in the brain were estimated from structural MRI, using tissue segmentation and deformation morphometry. A general linear model was fitted relating latency to measures of local anatomic size, covarying for intracranial vault volume. Longer P3b latencies were related to contractions in thalamus extending superiorly into the corpus callosum, white matter (WM) anterior to the central sulcus on the left and right, left temporal WM, the right anterior limb of the internal capsule extending into the lenticular nucleus, and larger cerebrospinal fluid volumes. There was no evidence for a relationship between gray matter (GM) volumes and P3b latency. Longer P3a latencies were related to contractions in left temporal WM, and left parietal GM and WM near the interhemispheric fissure. P3b latency variability is related chiefly to WM, thalamus, and lenticular nucleus, whereas P3a latency variability is not related as strongly to anatomy. These results imply that the WM connectivity between generators influences P3b latency more than the generators themselves do. PMID:15834860

  10. Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler☆

    PubMed Central

    Bindewald, Eckart; Grunewald, Calvin; Boyle, Brett; O’Connor, Mary; Shapiro, Bruce A.

    2013-01-01

    One approach to designing RNA nanoscale structures is to use known RNA structural motifs such as junctions, kissing loops or bulges and to construct a molecular model by connecting these building blocks with helical struts. We previously developed an algorithm for detecting internal loops, junctions and kissing loops in RNA structures. Here we present algorithms for automating or assisting many of the steps that are involved in creating RNA structures from building blocks: (1) assembling building blocks into nanostructures using either a combinatorial search or constraint satisfaction; (2) optimizing RNA 3D ring structures to improve ring closure; (3) sequence optimisation; (4) creating a unique non-degenerate RNA topology descriptor. This effectively creates a computational pipeline for generating molecular models of RNA nanostructures and more specifically RNA ring structures with optimized sequences from RNA building blocks. We show several examples of how the algorithms can be utilized to generate RNA tecto-shapes. PMID:18838281

  11. Ichnofabric and siliciclastic depositional systems: Integration for sequence stratigraphic analysis

    SciTech Connect

    Bottjer, D.J. ); Droser, M.L. )

    1991-03-01

    Much previous research on biogenic sedimentary structures has established how ichnofacies (assemblages of discrete trace fossils) vary within marine depositional systems. However, studies aimed at understanding the distribution of ichnofabric (sedimentary rock fabric resulting from biogenic reworking) have only recently been attempted. Because ichnofabric can be recorded using a semi-quantitative series of ichnofabric indices (ii), its distribution in marine sedimentary rocks can be easily recorded through vertical sequence analysis. Thicknesses of strata recording different ichnofabric indices can be logged from stratigraphic sections or cores. These data are best displayed in histograms as percent of ii recorded from the total thickness measured. These ichnofabric histograms (ichnograms) show variable but distinctive distributions for genetic units such as facies within systems tracts of siliciclastic depositional sequences. An average ichnofabric index for any genetic sedimentary unit can also be computed from the data used to construct ichnograms. Because skeletal fossils are typically much less commonly preserved in siliciclastic than carbonate depositional systems, such ichnofabric analyses have the potential of providing an important new line of evidence for depositional systems and sequence stratigraphic analysis of siliciclastic strata. In petroleum exploration results from completing analyses of ichnofabric distribution could provide important information including: (1) systems tracts with fine-grained facies that have relatively low ichnofabric values are potential source beds; and (2) petroleum reservoirs that occur in coarse episodically deposited beds are more likely to from in systems tracts with facies that have low rather than high ichnofabric values.

  12. Latest Quaternary stratigraphic framework of the Mississippi River delta region

    USGS Publications Warehouse

    Kulp, Mark; Howell, Paul; Adiau, Sandra; Penland, Shea; Kindinger, Jack; Williams, S. Jeffress

    2002-01-01

    Previous researchers separated the uppermost Quaternary stratigraphy of the Mississippi River delta region into two major lithofacies. The stratigraphically lower of these, "substratum," primarily consists of coarse-grained sediment deposited within lowstand-incised stream valleys. Relatively finer-grained "topstratum" overlies substratum; above interfluves, topstratum directly overlies weathered late Pleistocene sediments. However, the onshore to offshore distribution and architecture of these lithofacies was not well constrained. This study integrates published and unpublished lithostratigraphic data with high-resolution seismic profiles from the continental shelf to aid in mapping the regional distribution of major substratum deposits and thickness of topstratum sediments. A transgressive sand sheet commonly marks the base of the topstratum deposits, providing a stratigraphic marker to aid in regional lithostratigraphic correlations. Radiocarbondated deposits and boreholes tied to oxygen isotope chronologies provide chronostratigraphic control. Excellent correlation between these multiple datasets has been found to exist, enabling construction of regional isopachous and structural elevation maps and cross sections detailing elements of the Late Quaternary stratigraphy.

  13. Automated Sample Exchange Robots for the Structural Biology Beam Lines at the Photon Factory

    SciTech Connect

    Hiraki, Masahiko; Watanabe, Shokei; Yamada, Yusuke; Matsugaki, Naohiro; Igarashi, Noriyuki; Gaponov, Yurii; Wakatsuki, Soichi

    2007-01-19

    We are now developing automated sample exchange robots for high-throughput protein crystallographic experiments for onsite use at synchrotron beam lines. It is part of the fully automated robotics systems being developed at the Photon Factory, for the purposes of protein crystallization, monitoring crystal growth, harvesting and freezing crystals, mounting the crystals inside a hutch and for data collection. We have already installed the sample exchange robots based on the SSRL automated mounting system at our insertion device beam lines BL-5A and AR-NW12A at the Photon Factory. In order to reduce the time required for sample exchange further, a prototype of a double-tonged system was developed. As a result of preliminary experiments with double-tonged robots, the sample exchange time was successfully reduced from 70 seconds to 10 seconds with the exception of the time required for pre-cooling and warming up the tongs.

  14. Analysing the archaeological context: Reconstructing stratigraphic layers

    NASA Astrophysics Data System (ADS)

    Schubert, Lutz; Predoi, Ana; Jeffery, Keith

    2017-07-01

    The stratigraphic layout of an excavation determines how finds can be interpreted regarding their timeline and relationships with each other. Older excavation reports do not fully record this layout however and reconstructing the relationships is often subject to conjecture. In this paper we present a first approach for reasoning over and visualizing the stratigraphy given only profile information. We will demonstrate how this can be used for spatial analysis, but also for reasoning over different processes contributing to the found layout, including potential influences that left no visible traces.

  15. AutoQSAR: an automated machine learning tool for best-practice quantitative structure-activity relationship modeling.

    PubMed

    Dixon, Steven L; Duan, Jianxin; Smith, Ethan; Von Bargen, Christopher D; Sherman, Woody; Repasky, Matthew P

    2016-10-01

    We introduce AutoQSAR, an automated machine-learning application to build, validate and deploy quantitative structure-activity relationship (QSAR) models. The process of descriptor generation, feature selection and the creation of a large number of QSAR models has been automated into a single workflow within AutoQSAR. The models are built using a variety of machine-learning methods, and each model is scored using a novel approach. Effectiveness of the method is demonstrated through comparison with literature QSAR models using identical datasets for six end points: protein-ligand binding affinity, solubility, blood-brain barrier permeability, carcinogenicity, mutagenicity and bioaccumulation in fish. AutoQSAR demonstrates similar or better predictive performance as compared with published results for four of the six endpoints while requiring minimal human time and expertise.

  16. Automated longitudinal registration of high resolution structural MRI brain sub-volumes in non-human primates

    PubMed Central

    Lecoeur, Jérémy; Wang, Feng; Chen, Li Min; Li, Rui; Avison, Malcolm J.; Dawant, Benoit M.

    2011-01-01

    Accurate anatomic co-registration is a prerequisite for identifying structural and functional changes in longitudinal studies of brain plasticity. Current MRI methods permit collection of brain images across multiple scales, ranging from whole brain at relatively low resolution (≥1 mm), to local brain areas at the level of cortical layers and columns (~100 µm) in the same session, allowing detection of subtle structural changes on a similar spatial scale. To measure these changes reliably, high resolution structural and functional images of local brain regions must be registered accurately across imaging sessions. The present study describes a robust fully automated strategy for the registration of high resolution structural images of brain sub-volumes to lower resolution whole brain images collected within a session, and the registration of partially overlapping high resolution MRI sub-volumes (“slabs”) across imaging sessions. In high field (9.4 T) reduced field-of-view high resolution structural imaging studies using a surface coil in an anesthetized non-human primate model, this fully automated coregistration pipeline was robust in the face of significant inhomogeneities in image intensity and tissue contrast arising from the spatially inhomogeneous transmit and receive properties of the surface coil, achieving a registration accuracy of 30 ± 15 µm between sessions. PMID:21920386

  17. Cryo automated electron tomography: towards high-resolution reconstructions of plastic-embedded structures.

    PubMed

    Braunfeld, M B; Koster, A J; Sedat, J W; Agard, D A

    1994-05-01

    The use of fully automated data collection methods for electron tomography allows a substantial reduction in beam dose. The goal has been to develop new protocols for data collection defining optimal approaches for maintaining data self-consistency and maximizing the useful resolution of the reconstruction. The effects of irradiation and post-cure microwaving were examined for a variety of embedding media (Epon, Epox, Lowicryl) in order to quantify beam damage with the goal of identifying the most beam stable embedding medium. Surprisingly, the substantial dose reduction made possible by automated data collection did not result in a significant decrease in specimen shrinkage even for samples stabilized by pre-irradiation. We believe that the accelerated shrinkage is a direct consequence of the stroboscopic illumination patterns inherent to automated data collection. Furthermore neither the choice of embedding resin nor microwave post-curing greatly affected shrinkage. Finally, cryogenic data collection was investigated as a means to minimize the effects of secondary radiation damage. Minimal pre-irradiation coupled with low-temperature automated data collection greatly reduces shrinkage and should result in high-quality data for three-dimensional reconstructions.

  18. Leveraging 3D Wheeler Diagrams and relative time mapping in seismic data to improve stratigraphic interpretation: Application, Assumptions, and Sequence Stratigraphic Revelations

    NASA Astrophysics Data System (ADS)

    Goggin, L. R.

    2014-12-01

    Our understanding of subsurface stratigraphic relationships is guided by stratigraphic concepts that were developed using many varieties and scales of data including paleontological samples, cuttings and core, outcrop analogs, well logs, and seismic. Subsurface stratigraphic correlations are strongly influenced by the type, density, and distribution of the data available. The exploration geologist typically interprets 2D and 3D seismic reflections to define prospects and plays. In structurally simple areas, he or she often assumes that seismic reflectors mark depositional boundaries that are essentially time-synchronous events represented by a single wavelet character. In reality, seismic reflectors usually display spatial wavelet variability, seldom resolve individual beds and are the product of the amplitude expression of a range of lithologic changes that encompasses a range of geologic time and depositional processes. Our assumption that seismic reflections are time-synchronous can lead to errors in stratigraphic correlation that only become evident when our prediction of well or field performance is unrealized. To mitigate the potential for this correlation error, we must modify how we interpret seismic data. In this presentation we will focus on the concept of defining or approximating time-correlative surfaces in seismic data, leverage concepts of the Wheeler transform to place these seismic reflectors into the relative time domain and then examine the diachronous nature of these time-mapped surfaces in 3D. We will then explore how the 3D mapping of time-correlative surfaces fits sequence stratigraphic concepts and discuss whether this new approach requires us to change our interpretation paradigms.

  19. Computer Automated Structure Evaluation (CASE) of the teratogenicity of retinoids with the aid of a novel geometry index

    NASA Astrophysics Data System (ADS)

    Klopman, Gilles; Dimayuga, Mario L.

    1990-06-01

    The CASE (Computer Automated Structure Evaluation) program, with the aid of a geometry index for discriminating cis and trans isomers, has been used to study a set of retinoids tested for teratogenicity in hamsters. CASE identified 8 fragments, the most important representing the non-polar terminus of a retinoid with an additional ring system which introduces some rigidity in the isoprenoid side chain. The geometry index helped to identify relevant fragments with an all- trans configuration and to distinguish them from irrelevant fragments with other configurations.

  20. Sedimentological indicators of paleoenvironments and siliciclastic stratigraphic sequences in some Miocene deposits of the Calvert Cliffs, southern Maryland

    USGS Publications Warehouse

    Shideler, G.L.

    1994-01-01

    Middle Miocene siliciclastic deposits comprising the Calvert Cliffs section at the Baltimore Gas and Electric Company's (BG&E) nuclear power plant site in southern Maryland were analyzed in terms of lithostratigraphy, sedimentary structures, and granulometric parameters, to interprete paleo-environments within a sequence-stratigraphic framework. In terms of sequence-stratigraphic models, the BG&E section can be interpreted as consisting of two genetic stratigraphic sequences (Galloway model), namely, a shelf sequence and an overlying deltaic sequence. Using the Exxon model, the section consists of two third-order (1-5 m.y. duration) depositional sequences. The stratigraphic sequences of the BG&E section reflect both relatively short-term eustatic transgressive events, as well as a long-term regressive trend with associated local deltation and coastal progradation. The regression probably signified a regional basinward shift of depocenters within the Salisbury embayment during Miocene time. -from Author

  1. Development of automated extraction method of biliary tract from abdominal CT volumes based on local intensity structure analysis

    NASA Astrophysics Data System (ADS)

    Koga, Kusuto; Hayashi, Yuichiro; Hirose, Tomoaki; Oda, Masahiro; Kitasaka, Takayuki; Igami, Tsuyoshi; Nagino, Masato; Mori, Kensaku

    2014-03-01

    In this paper, we propose an automated biliary tract extraction method from abdominal CT volumes. The biliary tract is the path by which bile is transported from liver to the duodenum. No extraction method have been reported for the automated extraction of the biliary tract from common contrast CT volumes. Our method consists of three steps including: (1) extraction of extrahepatic bile duct (EHBD) candidate regions, (2) extraction of intrahepatic bile duct (IHBD) candidate regions, and (3) combination of these candidate regions. The IHBD has linear structures and intensities of the IHBD are low in CT volumes. We use a dark linear structure enhancement (DLSE) filter based on a local intensity structure analysis method using the eigenvalues of the Hessian matrix for the IHBD candidate region extraction. The EHBD region is extracted using a thresholding process and a connected component analysis. In the combination process, we connect the IHBD candidate regions to each EHBD candidate region and select a bile duct region from the connected candidate regions. We applied the proposed method to 22 cases of CT volumes. An average Dice coefficient of extraction result was 66.7%.

  2. Revisiting automated G-protein coupled receptor modeling: the benefit of additional template structures for a neurokinin-1 receptor model.

    PubMed

    Kneissl, Benny; Leonhardt, Bettina; Hildebrandt, Andreas; Tautermann, Christofer S

    2009-05-28

    The feasibility of automated procedures for the modeling of G-protein coupled receptors (GPCR) is investigated on the example of the human neurokinin-1 (NK1) receptor. We use a combined method of homology modeling and molecular docking and analyze the information content of the resulting docking complexes regarding the binding mode for further refinements. Moreover, we explore the impact of different template structures, the bovine rhodopsin structure, the human beta(2) adrenergic receptor, and in particular a combination of both templates to include backbone flexibility in the target conformational space. Our results for NK1 modeling demonstrate that model selection from a set of decoys can in general not solely rely on docking experiments but still requires additional mutagenesis data. However, an enrichment factor of 2.6 in a nearly fully automated approach indicates that reasonable models can be created automatically if both available templates are used for model construction. Thus, the recently resolved GPCR structures open new ways to improve the model building fundamentally.

  3. 3D Stratigraphic Modeling of Central Aachen

    NASA Astrophysics Data System (ADS)

    Dong, M.; Neukum, C.; Azzam, R.; Hu, H.

    2010-05-01

    Since 1980s, advanced computer hardware and software technologies, as well as multidisciplinary research have provided possibilities to develop advanced three dimensional (3D) simulation software for geosciences application. Some countries, such as USA1) and Canada2) 3), have built up regional 3D geological models based on archival geological data. Such models have played huge roles in engineering geology2), hydrogeology2) 3), geothermal industry1) and so on. In cooperating with the Municipality of Aachen, the Department of Engineering Geology of RWTH Aachen University have built up a computer-based 3D stratigraphic model of 50 meter' depth for the center of Aachen, which is a 5 km by 7 km geologically complex area. The uncorrelated data from multi-resources, discontinuous nature and unconformable connection of the units are main challenges for geological modeling in this area. The reliability of 3D geological models largely depends on the quality and quantity of data. Existing 1D and 2D geological data were collected, including 1) approximately 6970 borehole data of different depth compiled in Microsoft Access database and MapInfo database; 2) a Digital Elevation Model (DEM); 3) geological cross sections; and 4) stratigraphic maps in 1m, 2m and 5m depth. Since acquired data are of variable origins, they were managed step by step. The main processes are described below: 1) Typing errors of borehole data were identified and the corrected data were exported to Variowin2.2 to distinguish duplicate points; 2) The surface elevation of borehole data was compared to the DEM, and differences larger than 3m were eliminated. Moreover, where elevation data missed, it was read from the DEM; 3) Considerable data were collected from municipal constructions, such as residential buildings, factories, and roads. Therefore, many boreholes are spatially clustered, and only one or two representative points were picked out in such areas; After above procedures, 5839 boreholes with -x

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  5. Stratigraphic and structural data for the Conasauga Group and the Rome Formation on the Copper Creek fault block near Oak Ridge, Tennessee: preliminary results from test borehole ORNL-JOY No. 2

    SciTech Connect

    Haase, C.S.; Walls, E.C.; Farmer, C.D.

    1985-06-01

    To resolve long-standing problems with the stratigraphy of the Conasauga Group and the Rome Formation on the Copper Creek fault block near Oak Ridge National Laboratory (ORNL), an 828.5-m-deep test borehole was drilled. Continuous rock core was recovered from the 17.7- to 828.5-m-deep interval; temperature, caliper, neutron, gamma-ray, and acoustic (velocity and televiewer) logs were obtained. The Conasauga Group at the study site is 572.4 m thick and comprises six formations that are - in descending stratigraphic order - Maynardville Limestone (98.8 m), Nolichucky Shale (167.9 m), Maryville Limestone (141.1 m), Rogersville Shale (39.6 m), Rutledge Limestone (30.8 m), and Pumpkin Valley Shale (94.2 m). The formations are lithologically complex, ranging from clastics that consist of shales, mudstones, and siltstones to carbonates that consist of micrites, wackestones, packstones, and conglomerates. The Rome Formation is 188.1 m thick and consists of variably bedded mudstones, siltstones, and sandstones. The Rome Formation thickness represents 88.1 m of relatively undeformed section and 100.0 m of highly deformed, jumbled, and partially repeated section. The bottom of the Rome Formation is marked by a tectonic disconformity that occurs within a 46-m-thick, intensely deformed interval caused by motion along the Copper Creek fault. Results from this study establish the stratigraphy and the lithology of the Conasauga Group and the Rome Formation near ORNL and, for the first time, allow for the unambiguous correlation of cores and geophysical logs from boreholes elsewhere in the ORNL vicinity. 45 refs., 26 figs., 2 tabs.

  6. The scheme of combined application of optimization and simulation models for formation of an optimum structure of an automated control system of space systems

    NASA Astrophysics Data System (ADS)

    Chernigovskiy, A. S.; Tsarev, R. Yu; Nikiforov, A. Yu; Zelenkov, P. V.

    2016-11-01

    With the development of automated control systems of space systems, there are new classes of spacecraft that requires improvement of their structure and expand their functions. When designing the automated control system of space systems occurs various tasks such as: determining location of elements and subsystems in the space, hardware selection, the distribution of the set of functions performed by the system units, all of this under certain conditions on the quality of control and connectivity of components. The problem of synthesis of structure of automated control system of space systems formalized using discrete variables at various levels of system detalization. A sequence of tasks and stages of the formation of automated control system of space systems structure is developed. The authors have developed and proposed a scheme of the combined implementation of optimization and simulation models to ensure rational distribution of functions between the automated control system complex and the rest of the system units. The proposed approach allows to make reasonable hardware selection, taking into account the different requirements for the operation of automated control systems of space systems.

  7. Evaluation of stereo-array isotope labeling (SAIL) patterns for automated structural analysis of proteins with CYANA.

    PubMed

    Ikeya, Teppei; Terauchi, Tsutomu; Güntert, Peter; Kainosho, Masatsune

    2006-07-01

    Recently we have developed the stereo-array isotope labeling (SAIL) technique to overcome the conventional molecular size limitation in NMR protein structure determination by employing complete stereo- and regiospecific patterns of stable isotopes. SAIL sharpens signals and simplifies spectra without the loss of requisite structural information, thus making large classes of proteins newly accessible to detailed solution structure determination. The automated structure calculation program CYANA can efficiently analyze SAIL-NOESY spectra and calculate structures without manual analysis. Nevertheless, the original SAIL method might not be capable of determining the structures of proteins larger than 50 kDa or membrane proteins, for which the spectra are characterized by many broadened and overlapped peaks. Here we have carried out simulations of new SAIL patterns optimized for minimal relaxation and overlap, to evaluate the combined use of SAIL and CYANA for solving the structures of larger proteins and membrane proteins. The modified approach reduces the number of peaks to nearly half of that observed with uniform labeling, while still yielding well-defined structures and is expected to enable NMR structure determinations of these challenging systems.

  8. PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination.

    PubMed

    Lee, Woonghee; Stark, Jaime L; Markley, John L

    2014-11-01

    Peak-picking Of Noe Data Enabled by Restriction Of Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727-1728. doi: 10.1093/bioinformatics/btr200, 2011) and includes improved features for structure calculation and refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein sequence, a list of assigned chemical shifts, and nuclear Overhauser data sets ((13)C- and/or (15)N-NOESY). The output is a set of assigned NOEs and 3D structural models for the protein. Ponderosa Analyzer supports the visualization, validation, and refinement of the results from Ponderosa Server. These tools enable semi-automated NMR-based structure determination of proteins in a rapid and robust fashion. We present examples showing the use of PONDEROSA-C/S in solving structures of four proteins: two that enable comparison with the original PONDEROSA package, and two from the Critical Assessment of automated Structure Determination by NMR (Rosato et al. in Nat Methods 6:625-626. doi: 10.1038/nmeth0909-625 , 2009) competition. The software package can be downloaded freely in binary format from http://pine.nmrfam.wisc.edu/download_packages.html. Registered users of the National Magnetic Resonance Facility at Madison can submit jobs to the PONDEROSA-C/S server at http://ponderosa.nmrfam.wisc.edu, where instructions, tutorials, and instructions can be found. Structures are normally returned within 1-2 days.

  9. Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement.

    PubMed

    Xu, Dong; Zhang, Jian; Roy, Ambrish; Zhang, Yang

    2011-01-01

    I-TASSER is an automated pipeline for protein tertiary structure prediction using multiple threading alignments and iterative structure assembly simulations. In CASP9 experiments, two new algorithms, QUARK and fragment-guided molecular dynamics (FG-MD), were added to the I-TASSER pipeline for improving the structural modeling accuracy. QUARK is a de novo structure prediction algorithm used for structure modeling of proteins that lack detectable template structures. For distantly homologous targets, QUARK models are found useful as a reference structure for selecting good threading alignments and guiding the I-TASSER structure assembly simulations. FG-MD is an atomic-level structural refinement program that uses structural fragments collected from the PDB structures to guide molecular dynamics simulation and improve the local structure of predicted model, including hydrogen-bonding networks, torsion angles, and steric clashes. Despite considerable progress in both the template-based and template-free structure modeling, significant improvements on protein target classification, domain parsing, model selection, and ab initio folding of β-proteins are still needed to further improve the I-TASSER pipeline. Copyright © 2011 Wiley-Liss, Inc.

  10. Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement

    PubMed Central

    Xu, Dong; Zhang, Jian; Roy, Ambrish; Zhang, Yang

    2011-01-01

    I-TASSER is an automated pipeline for protein tertiary structure prediction using multiple threading alignments and iterative structure assembly simulations. In CASP9 experiments, two new algorithms, QUARK and FG-MD, were added to the I-TASSER pipeline for improving the structural modeling accuracy. QUARK is a de novo structure prediction algorithm used for structure modeling of proteins that lack detectable template structures. For distantly homologous targets, QUARK models are found useful as a reference structure for selecting good threading alignments and guiding the I-TASSER structure assembly simulations. FG-MD is an atomic-level structural refinement program that uses structural fragments collected from the PDB structures to guide molecular dynamics simulation and improve the local structure of predicted model, including hydrogen-bonding networks, torsion angles and steric clashes. Despite considerable progress in both the template-based and template-free structure modeling, significant improvements on protein target classification, domain parsing, model selection, and ab initio folding of beta-proteins are still needed to further improve the I-TASSER pipeline. PMID:22069036

  11. The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013.

    PubMed

    Rosato, Antonio; Vranken, Wim; Fogh, Rasmus H; Ragan, Timothy J; Tejero, Roberto; Pederson, Kari; Lee, Hsiau-Wei; Prestegard, James H; Yee, Adelinda; Wu, Bin; Lemak, Alexander; Houliston, Scott; Arrowsmith, Cheryl H; Kennedy, Michael; Acton, Thomas B; Xiao, Rong; Liu, Gaohua; Montelione, Gaetano T; Vuister, Geerten W

    2015-08-01

    The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could be established by comparing them to the corresponding manually solved structure of each target, which was not available at the time the data were provided. Across the entire data set, 71 % of all entries submitted achieved an accuracy relative to the reference NMR structure better than 1.5 Å. Methods based on NOESY peak lists achieved even better results with up to 100% of the entries within the 1.5 Å threshold for some programs. However, some methods did not converge for some targets using un-curated NOESY peak lists. Over 90% of the entries achieved an accuracy better than the more relaxed threshold of 2.5 Å that was used in the previous CASD-NMR-2010 round. Comparisons between entries generated with un-curated versus curated peaks show only marginal improvements for the latter in those cases where both calculations converged.

  12. Seismic attenuation of the inner core: Viscoelastic or stratigraphic?

    USGS Publications Warehouse

    Cormier, V.F.; Xu, L.; Choy, G.L.

    1998-01-01

    Broadband velocity waveforms of PKIKP in the distance range 150??to 180??are inverted for inner core attenuation. A mean Q?? of 244 is determined at 1 Hz from 8 polar and 9 equatorial paths. The scatter in measured Q-1 exceeds individual error estimates, suggesting significant variation in attenuation with path. These results are interpreted by (1) viscoelasticity, in which the relaxation spectrum has a low-frequency corner near or slightly above the frequency band of short-period body waves, and by (2) stratigraphic (scattering) attenuation, in which attenuation and pulse broadening are caused by the interference of scattered multiples in a velocity structure having rapid fluctuations along a PKIKP path. In the scattering interpretation, PKIKP attenuation is only weakly affected by the intrinsic shear attenuation measured in the free-oscillation band. Instead, its frequency dependence, path variations, and fluctuations are all explained by scattering attenuation in a heterogeneous fabric resulting from solidification texturing of intrinsically anisotropic iron. The requisite fabric may consist of either single or ordered groups of crystals with P velocity differences of at least 5% and as much as 12% between two crystallographic axes at scale lengths of 0.5 to 2 km in the direction parallel to the axis of rotation and longer in the cylindrically radial direction, perpendicular to the axis of rotation.Broadband velocity waveforms of PKIKP in the distance range 150?? to 180?? are inverted for inner core attenuation. A mean Q?? of 244 is determined at 1 Hz from 8 polar and 9 equatorial paths. The scatter in the measured Q-1 exceeds individual error estimates, indicating significant variation in attenuation with path. The results are interpreted by viscoelasticity and stratigraphic (scattering) attenuation.

  13. Automated Processing of Imaging Data through Multi-tiered Classification of Biological Structures Illustrated Using Caenorhabditis elegans

    PubMed Central

    Zhan, Mei; Crane, Matthew M.; Entchev, Eugeni V.; Caballero, Antonio; Fernandes de Abreu, Diana Andrea; Ch’ng, QueeLim; Lu, Hang

    2015-01-01

    Quantitative imaging has become a vital technique in biological discovery and clinical diagnostics; a plethora of tools have recently been developed to enable new and accelerated forms of biological investigation. Increasingly, the capacity for high-throughput experimentation provided by new imaging modalities, contrast techniques, microscopy tools, microfluidics and computer controlled systems shifts the experimental bottleneck from the level of physical manipulation and raw data collection to automated recognition and data processing. Yet, despite their broad importance, image analysis solutions to address these needs have been narrowly tailored. Here, we present a generalizable formulation for autonomous identification of specific biological structures that is applicable for many problems. The process flow architecture we present here utilizes standard image processing techniques and the multi-tiered application of classification models such as support vector machines (SVM). These low-level functions are readily available in a large array of image processing software packages and programming languages. Our framework is thus both easy to implement at the modular level and provides specific high-level architecture to guide the solution of more complicated image-processing problems. We demonstrate the utility of the classification routine by developing two specific classifiers as a toolset for automation and cell identification in the model organism Caenorhabditis elegans. To serve a common need for automated high-resolution imaging and behavior applications in the C. elegans research community, we contribute a ready-to-use classifier for the identification of the head of the animal under bright field imaging. Furthermore, we extend our framework to address the pervasive problem of cell-specific identification under fluorescent imaging, which is critical for biological investigation in multicellular organisms or tissues. Using these examples as a guide, we envision

  14. Semi-automated processing and routing within indoor structures for emergency response applications

    NASA Astrophysics Data System (ADS)

    Liu, Jianfei; Lyons, Kyle; Subramanian, Kalpathi; Ribarsky, William

    2010-04-01

    In this work, we propose new automation tools to process 2D building geometry data for effective communication and timely response to critical events in commercial buildings. Given the scale and complexity of commercial buildings, robust and visually rich tools are needed during an emergency. Our data processing pipeline consists of three major components, (1) adjacency graph construction, representing spatial relationships within a building (between hallways, offices, stairways, elevators), (2) identification of elements involved in evacuation routes (hallways, stairways), (3) 3D building network construction, by connecting the oor elements via stairways and elevators. We have used these tools to process a cluster of five academic buildings. Our automation tools (despite some needed manual processing) show a significant advantage over manual processing (a few minutes vs. 2-4 hours). Designed as a client-server model, our system supports analytical capabilities to determine dynamic routing within a building under constraints(parts of the building blocked during emergencies, for instance). Visualization capabilities are provided for easy interaction with the system, on both desktop (command post) stations as well as mobile hand-held devices, simulating a command post-responder scenario.

  15. Integration of the stratigraphic aspects of very large sea-floor databases using information processing

    USGS Publications Warehouse

    Jenkins, Clinton N.; Flocks, J.; Kulp, M.; ,

    2006-01-01

    Information-processing methods are described that integrate the stratigraphic aspects of large and diverse collections of sea-floor sample data. They efficiently convert common types of sea-floor data into database and GIS (geographical information system) tables, visual core logs, stratigraphic fence diagrams and sophisticated stratigraphic statistics. The input data are held in structured documents, essentially written core logs that are particularly efficient to create from raw input datasets. Techniques are described that permit efficient construction of regional databases consisting of hundreds of cores. The sedimentological observations in each core are located by their downhole depths (metres below sea floor - mbsf) and also by a verbal term that describes the sample 'situation' - a special fraction of the sediment or position in the core. The main processing creates a separate output event for each instance of top, bottom and situation, assigning top-base mbsf values from numeric or, where possible, from word-based relative locational information such as 'core catcher' in reference to sampler device, and recovery or penetration length. The processing outputs represent the sub-bottom as a sparse matrix of over 20 sediment properties of interest, such as grain size, porosity and colour. They can be plotted in a range of core-log programs including an in-built facility that better suits the requirements of sea-floor data. Finally, a suite of stratigraphic statistics are computed, including volumetric grades, overburdens, thicknesses and degrees of layering. ?? The Geological Society of London 2006.

  16. Regional correlations in the South Caspian Sea -implications for stratigraphic nomenclature

    SciTech Connect

    Murphy, J. Rukhsara, K.

    1995-08-01

    Regional Correlations in the South Caspian Sea - Implications for Stratigraphic Nomenclature Detailed sequence boundary correlations in the South Caspian sea have led to a better understanding of the relationships between stratigraphic units identified in wells throughout the basin. With the aid of synthetic seismograms, used to tie the logs to the seismic data, lithologic units have been identified seismically and have been mapped across the basin. The synthetic seismograms were created from pseudo-sonic logs which were transformed from resistivity logs with the Faust equation. Checkshots and VSP surveys supplied the velocity control. The sequence boundary correlations revealed substantial facies changes across the basin and led to the creation of a new stratigraphic correlation chart which relates local formation names to their time correlative boundaries. A recognition of these facies changes has led to a better understanding of the lithologic relationships within the basin, the depositional history of the basin, and the source and distribution of potential reservoir sands. Previous well log correlations, made primarily by matching tops of sand and shale sequences, frequently crossed sequence boundaries mapped from seismic data. Lithologic units, deposited under similar geologic conditions, often looked the same but were not time equivalent. Seismic sequence analyses have shown that tectonic movements, as evidenced by rising domes, created barriers to sediment distribution and led to pronounced thickness changes on opposite sides of a high. New log correlations, incorporating these concepts, are helping to unravel the complex structural and stratigraphic history of the South Caspian Sea.

  17. Shearing along faults and stratigraphic joints controlled by land subsidence in the Valley of Queretaro, Mexico

    NASA Astrophysics Data System (ADS)

    Carreón-Freyre, D.; Cerca, M.; Ochoa-González, G.; Teatini, P.; Zuñiga, F. R.

    2016-05-01

    Slip of nearly vertical faults or horizontal stratigraphic joints has provoked the shearing of at least 16 well casings in a period of over 10 years in the Valley of Queretaro aquifer, Mexico. Evidence integrated from field observations, remote surface-deformation monitoring, in-situ monitoring, stratigraphic correlation, and numerical modeling indicate that groundwater depletion and land subsidence induce shearing. Two main factors conditioning the stress distribution and the location of sheared well casings have been identified: (1) slip on fault planes, and (2) slip on stratigraphic joints. Additionally, the distribution of piezometric gradients may be a factor that enhances shearing. Slip on faults can be generated either by the compaction of sedimentary units (passive faulting) or by slip of blocks delimited by pre-existing faults (reactivation). Major piezometric-level declines and the distribution of hydraulic gradients can also be associated with slip at stratigraphic joints. Faults and hydraulic contrasts in the heterogeneous rock sequence, along with groundwater extraction, influence the distribution of the gradients and delimit the compartments of groundwater in the aquifer. Analogue modeling allowed assessment of the distribution of stress-strain and displacements associated with the increase of the vertical stress. Fault-bounded aquifers in grabens are common in the central part of Mexico and the results obtained can be applied to other subsiding, structurally controlled aquifer systems elsewhere.

  18. Probabilistic sequence alignment of stratigraphic records

    NASA Astrophysics Data System (ADS)

    Lin, Luan; Khider, Deborah; Lisiecki, Lorraine E.; Lawrence, Charles E.

    2014-10-01

    The assessment of age uncertainty in stratigraphically aligned records is a pressing need in paleoceanographic research. The alignment of ocean sediment cores is used to develop mutually consistent age models for climate proxies and is often based on the δ18O of calcite from benthic foraminifera, which records a global ice volume and deep water temperature signal. To date, δ18O alignment has been performed by manual, qualitative comparison or by deterministic algorithms. Here we present a hidden Markov model (HMM) probabilistic algorithm to find 95% confidence bands for δ18O alignment. This model considers the probability of every possible alignment based on its fit to the δ18O data and transition probabilities for sedimentation rate changes obtained from radiocarbon-based estimates for 37 cores. Uncertainty is assessed using a stochastic back trace recursion to sample alignments in exact proportion to their probability. We applied the algorithm to align 35 late Pleistocene records to a global benthic δ18O stack and found that the mean width of 95% confidence intervals varies between 3 and 23 kyr depending on the resolution and noisiness of the record's δ18O signal. Confidence bands within individual cores also vary greatly, ranging from ~0 to >40 kyr. These alignment uncertainty estimates will allow researchers to examine the robustness of their conclusions, including the statistical evaluation of lead-lag relationships between events observed in different cores.

  19. Tectono-stratigraphic terrane map of Alaska

    SciTech Connect

    Nokleberg, W.J.; Brew, D.A.; Grantz, A.; Plafker, G.; Moore, T.E.; Patton, W.W. Jr. ); Mollstalcup, E.J. ); Miller, T.P. )

    1993-04-01

    A new terrane map compelled at a scale of 2.5 million is a comprehensive portrayal of the major tectono-stratigraphic terranes, pre-accretionary plutonic rocks, faults or sutures that bound terranes, and younger overlap sedimentary , volcanic, and plutonic assemblages of Alaska. Terranes are divided by tectonic affinity into cratonal, passive continental margin, metamorphosed continental margin, continental margin arc, island arc, oceanic crust, sea mount, ophiolite, accretionary wedge, subduction zone, turbidite basin, and metamorphic environments. Overlap assemblages consist of sequences of sedimentary, volcanic, and plutonic rocks that link or weld together adjacent terranes after emplacement, and provide important constraints on the timing of tectonic juxtaposition. Groups of terranes and overlap assemblages, with similar tectonic environments and geologic histories, can be correlated within Alaska and into the adjacent Canadian Cordillera. These groups include: (1) highly deformed and metamorphosed continental margin terranes (Seward, Coldfoot, Ruby, Yukon-Tanana, Kootenay) that are interpreted either as displaced fragments of the North American or other continental margins; (2) ophiolite terranes (Angayucham, Tozitna, Inoko, Seventymile, Slide Mountain) that are interpreted as remnants of one or more major, long-lived, Paleozoic and early Mesozoic oceanic basins; (3) Jurassic and Early Cretaceous island arc terranes (Koyukuk, Togiak, Nyac) that are interpreted as remnants of a discontinuous, short-lived, Mesoxoic island arc system; and (4) the Late Jurassic and Early Cretaceous Kahiltna and Gravina-Nutzotin overlap assemblages that are interpreted as parts of a major arc and flysch sequence.

  20. Stratigraphic evolution of paleozoic erathem, northern Florida

    SciTech Connect

    Coleman, J.L. Jr.

    1985-02-01

    Unmetamorphosed Paleozoic sedimentary and volcanic rocks have been drilled in numerous wells throughout northern Florida and southern Georgia, in what is today a gently folded and block-faulted relict continental fragment of northwest Africa and northeast South America. Stratigraphic and lithologic equivalents of these North American Paleozoic units are prolific hydrocarbon producers in North Africa. The northern Florida Paleozoic sediments were deposited on Pan-African and Cadoman basement. Widespread continental glaciation from late Precambrian to Early Cambrian introduced a thick sequence of fine-grained marine sandstones (glacial flour), which overlie medium to coarse-grained glaciofluvial sandstones. Basinward of the sand shelf, the accretion of a volcanic island arc complex began during the Ordovician. A fluctuating transgression, accompanying a major glacial minimum, brought open-marine, graptolitic, black shales onto the sand shelf, producing an interbedded shoreface-shelf sand and black shale section during the Middle and Late Ordovician. At the Ordovician-Silurian boundary, renewed continental glaciation lowered sea level, producing a widespread unconformity. A Late Silurian major marine transgression returned black, graptolitic, highly organic shales onto the sand shelf. Devonian deltaic sands from Avalonia(.) to the north and the craton to the south closed the Paleozoic sedimentary record of northern Florida.

  1. Economics of Developing Hot Stratigraphic Reservoirs

    SciTech Connect

    Greg Mines; Hillary Hanson; Rick Allis; Joseph Moore

    2014-09-01

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

  2. New stratigraphic technologies in exploration/exploitation

    SciTech Connect

    Scott, R.W.; Lane, H.R.

    1995-09-01

    With the demand for increased accuracy and precision in the interpretation of seismic sections for the prediction of reservoirs and traps, traditional paleontologic and new non-paleontologic stratigraphic data have assumed a greater role in exploration/exploitation. Strata bounded by sequence boundaries can be dated have assumed a greater role in exploration/exploitation. Strata bounded by sequence boundaries can be dated precisely by the graphic correlation technique. For example, Arabian Cretaceous reservoirs pinch out by facies change and diagenesis into coeval strata. But Pliocene sands in the Gulf Coast are truncated by regional unconformities accentuated by salt dome movement. In this Plio-Pleistocene section high precision chronostratigraphy is achieved by the integration of paleontological and geochemical data. Detailed biostratigraphic analysis of many sections of Mississippian carbonates along the eastern side of the Transcontinental Arch allows for the recognition of four unconformity-bounded units (biothems of Lane and others, 1994). These biotherms have been traced form Illinois to New Mexico and are not easily detected in the subsurface by using seismic or electric log technology because of the rather uniform carbonate lithologies composing the entire Mississippian in the region. Mississippian hydrocarbon production in western Kansas can be shown to be associated with these intra-Mississippian carbonate-on-carbonate unconformities that are easily detected biostratigraphically.

  3. Stratigraphic Feedbacks on Alternate Bar Morphology

    NASA Astrophysics Data System (ADS)

    Brown, R.; Nelson, P. A.

    2016-12-01

    As rivers aggrade, they can develop subsurface stratigraphy consisting of heterogeneous grain-size distributions in the downstream, cross-stream, and vertical directions. During subsequent periods of degradation, this stratigraphy may be exhumed and potentially feed back on the processes that drive morphodynamic evolution, but these surface-stratigraphy feedbacks are poorly understood and difficult to predict. Here we investigate these feedbacks by implementing the ability to store, track, and access bed stratigraphy in the 2-dimensional morphodynamic model FaSTMECH. We use a modified active layer approach, in which the active layer is allowed to exchange sediment with bedload as well as the highest stratigraphy layer. In cases of aggradation, a fraction of the active layer and bedload is released to the highest stratigraphy layer. During degradation, the active layer takes on the sediment properties stored in the stratigraphy. We validate this new model against flume experiments of migrating, alternate bars in which detailed topography and stratigraphy measurements were collected. We then investigate the effects of stratigraphic feedbacks on the coevolution of fixed patches and alternate bar morphology. Initial model results suggest that including dynamic stratigraphy in morphodynamic models enables prediction of fine grain-size surface patches observed in experiments, but not predicted in simulations without stratigraphy. Our findings suggest that surface-subsurface interactions can play an important role in river morphodynamics.

  4. Stratigraphic test well, Nantucket Island, Massachusetts

    USGS Publications Warehouse

    Folger, David W.; Hathaway, J.C.; Christopher, R.A.; Valentine, P.C.; Poag, C.W.

    1978-01-01

    The U.S. Geological Survey, in cooperation with the Massachusetts Water Resources Commission and the Nantucket Conservation Foundation, continuously cored 514 m of sediment and volcanic rock in a stratigraphic and water-quality test near the geographic center of Nantucket Island. Stratified sediments were divided texturally into three zones: the upper zone (0-128 m) contains mostly coarse sand and gravel; the middle zone (128-349 m) contains mostly silty clay and a few beds of sand and silt; and the lower zone (349-457 m) contains soft, unconsolidated, clayey sand. Below the lower zone, a saprolite, composed mostly of clay, grades abruptly downward at 470 m into partially altered basalt that extends to the bottom of the hole at 514 m. Calculations based on the Ghyben-Herzberg principle predicted a zone of freshwater 120-150 m thick. This principle is the theory of hydrostatic equilibrium between freshwater and more dense seawater in a coastal aquifer; it states that for each meter of ground-water elevation above sea level, the freshwater lens will depress the saltwater interface about 40 m below sea level. Freshwater or low-salinity brackish water was found in sediments far below the depth predicted by the Ghyben-Herzberg principle. These interstitial waters are probably relict ground water emplaced during times of low sea level during the Pleistocene. (Woodard-USGS)

  5. Production implementation of fully automated, closed loop cure control for advanced composite structures

    NASA Astrophysics Data System (ADS)

    Johnson, Sean A.; Roberts, Nancy K.

    Economic of advanced composite part production requires development and use of the most aggressive cure cycles possible without sacrificing quality. As cure cycles are shortened and heating rates increase, tolerance windows for process parameters become increasingly narrow. These factors are intensified by condensation curing systems which generate large amounts of volatiles. Management of the situation requires fully automated, closed loop process control and a fundamental understanding of the material system used for the application. No turnkey system for this application is currently available. General Dynamics Pomona Division (GD/PD) has developed an integrated closed loop control system which is now being proofed in production. Realization of this system will enable cure time reductions of nearly 50 percent, while increasing yield and maintaining quality.

  6. Automating tasks in protein structure determination with the Clipper Python module.

    PubMed

    McNicholas, Stuart; Croll, Tristan; Burnley, Tom; Palmer, Colin M; Hoh, Soon Wen; Jenkins, Huw T; Dodson, Eleanor; Cowtan, Kevin; Agirre, Jon

    2017-09-13

    Scripting programming languages provide the fastest means of prototyping complex functionality. Those with a syntax and grammar resembling human language also greatly enhance the maintainability of the produced source code. Furthermore, the combination of a powerful, machine-independent scripting language with binary libraries tailored for each computer architecture allows programs to break free from the tight boundaries of efficiency traditionally associated with scripts. In the present work, we describe how an efficient C++ crystallographic library such as Clipper can be wrapped, adapted and generalised for use in both crystallographic and electron cryo-microscopy applications, scripted with the Python language. We shall also place an emphasis on best practices in automation, illustrating how this can be achieved with this new Python module. This article is protected by copyright. All rights reserved. © 2017 The Protein Society.

  7. SDAR 1.0 a New Quantitative Toolkit for Analyze Stratigraphic Data

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  8. Towards a stratigraphic record of dynamic topography

    NASA Astrophysics Data System (ADS)

    Armitage, J. J.; Duller, R. A.

    2012-12-01

    The erosion of mountainous terrain and contemporaneous deposition of sediment within the adjacent basins modifies the applied load upon the surface of the Earth. A simple argument can then be made that an increase in rainfall would lead to increased erosion and deposition, and would therefore directly impact the dynamics and evolution of the linked mountain-basin system. Key to the exploration of this argument is an understanding of how efficient erosion is and the acceptable way to model long-term (> million years) Earth surface processes at relatively large spatial scales (100's of kilometres). Surface processes are complex and chaotic, and up-scaling from individual bed-load processes to the scale of a single river system has yet to be achieved. To overcome this we attempt to find the laws that describe sediment transport on a gross scale. We develop a general and simple length dependent diffusive sediment transport law to model both erosion and deposition that includes the concentrative effects of river systems. This allows us to collapse sediment transport onto a line and couple erosion and deposition with plate flexure. We use this model to interogate the impact of long-term (millions of years) change in rainfall and uplift rate on the stratigraphic archive of continental interior basins. Tilting of the interior of the North American continent due mantle flow, be it lithosphere instability or remnant subducting slabs, has been invoked to be the driver of change in rates and magnitude of river incision observed within the Great Plains. But, an increase in rainfall would also lead to an increase in river incision. Assuming that grains are deposited selectively by size we explore the signals recorded in the stratigraphic record by change in long-wavelength uplift and long-term rainfall. We find that under simple forcing conditions the modelled landscape is highly responsive to change in climate. Increase in rainfall causes incision of previously deposited

  9. Stratigraphic sequence analysis of the Antler foreland

    SciTech Connect

    Silberling, N.J.; Nichols, K.M.; Macke, D.L. )

    1993-04-01

    Mid-Upper Devonian to Upper Mississippian strata in western Utah were deposited in the distal Antler foreland. They record lateral and vertical changes in depositional environments that define five successive stratigraphic sequences, each representing a third-order transgressive-regressive cycle. In ascending order, these sequences are informally named the Langenheim (LA) of late Frasnian to mid-Famennian age, the Gutschick (GU) of late Famennian to early Kinderhookian age, the Morris (MO) of late Kinderhookian age; the Sadlick (SA) of Osagean to early Meramecian age, and the Maughan (MA) of mid-Meramecian to Chesterian age. MO is widespread and recognized within carbonate rocks of the Fitchville Formation and Joana Limestone. SA formed in concert with and to the east and south of the Wendover foreland high; the Delle phosphatic event marks maximum marine flooding during SA deposition. The transgressive systems tract of MA includes rhythmic-bedded limestone in the upper part of the Deseret Limestone in west-central Utah and, farther west, the hypoxic limestone and black shale of the Skunk Spring Limestone Bed and part of the overlying Chainman Shale. Traced westward into Nevada, MA first oversteps SA and then MO. Lithostratigraphic correlation of these sequences still farther west into the Eureka thrust belt (ETB) could mean that the youngest strata truncated by the Roberts Mountains thrust belong to the MA and that this thrust is simply part of the post-Mississippian ETB. However, some strata in central Nevada that lithically resemble those of the MA are paleontologically dated as Early Mississippian, the age of sequences overstepped by MA not far to the east. Thus, at least some imbricates of the ETB may contain a sequence stratigraphy which reflects local tectonic control.

  10. Submarine fans in a sequence stratigraphic framework

    SciTech Connect

    Posamentier, H.W.; Erskine, R.D.; Mitchum, R.M.; Vail, P.R.

    1987-05-01

    Submarine fans are fan- or cone-shaped turbiditic deposits formed in upper bathyal or deeper water depths. Within a sequence stratigraphic framework, these basin-floor turbidites can occur during lowstand-fan or lowstand-wedge systems tract time. During lowstand fan time, streams are rejuvenated and depocenters shift from the coastal plain to the upper slope, causing retrogradational slope failure and canyon formation. The sediment delivered here bypasses the canyon and continues down the slope as a succession of gravity flows and is deposited as fan-shaped turbiditic deposits at the base of the slope. Seismic and outcrop evidence suggest that these sand-prone deposits are abruptly introduced into the basin and are generally characterized by subtle external mounding and internal bidirectionally down lapping seismic reflections where seismically resolvable. Deep-water sediment deposited during this interval has no coeval shelf equivalent. During lowstand wedge time, streams cease down cutting and valleys which have been freshly incised begin to fill. Because coarse sediment will preferentially be deposited within these incised valleys, the sand-to-mud ratio delivered to the upper slope will be decreased and, consequently, there is an inherent difference between submarine fans deposited at this time and those deposited during lowstand fan time. Deposition during lowstand wedge time is characterized seismically by slope front fill or wedge-shaped geometries down lapping the earlier submarine fan (i.e., deposited during lowstand fan time). These shale-prone deposits are largely comprised of thinner-bedded turbidites as well as the occasional leveed channel.

  11. Major marine source rocks and stratigraphic cycles

    SciTech Connect

    Duval, B.C.

    1995-11-01

    The identification of continental encroachment cycles and subcycles by using sequence stratigraphy can assist explorationists in locating source rocks. The continental encroachment cycles are associated with the breakup of the supercontinents and fit a smooth long-term eustatic curve. They are first order, with a duration greater than 50 m.y., and are composed of transgressive and regressive phases inducing major changes in shoreline. The limit between the transgressive and regressive phases corresponds to a major downlap surface, and major marine source rocks are often found in association with this surface, particularly in the northern hemisphere. Potential {open_quotes}secondary{close_quotes} source rock intervals can also be sought by sequence stratigraphy because each continental encroachment cycle is composed of several subcycles, and the same configuration of a regressive forestepping phase overlying a transgressive backstepping phase also creates a downlap surface that may correspond with organic-rich intervals. The stratigraphic distribution of source rocks and related reserves fits reasonably well with continental encroachment cycles and subcycles. For instance, source rocks of Silurian, Upper Jurassic, and Middle-Upper Cretaceous are associated with eustatic highs and bear witness to this relationship. The recognition and mapping of such downlap surfaces is therefore a useful step to help map source rocks. The interpretation of sequence stratigraphy from regional seismic lines, properly calibrated with geochernical data whenever possible, can be of considerable help in the process. Several examples from around the world illustrate the power of the method: off-shore of eastern Venezuela, coastal basin of Angola, western Africa, the North Sea, south Algeria, and the North Caucasian trough.

  12. The role of social and ecological processes in structuring animal populations: a case study from automated tracking of wild birds

    PubMed Central

    Farine, Damien R.; Firth, Josh A.; Aplin, Lucy M.; Crates, Ross A.; Culina, Antica; Garroway, Colin J.; Hinde, Camilla A.; Kidd, Lindall R.; Milligan, Nicole D.; Psorakis, Ioannis; Radersma, Reinder; Verhelst, Brecht; Voelkl, Bernhard; Sheldon, Ben C.

    2015-01-01

    Both social and ecological factors influence population process and structure, with resultant consequences for phenotypic selection on individuals. Understanding the scale and relative contribution of these two factors is thus a central aim in evolutionary ecology. In this study, we develop a framework using null models to identify the social and spatial patterns that contribute to phenotypic structure in a wild population of songbirds. We used automated technologies to track 1053 individuals that formed 73 737 groups from which we inferred a social network. Our framework identified that both social and spatial drivers contributed to assortment in the network. In particular, groups had a more even sex ratio than expected and exhibited a consistent age structure that suggested local association preferences, such as preferential attachment or avoidance. By contrast, recent immigrants were spatially partitioned from locally born individuals, suggesting differential dispersal strategies by phenotype. Our results highlight how different scales of social decision-making, ranging from post-natal dispersal settlement to fission–fusion dynamics, can interact to drive phenotypic structure in animal populations. PMID:26064644

  13. AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain–domain interaction prediction

    PubMed Central

    Xu, Dong; Jaroszewski, Lukasz; Li, Zhanwen; Godzik, Adam

    2015-01-01

    Motivation: Most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. Template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available. Results: We have developed a fast docking algorithm ab initio domain assembly (AIDA) for assembling multi-domain protein structures, guided by the ab initio folding potential. This approach can be extended to discontinuous domains (i.e. domains with ‘inserted’ domains). When tested on experimentally solved structures of multi-domain proteins, the relative domain positions were accurately found among top 5000 models in 86% of cases. AIDA server can use domain assignments provided by the user or predict them from the provided sequence. The latter approach is particularly useful for automated protein structure prediction servers. The blind test consisting of 95 CASP10 targets shows that domain boundaries could be successfully determined for 97% of targets. Availability and implementation: The AIDA package as well as the benchmark sets used here are available for download at http://ffas.burnham.org/AIDA/. Contact: adam@sanfordburnham.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25701568

  14. The role of social and ecological processes in structuring animal populations: a case study from automated tracking of wild birds.

    PubMed

    Farine, Damien R; Firth, Josh A; Aplin, Lucy M; Crates, Ross A; Culina, Antica; Garroway, Colin J; Hinde, Camilla A; Kidd, Lindall R; Milligan, Nicole D; Psorakis, Ioannis; Radersma, Reinder; Verhelst, Brecht; Voelkl, Bernhard; Sheldon, Ben C

    2015-04-01

    Both social and ecological factors influence population process and structure, with resultant consequences for phenotypic selection on individuals. Understanding the scale and relative contribution of these two factors is thus a central aim in evolutionary ecology. In this study, we develop a framework using null models to identify the social and spatial patterns that contribute to phenotypic structure in a wild population of songbirds. We used automated technologies to track 1053 individuals that formed 73 737 groups from which we inferred a social network. Our framework identified that both social and spatial drivers contributed to assortment in the network. In particular, groups had a more even sex ratio than expected and exhibited a consistent age structure that suggested local association preferences, such as preferential attachment or avoidance. By contrast, recent immigrants were spatially partitioned from locally born individuals, suggesting differential dispersal strategies by phenotype. Our results highlight how different scales of social decision-making, ranging from post-natal dispersal settlement to fission-fusion dynamics, can interact to drive phenotypic structure in animal populations.

  15. The stratigraphic filter and bias in measurement of geologic rates

    USGS Publications Warehouse

    Schumer, R.; Jerolmack, D.; McElroy, B.

    2011-01-01

    Erosion and deposition rates estimated from the stratigraphic record frequently exhibit a power-law dependence on measurement interval. This dependence can result from a power-law distribution of stratigraphic hiatuses. By representing the stratigraphic filter as a stochastic process called a reverse ascending ladder, we describe a likely origin of power-law hiatuses, and thus, rate scaling. While power-law hiatuses in certain environments can be a direct result of power-law periods of stasis (no deposition or erosion), they are more generally the result of randomness in surface fluctuations irrespective of mean subsidence or uplift. Autocorrelation in fluctuations can make hiatuses more or less heavy-tailed, but still exhibit power-law characteristics. In addition we show that by passing stratigraphic data backward through the filter, certain statistics of surface kinematics from their formative environments can be inferred. Copyright ?? 2011 by the American Geophysical Union.

  16. The stratigraphic filter and bias in measurement of geologic rates

    USGS Publications Warehouse

    Schumer, Rina; Jerolmack, Douglas; McElroy, Brandon

    2011-01-01

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

  17. Advances in inspection automation

    NASA Astrophysics Data System (ADS)

    Weber, Walter H.; Mair, H. Douglas; Jansen, Dion; Lombardi, Luciano

    2013-01-01

    This new session at QNDE reflects the growing interest in inspection automation. Our paper describes a newly developed platform that makes the complex NDE automation possible without the need for software programmers. Inspection tasks that are tedious, error-prone or impossible for humans to perform can now be automated using a form of drag and drop visual scripting. Our work attempts to rectify the problem that NDE is not keeping pace with the rest of factory automation. Outside of NDE, robots routinely and autonomously machine parts, assemble components, weld structures and report progress to corporate databases. By contrast, components arriving in the NDT department typically require manual part handling, calibrations and analysis. The automation examples in this paper cover the development of robotic thickness gauging and the use of adaptive contour following on the NRU reactor inspection at Chalk River.

  18. Method and system for automated on-chip material and structural certification of MEMS devices

    DOEpatents

    Sinclair, Michael B.; DeBoer, Maarten P.; Smith, Norman F.; Jensen, Brian D.; Miller, Samuel L.

    2003-05-20

    A new approach toward MEMS quality control and materials characterization is provided by a combined test structure measurement and mechanical response modeling approach. Simple test structures are cofabricated with the MEMS devices being produced. These test structures are designed to isolate certain types of physical response, so that measurement of their behavior under applied stress can be easily interpreted as quality control and material properties information.

  19. Automated detection and labeling of high-density EEG electrodes from structural MR images

    NASA Astrophysics Data System (ADS)

    Marino, Marco; Liu, Quanying; Brem, Silvia; Wenderoth, Nicole; Mantini, Dante

    2016-10-01

    Objective. Accurate knowledge about the positions of electrodes in electroencephalography (EEG) is very important for precise source localizations. Direct detection of electrodes from magnetic resonance (MR) images is particularly interesting, as it is possible to avoid errors of co-registration between electrode and head coordinate systems. In this study, we propose an automated MR-based method for electrode detection and labeling, particularly tailored to high-density montages. Approach. Anatomical MR images were processed to create an electrode-enhanced image in individual space. Image processing included intensity non-uniformity correction, background noise and goggles artifact removal. Next, we defined a search volume around the head where electrode positions were detected. Electrodes were identified as local maxima in the search volume and registered to the Montreal Neurological Institute standard space using an affine transformation. This allowed the matching of the detected points with the specific EEG montage template, as well as their labeling. Matching and labeling were performed by the coherent point drift method. Our method was assessed on 8 MR images collected in subjects wearing a 256-channel EEG net, using the displacement with respect to manually selected electrodes as performance metric. Main results. Average displacement achieved by our method was significantly lower compared to alternative techniques, such as the photogrammetry technique. The maximum displacement was for more than 99% of the electrodes lower than 1 cm, which is typically considered an acceptable upper limit for errors in electrode positioning. Our method showed robustness and reliability, even in suboptimal conditions, such as in the case of net rotation, imprecisely gathered wires, electrode detachment from the head, and MR image ghosting. Significance. We showed that our method provides objective, repeatable and precise estimates of EEG electrode coordinates. We hope our work

  20. Distributed cyberinfrastructure tools for automated data processing of structural monitoring data

    NASA Astrophysics Data System (ADS)

    Zhang, Yilan; Kurata, Masahiro; Lynch, Jerome P.; van der Linden, Gwendolyn; Sederat, Hassan; Prakash, Atul

    2012-04-01

    The emergence of cost-effective sensing technologies has now enabled the use of dense arrays of sensors to monitor the behavior and condition of large-scale bridges. The continuous operation of dense networks of sensors presents a number of new challenges including how to manage such massive amounts of data that can be created by the system. This paper reports on the progress of the creation of cyberinfrastructure tools which hierarchically control networks of wireless sensors deployed in a long-span bridge. The internet-enabled cyberinfrastructure is centrally managed by a powerful database which controls the flow of data in the entire monitoring system architecture. A client-server model built upon the database provides both data-provider and system end-users with secured access to various levels of information of a bridge. In the system, information on bridge behavior (e.g., acceleration, strain, displacement) and environmental condition (e.g., wind speed, wind direction, temperature, humidity) are uploaded to the database from sensor networks installed in the bridge. Then, data interrogation services interface with the database via client APIs to autonomously process data. The current research effort focuses on an assessment of the scalability and long-term robustness of the proposed cyberinfrastructure framework that has been implemented along with a permanent wireless monitoring system on the New Carquinez (Alfred Zampa Memorial) Suspension Bridge in Vallejo, CA. Many data interrogation tools are under development using sensor data and bridge metadata (e.g., geometric details, material properties, etc.) Sample data interrogation clients including those for the detection of faulty sensors, automated modal parameter extraction.

  1. Semi-automated measurement of anatomical structures using statistical and morphological priors

    NASA Astrophysics Data System (ADS)

    Ashton, Edward A.; Du, Tong

    2004-05-01

    Rapid, accurate and reproducible delineation and measurement of arbitrary anatomical structures in medical images is a widely held goal, with important applications in both clinical diagnostics and, perhaps more significantly, pharmaceutical trial evaluation. This process requires the ability first to localize a structure within the body, and then to find a best approximation of the structure"s boundaries within a given scan. Structures that are tortuous and small in cross section, such as the hippocampus in the brain or the abdominal aorta, present a particular challenge. Their apparent shape and position can change significantly from slice to slice, and accurate prior shape models for such structures are often difficult to form. In this work, we have developed a system that makes use of both a user-defined shape model and a statistical maximum likelihood classifier to identify and measure structures of this sort in MRI and CT images. Experiments show that this system can reduce analysis time by 75% or more with respect to manual tracing with no loss of precision or accuracy.

  2. Poncho field - Cretaceous J sandstone stratigraphic traps - Denver basin, Colorado

    SciTech Connect

    Ethridge, F.G.; Ziegler, J.R.

    1983-08-01

    Distributary channel and delta destructional sandstones of Early Cretaceous age are important reservoirs for stratigraphic traps in the J sandstone at Poncho field, Adams and Arapahoe Counties, Colorado. Cores and logs from the field area reveal a lowermost, nonproductive, northeast-trending delta front sandstoe (J-3); a middle complex of southeast- and east-trending, productive distributary channel sandstones (J-2) that grade into tightly cemented delta fringe marine sediments to the southeast and northeast; and an upper, northeast trending, productive delta destructional sandstone (J-1). Vertical and lateral sequences of sedimentary structures, textures, trace fossil assemblages, and geometry and trend of sandstone bodies suggest that these units were part of a wave-dominated delta complex that prograded to the east and southeast from the area of Lonetree field. Thin section and SEM analyses reveal that the principal cements in both reservoir sandstones are quartz overgrowths, kaolinite, and chlorite, and that the bulk of the porosity is secondary and related to dissolution of carbonate cement and feldspar grains. Porosities and permeabilities are most variable and lowest in the nonproductive delta front sandstones, averaging 15% and 7 md; variable and intermediate in the productive distributary channel sandstones, averaging 16% and 28 md; and most uniform and highest in the overlying delta destructional sandstones, averaging 21% and 88 md.

  3. Pleistocene sediments of Lake Baikal: Lithology and stratigraphic correlation

    NASA Astrophysics Data System (ADS)

    Akulov, N. I.; Mashchuk, I. M.; Akulova, V. V.

    2015-01-01

    The Cenozoic sediments of Lake Baikal penetrated by boreholes and investigated by the manned submersible Pisces, as well as coeval deposits cropping out in beach scarps, recovered by mine workings, and drilled in the coastal zone were the object of this investigation. The main attention was paid to Pleistocene bottom sediments penetrated by Borehole BDP-99-2. The investigations included the detailed analysis of the lithology (grain-size composition, immersion mineralogy of light and heavy fractions, X-ray structural analysis of clayey fraction) and palynological assemblages to specify facies features of Cenozoic sediments, correlate all their known stratigraphic units constituting the sedimentary section of the lake with their analogs in the onshore part of the Baikal rift zone, and compile the composite Cenozoic section. The following features of these sediments are noted: (1) as a whole, Pleistocene sediments are characterized by the hydromica-smectite composition of their clayey fraction with an insignificant share of kaoline; (2) the heavy fraction is dominated by the terrigenous epidote-amphibole association poorly resistant to weathering; (3) Pleistocene sediments of the lake contain siderite, vivianite, pyrite, and goethite concretions and micrometeorites, in addition to well-known ferromanganese nodules; (4) the presence of relict palynomorphs in Pleistocene sediments of Baikal is determined by their erosion from Miocene and Pliocene cavernous clays cropping out on underwater slopes of the Posol'skaya Bank and subsequent reburial along with Pleistocene palynological assemblages.

  4. The ocean-continent transition zones: Stratigraphic and paleoecosystem studies

    SciTech Connect

    Gladenkov, Yu.B. )

    1993-03-01

    The author uses the Cenozoic of the Russian Pacific coast, drawing particularly on his 30-year experience with the molluscan faunas, as the source of examples of the ways that regional and global changes in the inorganic world affect the living world, as reflected in the stratigraphic and paleontologic record. The shelf ecosystem, despite its relative stability, shows periods of rapid change, reflecting both migration and accelerated evolution. The shelf ecosystem of the boreal belt evolved during Cenozoic time in an environment of changing paleoclimatic and paleogeographic phenomena. In spite of all their complexity and the considerable stressed nature of situations during individual moments in geological time, the ecosystem displayed a relative stability. The composition and structure of biotic communities, judging by the mollusks, changed with a definite trend (since Oligocene time, mainly on the species level), with gradual replacement through time of some forms by others, and with an increase in the percentage of Holocene species. This linear process was complicated by moments when the process accelerated. The problems encountered require wider discussion. The observed patterns of development of abiotic and biotic phenomena in this region, with its definite cyclicity and synchroneity, may be valuable in deciphering such patterns in other regions of the globe. The trends seen in the evolution of the biotic communities during Cenozoic time may also provide a basis for predicting the development of shelf ecosystems in the forthcoming decades and centuries. 46 refs., 2 figs., 2 tabs.

  5. Tectono-Stratigraphic Evolution of the Lake Van, Turkey

    NASA Astrophysics Data System (ADS)

    Görür, Naci; Sakınç, Mehmet; Zabcı, Cengiz; Namık Çaǧatay, M.; Akkök, Remzi; Şile, Hande

    2014-05-01

    Lake Van is situated in eastern Anatolia. It is the largest soda lake in the world. It also ranks the fourth-lake on earth by volume. It formed during the Pleistocene when the volcanic edifice of the Nemrut Volcano locally blocked the valley of the River Euphrates. It has a closed drainage system with several perennial streams that carry large amounts of sediments from the surrounding high mountains and accumulate them in today's lake. However, these sediments also crop out as terraces at various altitudes of the surrounding elevated areas, indicating that a series of changes in base- or water-level of the lake occurred. The exposed sediments display characteristic facies, stratigraphic sequence, well-developed sedimentary structures and scattered fossils that provide invaluable data on physical, chemical and biological conditions of their depositional sub-environments. Recognition of these sub-environments and their arrangement in space and time may contribute tremendously to our understanding of local tectonics and paleoclimate of the Lake Van Basin. These presentation deals with such topics.

  6. Automating crystallographic structure solution and refinement of protein–ligand complexes

    PubMed Central

    Echols, Nathaniel; Moriarty, Nigel W.; Klei, Herbert E.; Afonine, Pavel V.; Bunkóczi, Gábor; Headd, Jeffrey J.; McCoy, Airlie J.; Oeffner, Robert D.; Read, Randy J.; Terwilliger, Thomas C.; Adams, Paul D.

    2014-01-01

    High-throughput drug-discovery and mechanistic studies often require the determination of multiple related crystal structures that only differ in the bound ligands, point mutations in the protein sequence and minor conformational changes. If performed manually, solution and refinement requires extensive repetition of the same tasks for each structure. To accelerate this process and minimize manual effort, a pipeline encompassing all stages of ligand building and refinement, starting from integrated and scaled diffraction intensities, has been implemented in Phenix. The resulting system is able to successfully solve and refine large collections of structures in parallel without extensive user intervention prior to the final stages of model completion and validation. PMID:24419387

  7. Automated Lipid A Structure Assignment from Hierarchical Tandem Mass Spectrometry Data

    NASA Astrophysics Data System (ADS)

    Ting, Ying S.; Shaffer, Scott A.; Jones, Jace W.; Ng, Wailap V.; Ernst, Robert K.; Goodlett, David R.

    2011-05-01

    Infusion-based electrospray ionization (ESI) coupled to multiple-stage tandem mass spectrometry (MS n ) is a standard methodology for investigating lipid A structural diversity (Shaffer et al. J. Am. Soc. Mass. Spectrom. 18(6), 1080-1092, 2007). Annotation of these MS n spectra, however, has remained a manual, expert-driven process. In order to keep up with the data acquisition rates of modern instruments, we devised a computational method to annotate lipid A MS n spectra rapidly and automatically, which we refer to as hierarchical tandem mass spectrometry (HiTMS) algorithm. As a first-pass tool, HiTMS aids expert interpretation of lipid A MS n data by providing the analyst with a set of candidate structures that may then be confirmed or rejected. HiTMS deciphers the signature ions (e.g., A-, Y-, and Z-type ions) and neutral losses of MS n spectra using a species-specific library based on general prior structural knowledge of the given lipid A species under investigation. Candidates are selected by calculating the correlation between theoretical and acquired MS n spectra. At a false discovery rate of less than 0.01, HiTMS correctly assigned 85% of the structures in a library of 133 manually annotated Francisella tularensis subspecies novicida lipid A structures. Additionally, HiTMS correctly assigned 85% of the structures in a smaller library of lipid A species from Yersinia pestis demonstrating that it may be used across species.

  8. Automated delineation of brain structures in patients undergoing radiotherapy for primary brain tumors: from atlas to dose-volume histograms.

    PubMed

    Conson, Manuel; Cella, Laura; Pacelli, Roberto; Comerci, Marco; Liuzzi, Raffaele; Salvatore, Marco; Quarantelli, Mario

    2014-09-01

    To implement and evaluate a magnetic resonance imaging atlas-based automated segmentation (MRI-ABAS) procedure for cortical and sub-cortical grey matter areas definition, suitable for dose-distribution analyses in brain tumor patients undergoing radiotherapy (RT). 3T-MRI scans performed before RT in ten brain tumor patients were used. The MRI-ABAS procedure consists of grey matter classification and atlas-based regions of interest definition. The Simultaneous Truth and Performance Level Estimation (STAPLE) algorithm was applied to structures manually delineated by four experts to generate the standard reference. Performance was assessed comparing multiple geometrical metrics (including Dice Similarity Coefficient - DSC). Dosimetric parameters from dose-volume-histograms were also generated and compared. Compared with manual delineation, MRI-ABAS showed excellent reproducibility [median DSCABAS=1 (95% CI, 0.97-1.0) vs. DSCMANUAL=0.90 (0.73-0.98)], acceptable accuracy [DSCABAS=0.81 (0.68-0.94) vs. DSCMANUAL=0.90 (0.76-0.98)], and an overall 90% reduction in delineation time. Dosimetric parameters obtained using MRI-ABAS were comparable with those obtained by manual contouring. The speed, reproducibility, and robustness of the process make MRI-ABAS a valuable tool for investigating radiation dose-volume effects in non-target brain structures providing additional standardized data without additional time-consuming procedures. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  9. CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

    PubMed Central

    Puton, Tomasz; Kozlowski, Lukasz P.; Rother, Kristian M.; Bujnicki, Janusz M.

    2013-01-01

    We present a continuous benchmarking approach for the assessment of RNA secondary structure prediction methods implemented in the CompaRNA web server. As of 3 October 2012, the performance of 28 single-sequence and 13 comparative methods has been evaluated on RNA sequences/structures released weekly by the Protein Data Bank. We also provide a static benchmark generated on RNA 2D structures derived from the RNAstrand database. Benchmarks on both data sets offer insight into the relative performance of RNA secondary structure prediction methods on RNAs of different size and with respect to different types of structure. According to our tests, on the average, the most accurate predictions obtained by a comparative approach are generated by CentroidAlifold, MXScarna, RNAalifold and TurboFold. On the average, the most accurate predictions obtained by single-sequence analyses are generated by CentroidFold, ContextFold and IPknot. The best comparative methods typically outperform the best single-sequence methods if an alignment of homologous RNA sequences is available. This article presents the results of our benchmarks as of 3 October 2012, whereas the rankings presented online are continuously updated. We will gladly include new prediction methods and new measures of accuracy in the new editions of CompaRNA benchmarks. PMID:23435231

  10. Direct-method SAD phasing with partial-structure iteration: towards automation.

    PubMed

    Wang, J W; Chen, J R; Gu, Y X; Zheng, C D; Fan, H F

    2004-11-01

    The probability formula of direct-method SAD (single-wavelength anomalous diffraction) phasing proposed by Fan & Gu (1985, Acta Cryst. A41, 280-284) contains partial-structure information in the form of a Sim-weighting term. Previously, only the substructure of anomalous scatterers has been included in this term. In the case that the subsequent density modification and model building yields only structure fragments, which do not straightforwardly lead to the complete solution, the partial structure can be fed back into the Sim-weighting term of the probability formula in order to strengthen its phasing power and to benefit the subsequent automatic model building. The procedure has been tested with experimental SAD data from two known proteins with copper and sulfur as the anomalous scatterers.

  11. Automated Aufbau of antibody structures from given sequences using Macromoltek's SmrtMolAntibody.

    PubMed

    Berrondo, Monica; Kaufmann, Susana; Berrondo, Manuel

    2014-08-01

    This study was a part of the second antibody modeling assessment. The assessment is a blind study of the performance of multiple software programs used for antibody homology modeling. In the study, research groups were given sequences for 11 antibodies and asked to predict their corresponding structures. The results were measured using root-mean-square deviation (rmsd) between the submitted models and X-ray crystal structures. In 10 of 11 cases, the results using SmrtMolAntibody show good agreement between the submitted models and X-ray crystal structures. In the first stage, the average rmsd was 1.4 Å. Average rmsd values for the framework was 1.2 Å and for the H3 loop was 3.0 Å. In stage two, there was a slight improvement with an rmsd for the H3 loop of 2.9 Å.

  12. Automated Quantification of Arbitrary Arm-Segment Structure in Spiral Galaxies

    NASA Astrophysics Data System (ADS)

    Davis, Darren Robert

    This thesis describes a system that, given approximately-centered images of spiral galaxies, produces quantitative descriptions of spiral galaxy structure without the need for per-image human input. This structure information consists of a list of spiral arm segments, each associated with a fitted logarithmic spiral arc and a pixel region. This list-of-arcs representation allows description of arbitrary spiral galaxy structure: the arms do not need to be symmetric, may have forks or bends, and, more generally, may be arranged in any manner with a consistent spiral-pattern center (non-merging galaxies have a sufficiently well-defined center). Such flexibility is important in order to accommodate the myriad structure variations observed in spiral galaxies. From the arcs produced from our method it is possible to calculate measures of spiral galaxy structure such as winding direction, winding tightness, arm counts, asymmetry, or other values of interest (including user-defined measures). In addition to providing information about the spiral arm "skeleton" of each galaxy, our method can enable analyses of brightness within individual spiral arms, since we provide the pixel regions associated with each spiral arm segment. For winding direction, arm tightness, and arm count, comparable information is available (to various extents) from previous efforts; to the extent that such information is available, we find strong correspondence with our output. We also characterize the changes to (and invariances in) our output as a function of modifications to important algorithm parameters. By enabling generation of extensive data about spiral galaxy structure from large-scale sky surveys, our method will enable new discoveries and tests regarding the nature of galaxies and the universe, and will facilitate subsequent work to automatically fit detailed brightness models of spiral galaxies.

  13. Digital tabulation of stratigraphic data from oil and gas wells in Cuyama Valley and surrounding areas, central California

    USGS Publications Warehouse

    Sweetkind, Donald S.; Bova, Shiera C.; Langenheim, V.E.; Shumaker, Lauren E.; Scheirer, Daniel S.

    2013-01-01

    Stratigraphic information from 391 oil and gas exploration wells from Cuyama Valley, California, and surrounding areas are herein compiled in digital form from reports that were released originally in paper form. The Cuyama Basin is located within the southeasternmost part of the Coast Ranges and north of the western Transverse Ranges, west of the San Andreas fault. Knowledge of the location and elevation of stratigraphic tops of formations throughout the basin is a first step toward understanding depositional trends and the structural evolution of the basin through time, and helps in understanding the slip history and partitioning of slip on San Andreas and related faults.

  14. Automated test bench for simulation of radiation electrification of spacecraft structural dielectrics

    NASA Astrophysics Data System (ADS)

    Vladimirov, A. M.; Bezhayev, A. Yu; Zykov, V. M.; Isaychenko, V. I.; Lukashchuk, A. A.; Lukonin, S. E.

    2017-01-01

    The paper describes the test bench “Prognoz-2” designed in Testing Center, Institute of Non-Destructive Testing, Tomsk Polytechnic University, which can be used: for ground testing of individual samples of spacecraft structural materials (e.g. thermal control coatings or cover glasses for solar batteries) or ceramics of the plasma thruster discharge channel), and whole spacecraft units or instruments (e.g. instruments of solar and stellar orientation or correcting plasma thrusters) exposed to radiation electrification factors; to verify the calculation mathematical models of radiation electrification of structural dielectrics under the impact of space factors in different orbits.

  15. A method for automated determination of the crystal structures from X-ray powder diffraction data

    SciTech Connect

    Hofmann, D. W. M. Kuleshova, L. N.

    2006-05-15

    An algorithm is proposed for determining the crystal structure of compounds. In the framework of this algorithm, X-ray powder diffraction patterns are compared using a new similarity index. Unlike the indices traditionally employed in X-ray powder diffraction analysis, the new similarity index can be applied even in the case of overlapping peaks and large differences in unit cell parameters. The capabilities of the proposed procedure are demonstrated by solving the crystal structures of a number of organic pigments (PY111, PR181, Me-PR170)

  16. Seismic model study of Patrick Draw field, Wyoming: a stratigraphic trap in the Upper Cretaceous Almond Formation

    USGS Publications Warehouse

    Anderson, Robert C.; Ryder, Robert T.

    1978-01-01

    The Patrick Draw field, located on the eastern flank of the Rock Springs uplift in the Washakie basin of southwestern Wyoming, was discovered in 1959 without the use of geophysical methods. The field is a classic example of a stratigraphic trap, where Upper Cretaceous porous sandstone units pinch out on a structural nose. Two-dimensional seismic modeling was used to construct the seismic waveform expressions of the Patrick Draw field, and to better understand how to explore for other 'Patrick Draw' fields. Interpretation of the model shows that the detection of the reservoir sand is very difficult, owing to a combination of acoustic contrasts and bed thickness. Because the model included other major stratigraphic units in the subsurface, several stratigraphic traps are suggested as potential exploration targets.

  17. Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates

    PubMed Central

    Matthew Ward, R.; Venner, Eric; Daines, Bryce; Murray, Stephen; Erdin, Serkan; Kristensen, David M.; Lichtarge, Olivier

    2009-01-01

    Summary:The Evolutionary Trace Annotation (ETA) Server predicts enzymatic activity. ETA starts with a structure of unknown function, such as those from structural genomics, and with no prior knowledge of its mechanism uses the phylogenetic Evolutionary Trace (ET) method to extract key functional residues and propose a function-associated 3D motif, called a 3D template. ETA then searches previously annotated structures for geometric template matches that suggest molecular and thus functional mimicry. In order to maximize the predictive value of these matches, ETA next applies distinctive specificity filters—evolutionary similarity, function plurality and match reciprocity. In large scale controls on enzymes, prediction coverage is 43% but the positive predictive value rises to 92%, thus minimizing false annotations. Users may modify any search parameter, including the template. ETA thus expands the ET suite for protein structure annotation, and can contribute to the annotation efforts of metaservers. Availability:The ETA Server is a web application available at http://mammoth.bcm.tmc.edu/eta/. Contact: lichtarge@bcm.edu PMID:19307237

  18. Combining structure and sequence information allows automated prediction of substrate specificities within enzyme families.

    PubMed

    Röttig, Marc; Rausch, Christian; Kohlbacher, Oliver

    2010-01-08

    An important aspect of the functional annotation of enzymes is not only the type of reaction catalysed by an enzyme, but also the substrate specificity, which can vary widely within the same family. In many cases, prediction of family membership and even substrate specificity is possible from enzyme sequence alone, using a nearest neighbour classification rule. However, the combination of structural information and sequence information can improve the interpretability and accuracy of predictive models. The method presented here, Active Site Classification (ASC), automatically extracts the residues lining the active site from one representative three-dimensional structure and the corresponding residues from sequences of other members of the family. From a set of representatives with known substrate specificity, a Support Vector Machine (SVM) can then learn a model of substrate specificity. Applied to a sequence of unknown specificity, the SVM can then predict the most likely substrate. The models can also be analysed to reveal the underlying structural reasons determining substrate specificities and thus yield valuable insights into mechanisms of enzyme specificity. We illustrate the high prediction accuracy achieved on two benchmark data sets and the structural insights gained from ASC by a detailed analysis of the family of decarboxylating dehydrogenases. The ASC web service is available at http://asc.informatik.uni-tuebingen.de/.

  19. Automated Remote Focusing, Drift Correction, and Photostimulation to Evaluate Structural Plasticity in Dendritic Spines

    PubMed Central

    Evans, Paul R.; Garrett, Tavita R.; Yan, Long; Yasuda, Ryohei

    2017-01-01

    Long-term structural plasticity of dendritic spines plays a key role in synaptic plasticity, the cellular basis for learning and memory. The biochemical step is mediated by a complex network of signaling proteins in spines. Two-photon imaging techniques combined with two-photon glutamate uncaging allows researchers to induce and quantify structural plasticity in single dendritic spines. However, this method is laborious and slow, making it unsuitable for high throughput screening of factors necessary for structural plasticity. Here we introduce a MATLAB-based module built for Scanimage to automatically track, image, and stimulate multiple dendritic spines. We implemented an electrically tunable lens in combination with a drift correction algorithm to rapidly and continuously track targeted spines and correct sample movements. With a straightforward user interface to design custom multi-position experiments, we were able to adequately image and produce targeted plasticity in multiple dendritic spines using glutamate uncaging. Our methods are inexpensive, open source, and provides up to a five-fold increase in throughput for quantifying structural plasticity of dendritic spines. PMID:28114380

  20. Automated assignment of NMR chemical shifts based on a known structure and 4D spectra.

    PubMed

    Trautwein, Matthias; Fredriksson, Kai; Möller, Heiko M; Exner, Thomas E

    2016-08-01

    Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is the basis for a number of applications, like chemical shift perturbation mapping and studies on the dynamics of proteins. This assignment is not a trivial task even if a 3D protein structure is known and needs almost as much effort as the assignment for structure prediction if performed manually. We present here a new algorithm based solely on 4D [(1)H,(15)N]-HSQC-NOESY-[(1)H,(15)N]-HSQC spectra which is able to assign a large percentage of chemical shifts (73-82 %) unambiguously, demonstrated with proteins up to a size of 250 residues. For the remaining residues, a small number of possible assignments is filtered out. This is done by comparing distances in the 3D structure to restraints obtained from the peak volumes in the 4D spectrum. Using dead-end elimination, assignments are removed in which at least one of the restraints is violated. Including additional information from chemical shift predictions, a complete unambiguous assignment was obtained for Ubiquitin and 95 % of the residues were correctly assigned in the 251 residue-long N-terminal domain of enzyme I. The program including source code is available at https://github.com/thomasexner/4Dassign .

  1. Low-Cost Impact Detection and Location for Automated Inspections of 3D Metallic Based Structures

    PubMed Central

    Morón, Carlos; Portilla, Marina P.; Somolinos, José A.; Morales, Rafael

    2015-01-01

    This paper describes a new low-cost means to detect and locate mechanical impacts (collisions) on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing) the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach. PMID:26029951

  2. Combining Structure and Sequence Information Allows Automated Prediction of Substrate Specificities within Enzyme Families

    PubMed Central

    Röttig, Marc; Rausch, Christian; Kohlbacher, Oliver

    2010-01-01

    An important aspect of the functional annotation of enzymes is not only the type of reaction catalysed by an enzyme, but also the substrate specificity, which can vary widely within the same family. In many cases, prediction of family membership and even substrate specificity is possible from enzyme sequence alone, using a nearest neighbour classification rule. However, the combination of structural information and sequence information can improve the interpretability and accuracy of predictive models. The method presented here, Active Site Classification (ASC), automatically extracts the residues lining the active site from one representative three-dimensional structure and the corresponding residues from sequences of other members of the family. From a set of representatives with known substrate specificity, a Support Vector Machine (SVM) can then learn a model of substrate specificity. Applied to a sequence of unknown specificity, the SVM can then predict the most likely substrate. The models can also be analysed to reveal the underlying structural reasons determining substrate specificities and thus yield valuable insights into mechanisms of enzyme specificity. We illustrate the high prediction accuracy achieved on two benchmark data sets and the structural insights gained from ASC by a detailed analysis of the family of decarboxylating dehydrogenases. The ASC web service is available at http://asc.informatik.uni-tuebingen.de/. PMID:20072606

  3. Low-cost impact detection and location for automated inspections of 3D metallic based structures.

    PubMed

    Morón, Carlos; Portilla, Marina P; Somolinos, José A; Morales, Rafael

    2015-05-28

    This paper describes a new low-cost means to detect and locate mechanical impacts (collisions) on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing) the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach.

  4. Using Structure-Based Organic Chemistry Online Tutorials with Automated Correction for Student Practice and Review

    ERIC Educational Resources Information Center

    O'Sullivan, Timothy P.; Hargaden, Gra´inne C.

    2014-01-01

    This article describes the development and implementation of an open-access organic chemistry question bank for online tutorials and assessments at University College Cork and Dublin Institute of Technology. SOCOT (structure-based organic chemistry online tutorials) may be used to supplement traditional small-group tutorials, thereby allowing…

  5. Using Structure-Based Organic Chemistry Online Tutorials with Automated Correction for Student Practice and Review

    ERIC Educational Resources Information Center

    O'Sullivan, Timothy P.; Hargaden, Gra´inne C.

    2014-01-01

    This article describes the development and implementation of an open-access organic chemistry question bank for online tutorials and assessments at University College Cork and Dublin Institute of Technology. SOCOT (structure-based organic chemistry online tutorials) may be used to supplement traditional small-group tutorials, thereby allowing…

  6. Automated antibody structure prediction using Accelrys tools: results and best practices.

    PubMed

    Fasnacht, Marc; Butenhof, Ken; Goupil-Lamy, Anne; Hernandez-Guzman, Francisco; Huang, Hongwei; Yan, Lisa

    2014-08-01

    We describe the methodology and results from our participation in the second Antibody Modeling Assessment experiment. During the experiment we predicted the structure of eleven unpublished antibody Fv fragments. Our prediction methods centered on template-based modeling; potential templates were selected from an antibody database based on their sequence similarity to the target in the framework regions. Depending on the quality of the templates, we constructed models of the antibody framework regions either using a single, chimeric or multiple template approach. The hypervariable loop regions in the initial models were rebuilt by grafting the corresponding regions from suitable templates onto the model. For the H3 loop region, we further refined models using ab initio methods. The final models were subjected to constrained energy minimization to resolve severe local structural problems. The analysis of the models submitted show that Accelrys tools allow for the construction of quite accurate models for the framework and the canonical CDR regions, with RMSDs to the X-ray structure on average below 1 Å for most of these regions. The results show that accurate prediction of the H3 hypervariable loops remains a challenge. Furthermore, model quality assessment of the submitted models show that the models are of quite high quality, with local geometry assessment scores similar to that of the target X-ray structures.

  7. Semi-automated structural analysis of high resolution magnetic and gamma-ray spectrometry airborne surveys

    NASA Astrophysics Data System (ADS)

    Debeglia, N.; Martelet, G.; Perrin, J.; Truffert, C.; Ledru, P.; Tourlière, B.

    2005-08-01

    A user-controlled procedure was implemented for the structural analysis of geophysical maps. Local edge segments are first extracted using a suitable edge detector function, then linked into straight discontinuities and, finally, organised in complex boundary lines best delineating geophysical features. Final boundary lines may be attributed by a geologist to lithological contacts and/or structural geological features. Tests of some edge detectors, (i) horizontal gradient magnitude (HGM), (ii) various orders of the analytic signal ( An), reduced to the pole or not, (iii) enhanced horizontal derivative (EHD), (iv) composite analytic signal (CAS), were performed on synthetic magnetic data (with and without noise). As a result of these comparisons, the horizontal gradient appears to remain the best operator for the analysis of magnetic data. Computation of gradients in the frequency domain, including filtering and upward continuation of noisy data, is well-suited to the extraction of magnetic gradients associated to deep sources, while space-domain smoothing and differentiation techniques is generally preferable in the case of shallow magnetic sources, or for gamma-ray spectrometry analysis. Algorithms for edge extraction, segment linking, and line following can be controlled by choosing adequate edge detector and processing parameters which allows adaptation to a desired scale of interpretation. Tests on synthetic and real case data demonstrate the adaptability of the procedure and its ability to produce basic layer for multi-data analysis. The method was applied to the interpretation of high-resolution airborne magnetic and gamma-ray spectrometry data collected in northern Namibia. It allowed the delineation of dyke networks concealed by superficial weathering and demonstrated the presence of lithological variations in alluvial flows. The output from the structural analysis procedure are compatible with standard GIS softwares and enable the geologist to (i) compare

  8. Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments.

    PubMed

    Akhmedov, Murodzhon; Çatay, Bülent; Apaydın, Mehmet Serkan

    2015-12-01

    Nuclear Magnetic Resonance (NMR) Spectroscopy is an important technique that allows determining protein structure in solution. An important problem in protein structure determination using NMR spectroscopy is the mapping of peaks to corresponding amino acids, also known as the assignment problem. Structure-Based Assignment (SBA) is an approach to solve this problem using a template structure that is homologous to the target. Our previously developed approach Nuclear Vector Replacement-Binary Integer Programming (NVR-BIP) computed the optimal solution for small proteins, but was unable to solve the assignments of large proteins. NVR-Ant Colony Optimization (ACO) extended the applicability of the NVR approach for such proteins. One of the input data utilized in these approaches is the Nuclear Overhauser Effect (NOE) data. NOE is an interaction observed between two protons if the protons are located close in space. These protons could be amide protons, protons attached to the alpha-carbon atom in the backbone of the protein, or side chain protons. NVR only uses backbone protons. In this paper, we reformulate the NVR-BIP model to distinguish the type of proton in NOE data and use the corresponding proton coordinates in the extended formulation. In addition, the threshold value over interproton distances is set in a standard manner for all proteins by extracting the NOE upper bound distance information from the data. We also convert NOE intensities into distance thresholds. Our new approach thus handles the NOE data correctly and without manually determined parameters. We accordingly adapt NVR-ACO solution methodology to these changes. Computational results show that our approaches obtain optimal solutions for small proteins. For the large proteins our ant colony optimization-based approach obtains promising results.

  9. Enhanced Aircraft Design Capability for the Automated Structural Optimization System. Phase 1.

    DTIC Science & Technology

    1996-01-31

    creation and evolution . The creation takes place in the GOA in the form of a finite number of designs randomly generated to form the initial population...are feasible or not. Evolution is then applied to the population to produce a new population of, hopefully, better designs. The evolution B-3 of a...chromosomal" diploid strings that are closer, in structure, to human codings than traditional GOA haploid strings. For example, the human code carries 23 pairs

  10. Automated conductivity profiler for multilayer GaAs-(AlGa)As structures

    NASA Astrophysics Data System (ADS)

    Stiles, K. R.; Lee, J. W.

    1982-09-01

    An apparatus for automatic conductivity profiling of GaAs-(AlGa)As multilayer structures is described. The apparatus includes a microprocessor which controls a solenoid valve sequence in order to chemically etch the sample, and a programmable calculator which calculates sample conductance versus number of etch steps from which layer conductivities are calculated. Conductivity profiles of multilayer GaAs-(AlGa)As heterostructure laser material are presented and compared to profiles done by an earlier manual technique.

  11. Identifying relevant biomarkers of brain injury from structural MRI: Validation using automated approaches in children with unilateral cerebral palsy.

    PubMed

    Pagnozzi, Alex M; Dowson, Nicholas; Doecke, James; Fiori, Simona; Bradley, Andrew P; Boyd, Roslyn N; Rose, Stephen

    2017-01-01

    Previous studies have proposed that the early elucidation of brain injury from structural Magnetic Resonance Images (sMRI) is critical for the clinical assessment of children with cerebral palsy (CP). Although distinct aetiologies, including cortical maldevelopments, white and grey matter lesions and ventricular enlargement, have been categorised, these injuries are commonly only assessed in a qualitative fashion. As a result, sMRI remains relatively underexploited for clinical assessments, despite its widespread use. In this study, several automated and validated techniques to automatically quantify these three classes of injury were generated in a large cohort of children (n = 139) aged 5-17, including 95 children diagnosed with unilateral CP. Using a feature selection approach on a training data set (n = 97) to find severity of injury biomarkers predictive of clinical function (motor, cognitive, communicative and visual function), cortical shape and regional lesion burden were most often chosen associated with clinical function. Validating the best models on the unseen test data (n = 42), correlation values ranged between 0.545 and 0.795 (p<0.008), indicating significant associations with clinical function. The measured prevalence of injury, including ventricular enlargement (70%), white and grey matter lesions (55%) and cortical malformations (30%), were similar to the prevalence observed in other cohorts of children with unilateral CP. These findings support the early characterisation of injury from sMRI into previously defined aetiologies as part of standard clinical assessment. Furthermore, the strong and significant association between quantifications of injury observed on structural MRI and multiple clinical scores accord with empirically established structure-function relationships.

  12. Automated polyp measurement based on colon structure decomposition for CT colonography

    NASA Astrophysics Data System (ADS)

    Wang, Huafeng; Li, Lihong C.; Han, Hao; Peng, Hao; Song, Bowen; Wei, Xinzhou; Liang, Zhengrong

    2014-03-01

    Accurate assessment of colorectal polyp size is of great significance for early diagnosis and management of colorectal cancers. Due to the complexity of colon structure, polyps with diverse geometric characteristics grow from different landform surfaces. In this paper, we present a new colon decomposition approach for polyp measurement. We first apply an efficient maximum a posteriori expectation-maximization (MAP-EM) partial volume segmentation algorithm to achieve an effective electronic cleansing on colon. The global colon structure is then decomposed into different kinds of morphological shapes, e.g. haustral folds or haustral wall. Meanwhile, the polyp location is identified by an automatic computer aided detection algorithm. By integrating the colon structure decomposition with the computer aided detection system, a patch volume of colon polyps is extracted. Thus, polyp size assessment can be achieved by finding abnormal protrusion on a relative uniform morphological surface from the decomposed colon landform. We evaluated our method via physical phantom and clinical datasets. Experiment results demonstrate the feasibility of our method in consistently quantifying the size of polyp volume and, therefore, facilitating characterizing for clinical management.

  13. Automated method for the identification and analysis of vascular tree structures in retinal vessel network

    NASA Astrophysics Data System (ADS)

    Joshi, Vinayak S.; Garvin, Mona K.; Reinhardt, Joseph M.; Abramoff, Michael D.

    2011-03-01

    Structural analysis of retinal vessel network has so far served in the diagnosis of retinopathies and systemic diseases. The retinopathies are known to affect the morphologic properties of retinal vessels such as course, shape, caliber, and tortuosity. Whether the arteries and the veins respond to these changes together or in tandem has always been a topic of discussion. However the diseases such as diabetic retinopathy and retinopathy of prematurity have been diagnosed with the morphologic changes specific either to arteries or to veins. Thus a method describing the separation of retinal vessel trees imaged in a two dimensional color fundus image may assist in artery-vein classification and quantitative assessment of morphologic changes particular to arteries or veins. We propose a method based on mathematical morphology and graph search to identify and label the retinal vessel trees, which provides a structural mapping of vessel network in terms of each individual primary vessel, its branches and spatial positions of branching and cross-over points. The method was evaluated on a dataset of 15 fundus images resulting into an accuracy of 92.87 % correctly assigned vessel pixels when compared with the manual labeling of separated vessel trees. Accordingly, the structural mapping method performs well and we are currently investigating its potential in evaluating the characteristic properties specific to arteries or veins.

  14. Automated preliminary design of simplified wing structures to satisfy strength and flutter requirements

    NASA Technical Reports Server (NTRS)

    Stroud, W. J.; Dexter, C. B.; Stein, M.

    1972-01-01

    A simple structural model of an aircraft wing is used to show the effects of strength (stress) and flutter requirements on the design of minimum-weight aircraft-wing structures. The wing is idealized as an isotropic sandwich plate with a variable cover thickness distribution and a variable depth between covers. Plate theory is used for the structural analysis, and piston theory is used for the unsteady aerodynamics in the flutter analysis. Mathematical programming techniques are used to find the minimum-weight cover thickness distribution which satisfies flutter, strength, and minimum-gage constraints. The method of solution, some sample results, and the computer program used to obtain these results are presented. The results indicate that the cover thickness distribution obtained when designing for the strength requirement alone may be quite different from the cover thickness distribution obtained when designing for either the flutter requirement alone or for both the strength and flutter requirements concurrently. This conclusion emphasizes the need for designing for both flutter and strength from the outset.

  15. Automated Voxel Model from Point Clouds for Structural Analysis of Cultural Heritage

    NASA Astrophysics Data System (ADS)

    Bitelli, G.; Castellazzi, G.; D'Altri, A. M.; De Miranda, S.; Lambertini, A.; Selvaggi, I.

    2016-06-01

    In the context of cultural heritage, an accurate and comprehensive digital survey of a historical building is today essential in order to measure its geometry in detail for documentation or restoration purposes, for supporting special studies regarding materials and constructive characteristics, and finally for structural analysis. Some proven geomatic techniques, such as photogrammetry and terrestrial laser scanning, are increasingly used to survey buildings with different complexity and dimensions; one typical product is in form of point clouds. We developed a semi-automatic procedure to convert point clouds, acquired from laserscan or digital photogrammetry, to a filled volume model of the whole structure. The filled volume model, in a voxel format, can be useful for further analysis and also for the generation of a Finite Element Model (FEM) of the surveyed building. In this paper a new approach is presented with the aim to decrease operator intervention in the workflow and obtain a better description of the structure. In order to achieve this result a voxel model with variable resolution is produced. Different parameters are compared and different steps of the procedure are tested and validated in the case study of the North tower of the San Felice sul Panaro Fortress, a monumental historical building located in San Felice sul Panaro (Modena, Italy) that was hit by an earthquake in 2012.

  16. Automated procedure for design of wing structures to satisfy strength and flutter requirements

    NASA Technical Reports Server (NTRS)

    Haftka, R. T.

    1973-01-01

    A pilot computer program was developed for the design of minimum mass wing structures under flutter, strength, and minimum gage constraints. The wing structure is idealized by finite elements, and second-order piston theory aerodynamics is used in the flutter calculation. Mathematical programing methods are used for the optimization. Computation times during the design process are reduced by three techniques. First, iterative analysis methods used to reduce significantly reanalysis times. Second, the number of design variables is kept small by not using a one-to-one correspondence between finite elements and design variables. Third, a technique for using approximate second derivatives with Newton's method for the optimization is incorporated. The program output is compared witH previous published results. It is found that some flutter characteristics, such as the flutter speed, can display discontinous dependence on the design variables (which are the thicknesses of the structural elements). It is concluded that it is undesirable to use such quantities in the formulation of the flutter constraint.

  17. Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability.

    PubMed

    Parrish, Robert M; Burns, Lori A; Smith, Daniel G A; Simmonett, Andrew C; DePrince, A Eugene; Hohenstein, Edward G; Bozkaya, Uğur; Sokolov, Alexander Yu; Di Remigio, Roberto; Richard, Ryan M; Gonthier, Jérôme F; James, Andrew M; McAlexander, Harley R; Kumar, Ashutosh; Saitow, Masaaki; Wang, Xiao; Pritchard, Benjamin P; Verma, Prakash; Schaefer, Henry F; Patkowski, Konrad; King, Rollin A; Valeev, Edward F; Evangelista, Francesco A; Turney, Justin M; Crawford, T Daniel; Sherrill, C David

    2017-07-11

    Psi4 is an ab initio electronic structure program providing methods such as Hartree-Fock, density functional theory, configuration interaction, and coupled-cluster theory. The 1.1 release represents a major update meant to automate complex tasks, such as geometry optimization using complete-basis-set extrapolation or focal-point methods. Conversion of the top-level code to a Python module means that Psi4 can now be used in complex workflows alongside other Python tools. Several new features have been added with the aid of libraries providing easy access to techniques such as density fitting, Cholesky decomposition, and Laplace denominators. The build system has been completely rewritten to simplify interoperability with independent, reusable software components for quantum chemistry. Finally, a wide range of new theoretical methods and analyses have been added to the code base, including functional-group and open-shell symmetry adapted perturbation theory, density-fitted coupled cluster with frozen natural orbitals, orbital-optimized perturbation and coupled-cluster methods (e.g., OO-MP2 and OO-LCCD), density-fitted multiconfigurational self-consistent field, density cumulant functional theory, algebraic-diagrammatic construction excited states, improvements to the geometry optimizer, and the "X2C" approach to relativistic corrections, among many other improvements.

  18. Upper-mantle shear-wave structure under East and Southeast Asia from Automated Multimode Inversion of waveforms

    NASA Astrophysics Data System (ADS)

    Legendre, C. P.; Zhao, L.; Chen, Q.-F.

    2015-10-01

    We present a new Sv-velocity model of the upper mantle under East and Southeast Asia constrained by the inversion of seismic waveforms recorded by broad-band stations. Seismograms from earthquakes occurred between 1977 and 2012 are collected from about 4786 permanent and temporary stations in the region whenever and wherever available. Automated Multimode Inversion of surface and multiple-S waveforms is applied to extract structural information from the seismograms, in the form of linear equations with uncorrelated uncertainties. The equations are then solved for the seismic velocity perturbations in the crust and upper mantle with respect to a three-dimensional (3-D) reference model and a realistic crust. Major features of the lithosphere-asthenosphere system in East and Southeast Asia are identified in the resulting model. At lithospheric depth, low velocities can be seen beneath Tibet, whereas high velocities are found beneath cratonic regions, such as the Siberian, North China, Yangtze,) Tarim, and Dharwarand cratons. A number of microplates are mapped and the interaction with neighbouring plates is discussed. Slabs from the Pacific and Indian Oceans can be seen in the upper mantle. Passive marginal basins and subduction zones are also properly resolved.

  19. Automated tracing of open-field coronal structures for an optimized large-scale magnetic field reconstruction

    NASA Astrophysics Data System (ADS)

    Uritsky, V. M.; Davila, J. M.; Jones, S. I.

    2014-12-01

    Solar Probe Plus and Solar Orbiter will provide detailed measurements in the inner heliosphere magnetically connected with the topologically complex and eruptive solar corona. Interpretation of these measurements will require accurate reconstruction of the large-scale coronal magnetic field. In a related presentation by S. Jones et al., we argue that such reconstruction can be performed using photospheric extrapolation methods constrained by white-light coronagraph images. Here, we present the image-processing component of this project dealing with an automated segmentation of fan-like coronal loop structures. In contrast to the existing segmentation codes designed for detecting small-scale closed loops in the vicinity of active regions, we focus on the large-scale geometry of the open-field coronal features observed at significant radial distances from the solar surface. The coronagraph images used for the loop segmentation are transformed into a polar coordinate system and undergo radial detrending and initial noise reduction. The preprocessed images are subject to an adaptive second order differentiation combining radial and azimuthal directions. An adjustable thresholding technique is applied to identify candidate coronagraph features associated with the large-scale coronal field. A blob detection algorithm is used to extract valid features and discard noisy data pixels. The obtained features are interpolated using higher-order polynomials which are used to derive empirical directional constraints for magnetic field extrapolation procedures based on photospheric magnetograms.

  20. The history of tectonism on Venus: A stratigraphic analysis

    NASA Astrophysics Data System (ADS)

    Ivanov, Mikhail A.; Head, James W.

    2015-08-01

    The surface of Venus displays several tectonized terrains in which the morphologic characteristics of the original materials are almost completely erased by superposed tectonic structures whose large dimensions (»100 km) suggest formation related to mantle convection. The characteristics of these tectonized terrains are in contrast to volcanic units in which tectonic structures are less significant or absent and thus do not obscure the volcanic character of the units. We describe the temporal distribution of tectonized terrains, their stratigraphic relationships with volcanic units, and how these outline the major episodes in the geological evolution of Venus. Five major tectonized units make up ~20% of the planet: (1) tessera (t, 7.3%), (2) densely lineated plains (pdl, 1.6%), (3) ridged plains/ridge belts (pr/rb, 2.4%), (4) groove belts (gb, 8.1%), and (5) rift zones (rz, 5.0%). Clear relationships of relative age are often seen among the tectonic and volcanic units at the global scale and define three contrasting regimes of volcanic and tectonic resurfacing. The majority of tectonized terrains (t through gb) are the products of tectonic resurfacing and are embayed by the vast volcanic plains and, thus, are older. There are no units with either mildly- or non-tectonized surfaces that interleave the tectonic terrains, which would be expected if the tectonic resurfacing operated only during specific repetitive phases in discrete regions. These tectonized terrains (t through gb) thus define a tectonically dominated regime of resurfacing that occurred at a global-scale near the beginning of the observable geological history of Venus. This ancient tectonic regime began with formation of tessera and was followed by formation of pdl and pr/rb. Groove belts formed near the end of this regime. Branches of groove belts compose the tectonic components of many coronae, suggesting that these features are genetically related (e.g., mutual development of mantle diapirs and

  1. A method of reconstructing complex stratigraphic surfaces with multitype fault constraints

    NASA Astrophysics Data System (ADS)

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

    2017-06-01

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

  2. Glaciotectonic deformation and reinterpretation of the Worth Point stratigraphic sequence: Banks Island, NT, Canada

    NASA Astrophysics Data System (ADS)

    Vaughan, Jessica M.; England, John H.; Evans, David J. A.

    2014-05-01

    Hill-hole pairs, comprising an ice-pushed hill and associated source depression, cluster in a belt along the west coast of Banks Island, NT. Ongoing coastal erosion at Worth Point, southwest Banks Island, has exposed a section (6 km long and ˜30 m high) through an ice-pushed hill that was transported ˜ 2 km from a corresponding source depression to the southeast. The exposed stratigraphic sequence is polydeformed and comprises folded and faulted rafts of Early Cretaceous and Late Tertiary bedrock, a prominent organic raft, Quaternary glacial sediments, and buried glacial ice. Three distinct structural domains can be identified within the stratigraphic sequence that represent proximal to distal deformation in an ice-marginal setting. Complex thrust sequences, interfering fold-sets, brecciated bedrock and widespread shear structures superimposed on this ice-marginally deformed sequence record subsequent deformation in a subglacial shear zone. Analysis of cross-cutting relationships within the stratigraphic sequence combined with OSL dating indicate that the Worth Point hill-hole pair was deformed during two separate glaciotectonic events. Firstly, ice sheet advance constructed the hill-hole pair and glaciotectonized the strata ice-marginally, producing a proximal to distal deformation sequence. A glacioisostatically forced marine transgression resulted in extensive reworking of the strata and the deposition of a glaciomarine diamict. A readvance during this initial stage redeformed the strata in a subglacial shear zone, overprinting complex deformation structures and depositing a glaciotectonite ˜20 m thick. Outwash channels that incise the subglacially deformed strata record a deglacial marine regression, whereas aggradation of glaciofluvial sand and gravel infilling the channels record a subsequent marine transgression. Secondly, a later, largely non-erosive ice margin overrode Worth Point, deforming only the most surficial units in the section and depositing a

  3. Automated transient thermography for the inspection of CFRP structures: experimental results and developed procedures

    NASA Astrophysics Data System (ADS)

    Theodorakeas, P.; Avdelidis, N. P.; Hrissagis, K.; Ibarra-Castanedo, C.; Koui, M.; Maldague, X.

    2011-05-01

    In thermography surveys, the inspector uses the camera to acquire images from the examined part. Common problems are the lack of repeatability when trying to repeat the scanning process, the need to carry the equipment during scanning, and long setting-up time. The aim of this paper is to present transient thermography results on CFRP plates for assessing different types of fabricated defects (impact damage, inclusions for delaminations, etc), as well as and to discuss and present a prototype robotic scanner to apply non destructive testing (thermographic scanning) on materials and structures. Currently, the scanning process is not automatic. The equipment to be developed, will be able to perform thermal NDT scanning on structures, create the appropriate scanning conditions (material thermal excitation), and ensure precision and tracking of scanning process. A thermographic camera that will be used for the image acquisition of the non destructive inspection, will be installed on a x, y, z, linear manipulator's end effector and would be surrounded by excitation sources (optical lamps), required for the application of transient thermography. In this work various CFRP samples of different shape, thickness and geometry were investigated using two different thermographic systems in order to compare and evaluate their effectiveness concerning the internal defect detectability under different testing conditions.

  4. Development of a Genetic Algorithm to Automate Clustering of a Dependency Structure Matrix

    NASA Technical Reports Server (NTRS)

    Rogers, James L.; Korte, John J.; Bilardo, Vincent J.

    2006-01-01

    Much technology assessment and organization design data exists in Microsoft Excel spreadsheets. Tools are needed to put this data into a form that can be used by design managers to make design decisions. One need is to cluster data that is highly coupled. Tools such as the Dependency Structure Matrix (DSM) and a Genetic Algorithm (GA) can be of great benefit. However, no tool currently combines the DSM and a GA to solve the clustering problem. This paper describes a new software tool that interfaces a GA written as an Excel macro with a DSM in spreadsheet format. The results of several test cases are included to demonstrate how well this new tool works.

  5. Endoscopic system for automated high dynamic range inspection of moving periodic structures

    NASA Astrophysics Data System (ADS)

    Hahlweg, Cornelius; Rothe, Hendrik

    2015-09-01

    In the current paper an advanced endoscopic system for high resolution and high dynamic range inspection of periodic structures in rotating machines is presented. We address the system architecture, short time illumination, special optical problems, such as excluding the specular reflex, image processing, forward velocity prediction and metrological image processing. There are several special requirements to be met, such as the thermal stability above 100°C, robustness of the image field, illumination in view direction and the separation of metallic surface diffuse scatter. To find a compromise between image resolution and frame rate, an external sensor system was applied for synchronization with the moving target. The system originally was intended for inspection of thermal engines, but turned out to be of a more general use. Beside the theoretical part and dimensioning issues, practical examples and measurement results are included.

  6. Automated diffeomorphic registration of anatomical structures with rigid parts: application to dynamic cervical MRI.

    PubMed

    Commowick, Olivier; Wiest-Daesslé, Nicolas; Prima, Sylvain

    2012-01-01

    We propose an iterative two-step method to compute a diffeomorphic non-rigid transformation between images of anatomical structures with rigid parts, without any user intervention or prior knowledge on the image intensities. First we compute spatially sparse, locally optimal rigid transformations between the two images using a new block matching strategy and an efficient numerical optimiser (BOBYQA). Then we derive a dense, regularised velocity field based on these local transformations using matrix logarithms and M-smoothing. These two steps are iterated until convergence and the final diffeomorphic transformation is defined as the exponential of the accumulated velocity field. We show our algorithm to outperform the state-of-the-art log-domain diffeomorphic demons method on dynamic cervical MRI data.

  7. Tectonic and stratigraphic evolution in South Alboran Sea (Morocco)

    NASA Astrophysics Data System (ADS)

    D'Acremont, E.; Gorini, C.; El Abbassi, M.; Farran, M.; Leroy, S.; Mercier De Lepinay, B. F.; Migeon, S.; Poort, J.; Ammar, A.; Smit, J.; Ercilla, G.; Alonso, B.; Scientific Team of the Marlboro project

    2011-12-01

    The Alboran Basin, in western Mediterranean, concentrates on a relatively small surface and densely-populated, a large structural complexity linked to seismic activity with recurrent mass-transport deposits that may trigger tsunamis. It was formed by Oligo-Miocene extension while tectonic inversion occurred since the Late Miocene (Tortonian) due to the African-European collision. This North-South compression produces a conjugated fault system located in the central area from Al Hoceima to Andalusia. Numerous instabilities are linked to the recent and present-day seismic activity and show the link between seismicity and erosion-sedimentation processes. On the Andalusia margin the active structures have been identified and recently mapped in detail by using MBES data (including backscatter), and high-resolution seismic data. Such detailed studies have not yet been carried out on the Moroccan margin. The Marlboro-1 oceanographic cruise (R/V Côtes de la Manche, July 2011) has imaged and constrained active structures and associated sedimentary systems through seismic reflection data (MCS). The Xauen/Tofino banks (growth folds), the Alboran Ridge, and the Al Hoceima basin offshore Morocco have been selected because they constitute key-study areas that record a complete deformation history since the Tortonian. Active features including faults, growth folds, channels, mass transport deposits, contourites and volcanoes has provided first order tectonic and sedimentary markers of the basin's evolution. A high chrono-stratigraphical resolution will constitute the basis for reconstructing the evolution of this tectonically active area marked by strong seismic activity. The Marlboro-1 cruise will allow determining key-study area of the Marlboro-2 cruise scheduled for 2012 (R/V Téthys-II, CNFC Call). These cruises should allow for the acquisition of data necessary to characterize basin morphology, active tectonic and sedimentary structures and also make the link with existing

  8. Sequence stratigraphic analysis of stratigraphic oil traps in the west Siberian Neocomian

    SciTech Connect

    Mkrtchyan, O.M.; Armentrout, J.M.

    1996-12-31

    Large depositional oil traps (Priob, Sugmut, etc.) have been discovered in the West Siberian Neocomian. Sequence stratigraphic analysis of well logs and seismic reflection profiles demonstrate that reservoirs of these fields represent sands deposited during lowstand, transgressive and highstand phases of relative sea level cycles. Transgressions and regressions advanced in regional longitudinal and local latitudinal directions. The regional longitudinal pattern is dominated by westward prograding clinoforms formed as the sediment supply exceeded the accommodation space. Local northward and northwestward prograding complexes appear to be controlled by local basin-floor topography. In each systems tract, the coastal zones were landward from the shelf-breaks resulting in dominance of marine facies at each depositional shelf-edge. Lowstand systems tracts are represented on the upper slope by prograding wedges with thin shelfal equivalents or correlative unconformities. Sands deposited in these lowstand regressive facies comprise the main reservoir at Sugmut and a subordinate reservoir at Priob. Transgressive systems tracts are dominantly shale but in the Priob field one early transgressive parasequence sand contains an oil accumulation where it immediately overlies a highstand shelf sand. Highstand systems tracts are represented by regional sheets over the shelf and by thick progradational complexes over the upper slope. Most of the sands occur within the late highstand parasequences and are difficult to correlate due to channel incision. Most Priob field reserves occur in the late highstand parasequences.

  9. Sequence stratigraphic analysis of stratigraphic oil traps in the west Siberian Neocomian

    SciTech Connect

    Mkrtchyan, O.M. ); Armentrout, J.M. )

    1996-01-01

    Large depositional oil traps (Priob, Sugmut, etc.) have been discovered in the West Siberian Neocomian. Sequence stratigraphic analysis of well logs and seismic reflection profiles demonstrate that reservoirs of these fields represent sands deposited during lowstand, transgressive and highstand phases of relative sea level cycles. Transgressions and regressions advanced in regional longitudinal and local latitudinal directions. The regional longitudinal pattern is dominated by westward prograding clinoforms formed as the sediment supply exceeded the accommodation space. Local northward and northwestward prograding complexes appear to be controlled by local basin-floor topography. In each systems tract, the coastal zones were landward from the shelf-breaks resulting in dominance of marine facies at each depositional shelf-edge. Lowstand systems tracts are represented on the upper slope by prograding wedges with thin shelfal equivalents or correlative unconformities. Sands deposited in these lowstand regressive facies comprise the main reservoir at Sugmut and a subordinate reservoir at Priob. Transgressive systems tracts are dominantly shale but in the Priob field one early transgressive parasequence sand contains an oil accumulation where it immediately overlies a highstand shelf sand. Highstand systems tracts are represented by regional sheets over the shelf and by thick progradational complexes over the upper slope. Most of the sands occur within the late highstand parasequences and are difficult to correlate due to channel incision. Most Priob field reserves occur in the late highstand parasequences.

  10. Exploration for stratigraphic traps in a foreland basin using a sequence stratigraphic simulation: Examples from the Eocene/Oligocene of the Apure-Llanos basin, Venezuela

    SciTech Connect

    Reistroffer, J.; Levine, P.A.; Kendall, C.G. ); Finno, A. )

    1996-01-01

    Foreland basin depositional sequences provide a sensitive record of the interaction between tectonism, eustatic sea level fluctuations, and sedimentation rates. Interplay between these controlling factors creates sedimentary geometries which are unique to this tectonic setting and form excellent stratigraphic hydrocarbon traps. Incised valley fill deposits, [open quote]forced regression[close quote] deposits, and combination structure-stratigraphic traps are the predominant reservoir types. In an effort to extend our understanding of the development of these traps, the sequence stratigraphy of a regional seismic transact through the Apure-Llanos basin was simulated. From the Late Eocene through Oligocene, the Apure-Llanos basin was Characterized by multiple phases of compression and a southeast migrating depocenter. Sands of the Mirador and Carbonera formations, which onlap the Arauca Arch to the southeast, were shed from the Guyana craton and were Cannibalized from sediments along the deformation front to the northwest. These sands comprise the principal reservoirs in the study area. Shales of the Leon Formation, which act as a regional seal, were deposited during rapid flexural subsidence and eustatic sea level rise during the early Oligocene. The Arauca Arch acted as a focal mechanism for east and southeast migrating hydrocarbons. Simulation results predict an important stratigraphic pinchout of the Mirador Formation sands against the Arauca Arch, which correlates with the Arauca Reid in Colombia to the southwest. Also, modeling indicates that minimal Tertiary oil production In the La Victoria Field to the east is due to the lack of an adequate seal. Our results provide a conceptual model which predicts hydrocarbon reservoir and seal relationships in a foreland basin setting with limited data control.

  11. Automated structure–activity relationship mining: connecting chemical structure to biological profiles

    PubMed Central

    Wawer, Mathias J.; Jaramillo, David E.; Dancik, Vlado; Fass, Daniel M.; Haggarty, Stephen J.; Shamji, Alykhan F.; Wagner, Bridget K.; Schreiber, Stuart L.; Clemons, Paul A.

    2017-01-01

    Understanding structure–activity relationships (SARs) of small molecules is important for developing probes and novel therapeutic agents in chemical biology and drug discovery. Increasingly multiplexed small-molecule profiling assays allow simultaneous measurement of many biological response parameters for the same compound, e.g. expression levels for many genes or binding constants against many proteins. While such methods promise to capture SARs with high granularity, few computational methods are available to support SAR analyses of high-dimensional compound activity profiles. Many of these methods are not generally applicable or reduce the activity space to scalar summary statistics before establishing SARs. In this article, we present a versatile computational method that automatically extracts interpretable SAR rules from high-dimensional profiling data. The rules connect chemical structural features of compounds to patterns in their biological activity profiles. We applied our method to data from novel cell-based gene-expression and imaging assays collected on more than 30,000 small molecules. Based on the rules identified for this dataset, we prioritized groups of compounds for further study, including a novel set of putative histone deacetylase inhibitors. PMID:24710340

  12. Automated grid generation from models of complex geologic structure and stratigraphy

    SciTech Connect

    Gable, C.; Trease, H.; Cherry, T.

    1996-04-01

    The construction of computational grids which accurately reflect complex geologic structure and stratigraphy for flow and transport models poses a formidable task. With an understanding of stratigraphy, material properties and boundary and initial conditions, the task of incorporating this data into a numerical model can be difficult and time consuming. Most GIS tools for representing complex geologic volumes and surfaces are not designed for producing optimal grids for flow and transport computation. We have developed a tool, GEOMESH, for generating finite element grids that maintain the geometric integrity of input volumes, surfaces, and geologic data and produce an optimal (Delaunay) tetrahedral grid that can be used for flow and transport computations. GEOMESH also satisfies the constraint that the geometric coupling coefficients of the grid are positive for all elements. GEOMESH generates grids for two dimensional cross sections, three dimensional regional models, represents faults and fractures, and has the capability of including finer grids representing tunnels and well bores into grids. GEOMESH also permits adaptive grid refinement in three dimensions. The tools to glue, merge and insert grids together demonstrate how complex grids can be built from simpler pieces. The resulting grid can be utilized by unstructured finite element or integrated finite difference computational physics codes.

  13. Automation or De-automation

    NASA Astrophysics Data System (ADS)

    Gorlach, Igor; Wessel, Oliver

    2008-09-01

    In the global automotive industry, for decades, vehicle manufacturers have continually increased the level of automation of production systems in order to be competitive. However, there is a new trend to decrease the level of automation, especially in final car assembly, for reasons of economy and flexibility. In this research, the final car assembly lines at three production sites of Volkswagen are analysed in order to determine the best level of automation for each, in terms of manufacturing costs, productivity, quality and flexibility. The case study is based on the methodology proposed by the Fraunhofer Institute. The results of the analysis indicate that fully automated assembly systems are not necessarily the best option in terms of cost, productivity and quality combined, which is attributed to high complexity of final car assembly systems; some de-automation is therefore recommended. On the other hand, the analysis shows that low automation can result in poor product quality due to reasons related to plant location, such as inadequate workers' skills, motivation, etc. Hence, the automation strategy should be formulated on the basis of analysis of all relevant aspects of the manufacturing process, such as costs, quality, productivity and flexibility in relation to the local context. A more balanced combination of automated and manual assembly operations provides better utilisation of equipment, reduces production costs and improves throughput.

  14. Traps and seals II. Stratigraphic/capillary traps

    SciTech Connect

    Foster, N.H.; Beaumont, E.A.

    1988-01-01

    This text is a reprint belonging to a series of reprint volumes which in turn are part of the Treatise of Petroleum Geology. This volume contains papers that describe different stratigraphically controlled trap types, the preservation of porosity, and the importance of capillarity in trapping hydrocarbons.

  15. A Proposed Time-Stratigraphic System for Protoplanet Vesta

    NASA Astrophysics Data System (ADS)

    Williams, David; Jaumann, Ralf; McSween, Harry; Raymond, Carol; Russell, Chris

    2014-05-01

    The Dawn Science Team completed a geologic mapping campaign during its nominal mission at Vesta, including production of a 1:500,000 global geologic map derived from High-Altitude Mapping Orbit (HAMO) images (70 m/pixel) [1] and 15 1:250,000 quadrangle maps derived from Low-Altitude Mapping Orbit (LAMO) images (20-25 m/pixel) [2]. In this abstract we propose a time-stratigraphic system and geologic time scale for the protoplanet Vesta, based on global geologic mapping and other analyses of NASA Dawn spacecraft data, supplemented with insights gained from laboratory studies of howardite-eucrite-diogenite (HED) meteorites and geophysical modeling. Our time-stratigraphic system for Vesta relates the geologic map (rock) units identified from geologic mapping to a series of time-rock units and corresponding time units that define a geologic time scale for Vesta. During the Dawn nominal mission it became clear that the south pole of Vesta hosts two large impact basins, the older Veneneia superposed by the younger Rheasilvia [3,4]. Two separate sets of large ridges and troughs were identified, one set encircling much of Vesta equatorial region (Divalia Fossae), and the other preserved in the heavily cratered northern terrain (Saturnalia Fossae). Structural analysis of these ridge-and-trough systems demonstrated that they are likely a tectonic response to the formation of the south polar basins: the Rheasilvia impact led to the formation of the Divalia Fossae, the Veneneia impact led to the Saturnalia Fossae [3,5]. Crater counts provide cratering model ages for the Rheasilvia impact of ~3.6 Ga and ~1 Ga, and ages for the Veneneia impact of ~3.8 Ga and >2.1 Ga using the lunar-derived and asteroid flux-derived chronologies, respectively. Despite the differences in absolute ages, it is clear that these two large impact events had global effects, and thus delineate the major periods of Vesta's geologic history. Zones of heavily cratered terrain (HCT: [6,7]) in the northern

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

    PubMed

    O'Connor, Anne; Wills, Matthew A

    2016-09-01

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

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

    PubMed Central

    O'Connor, Anne; Wills, Matthew A.

    2016-01-01

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

  18. Evaluation of software tools for automated identification of neuroanatomical structures in quantitative β-amyloid PET imaging to diagnose Alzheimer's disease.

    PubMed

    Tuszynski, Tobias; Rullmann, Michael; Luthardt, Julia; Butzke, Daniel; Tiepolt, Solveig; Gertz, Hermann-Josef; Hesse, Swen; Seese, Anita; Lobsien, Donald; Sabri, Osama; Barthel, Henryk

    2016-06-01

    For regional quantification of nuclear brain imaging data, defining volumes of interest (VOIs) by hand is still the gold standard. As this procedure is time-consuming and operator-dependent, a variety of software tools for automated identification of neuroanatomical structures were developed. As the quality and performance of those tools are poorly investigated so far in analyzing amyloid PET data, we compared in this project four algorithms for automated VOI definition (HERMES Brass, two PMOD approaches, and FreeSurfer) against the conventional method. We systematically analyzed florbetaben brain PET and MRI data of ten patients with probable Alzheimer's dementia (AD) and ten age-matched healthy controls (HCs) collected in a previous clinical study. VOIs were manually defined on the data as well as through the four automated workflows. Standardized uptake value ratios (SUVRs) with the cerebellar cortex as a reference region were obtained for each VOI. SUVR comparisons between ADs and HCs were carried out using Mann-Whitney-U tests, and effect sizes (Cohen's d) were calculated. SUVRs of automatically generated VOIs were correlated with SUVRs of conventionally derived VOIs (Pearson's tests). The composite neocortex SUVRs obtained by manually defined VOIs were significantly higher for ADs vs. HCs (p=0.010, d=1.53). This was also the case for the four tested automated approaches which achieved effect sizes of d=1.38 to d=1.62. SUVRs of automatically generated VOIs correlated significantly with those of the hand-drawn VOIs in a number of brain regions, with regional differences in the degree of these correlations. Best overall correlation was observed in the lateral temporal VOI for all tested software tools (r=0.82 to r=0.95, p<0.001). Automated VOI definition by the software tools tested has a great potential to substitute for the current standard procedure to manually define VOIs in β-amyloid PET data analysis.

  19. Stratigraphic framework for Pliocene paleoclimate reconstruction: The correlation conundrum

    USGS Publications Warehouse

    Dowsett, H.J.; Robinson, M.M.

    2006-01-01

    Pre-Holocene paleoclimate reconstructions face a correlation conundrum because complications inherent in the stratigraphic record impede the development of synchronous reconstruction. The Pliocene Research, Interpretation and Synoptic Mapping (PRISM) paleoenvironmental reconstructions have carefully balanced temporal resolution and paleoclimate proxy data to achieve a useful and reliable product and are the most comprehensive pre-Pleistocene data sets available for analysis of warmer-than-present climate and for climate modeling experiments. This paper documents the stratigraphic framework for the mid-Pliocene sea surface temperature (SST) reconstruction of the North Atlantic and explores the relationship between stratigraphic/temporal resolution and various paleoceanographic estimates of SST. The magnetobiostratigraphic framework for the PRISM North Atlantic region is constructed from planktic foraminifer, calcareous nannofossil and paleomagnetic reversal events recorded in deep-sea cores and calibrated to age. Planktic foraminifer census data from multiple samples within the mid-Pliocene yield multiple SST estimates for each site. Extracting a single SST value at each site from multiple estimates, given the limitations of the material and stratigraphic resolution, is problematic but necessary for climate model experiments. The PRISM reconstruction, unprecedented in its integration of many different types of data at a focused stratigraphic interval, utilizes a time slab approach and is based on warm peak average temperatures. A greater understanding of the dynamics of the climate system and significant advances in models now mandate more precise, globally distributed yet temporally synchronous SST estimates than are available through averaging techniques. Regardless of the precision used to correlate between sequences within the midd-Pliocene, a truly synoptic reconstruction in the temporal sense is unlikely. SST estimates from multiple proxies promise to further

  20. Petroleum system elements within the Late Cretaceous and Early Paleogene sediments of Nigeria's inland basins: An integrated sequence stratigraphic approach

    NASA Astrophysics Data System (ADS)

    Dim, Chidozie Izuchukwu Princeton; Onuoha, K. Mosto; Okeugo, Chukwudike Gabriel; Ozumba, Bertram Maduka

    2017-06-01

    Sequence stratigraphic studies have been carried out using subsurface well and 2D seismic data in the Late Cretaceous and Early Paleogene sediments of Anambra and proximal onshore section of Niger Delta Basin in the Southeastern Nigeria. The aim was to establish the stratigraphic framework for better understanding of the reservoir, source and seal rock presence and distribution in the basin. Thirteen stratigraphic bounding surfaces (consisting of six maximum flooding surfaces - MFSs and seven sequence boundaries - SBs) were recognized and calibrated using a newly modified chronostratigraphic chart. Stratigraphic surfaces were matched with corresponding foraminiferal and palynological biozones, aiding correlation across wells in this study. Well log sequence stratigraphic correlation reveals that stratal packages within the basin are segmented into six depositional sequences occurring from Late Cretaceous to Early Paleogene age. Generated gross depositional environment maps at various MFSs show that sediment packages deposited within shelfal to deep marine settings, reflect continuous rise and fall of sea levels within a regressive cycle. Each of these sequences consist of three system tracts (lowstand system tract - LST, transgressive system tract - TST and highstand system tract - HST) that are associated with mainly progradational and retrogradational sediment stacking patterns. Well correlation reveals that the sand and shale units of the LSTs, HSTs and TSTs, that constitute the reservoir and source/seal packages respectively are laterally continuous and thicken basinwards, due to structural influences. Result from interpretation of seismic section reveals the presence of hanging wall, footwall, horst block and collapsed crest structures. These structural features generally aid migration and offer entrapment mechanism for hydrocarbon accumulation. The combination of these reservoirs, sources, seals and trap elements form a good petroleum system that is viable

  1. Automation pilot

    NASA Technical Reports Server (NTRS)

    1983-01-01

    An important concept of the Action Information Management System (AIMS) approach is to evaluate office automation technology in the context of hands on use by technical program managers in the conduct of human acceptance difficulties which may accompany the transition to a significantly changing work environment. The improved productivity and communications which result from application of office automation technology are already well established for general office environments, but benefits unique to NASA are anticipated and these will be explored in detail.

  2. Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life

    PubMed Central

    Buchheim, Mark A.; Keller, Alexander; Koetschan, Christian; Förster, Frank; Merget, Benjamin; Wolf, Matthias

    2011-01-01

    Background Chloroplast-encoded genes (matK and rbcL) have been formally proposed for use in DNA barcoding efforts targeting embryophytes. Extending such a protocol to chlorophytan green algae, though, is fraught with problems including non homology (matK) and heterogeneity that prevents the creation of a universal PCR toolkit (rbcL). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta. Methodology/Principal Findings Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence structure-specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses. Conclusions/Significance Our observations on the power of automated, sequence-structure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated

  3. Seismic depth-domain stratigraphic classification of the Golan Heights, central Dead Sea Fault

    NASA Astrophysics Data System (ADS)

    Meiler, Miki; Reshef, Moshe; Shulman, Haim

    2011-10-01

    A set of twenty five 2-D seismic profiles acquired over the Golan Heights basaltic plateau, central Dead Sea Fault segment, was processed and analyzed in the depth domain. The data were processed by the Pre-Stack Depth Migration techniques and, despite the thick basaltic layer entirely covering the plateau, shows surprisingly good quality. The study presents stratigraphic identification of eleven seismic markers recognized on the output depth-domain sections and their correlation with the adjacent Syrian, Jordanian and Israeli stratigraphic columns. Based on this regional correlation, the deep-seated structure and stratigraphic column underlying the extensive basaltic cover are addressed through structural mapping and isopach calculations, as well as through compilation of regional geological cross-sections. Results of the depth-domain seismic interpretation suggest that the Golan Heights covers a structural depression in which more than 8500 m of Late Proterozoic to Neogene sedimentary succession has accumulated, amid the Jordanian Highlands and the Mt. Hermon Anticline. The Infracambrian-Paleozoic succession attains a thickness of 3000-3500 m, while as much as 1500 m of this figure is attributed to the Late Proterozoic Saramuj Formation. The Mesozoic succession, outlined by the significant northward and north-western thickening of the Triassic and Jurassic successions, attains a cumulative thickness of 5 km in the Northern Golan. The Senonian-Cenozoic succession outlines the syncline nature of the Golan Plateau, attaining a thickness of 1.5-2 km at the central parts of the plateau. The estimated thickness of the Plio-Pleistocene basalt flows that cover the study area locally exceeds 1000 m. Two fault strands of the Dead Sea Fault System are recognized in the subsurface of the plateau: the Sheikh-Ali and Shamir Faults. The strands are interpreted beneath the basalt cover, extending into the plateau at a considerable distance from their surface expression next to

  4. Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system.

    PubMed

    Ikeya, Teppei; Takeda, Mitsuhiro; Yoshida, Hitoshi; Terauchi, Tsutomu; Jee, Jun-Goo; Kainosho, Masatsune; Güntert, Peter

    2009-08-01

    Stereo-array isotope labeling (SAIL) has been combined with the fully automated NMR structure determination algorithm FLYA to determine the three-dimensional structure of the protein ubiquitin from different sets of input NMR spectra. SAIL provides a complete stereo- and regio-specific pattern of stable isotopes that results in sharper resonance lines and reduced signal overlap, without information loss. Here we show that as a result of the superior quality of the SAIL NMR spectra, reliable, fully automated analyses of the NMR spectra and structure calculations are possible using fewer input spectra than with conventional uniformly 13C/15N-labeled proteins. FLYA calculations with SAIL ubiquitin, using a single three-dimensional "through-bond" spectrum (and 2D HSQC spectra) in addition to the 13C-edited and 15N-edited NOESY spectra for conformational restraints, yielded structures with an accuracy of 0.83-1.15 A for the backbone RMSD to the conventionally determined solution structure of SAIL ubiquitin. NMR structures can thus be determined almost exclusively from the NOESY spectra that yield the conformational restraints, without the need to record many spectra only for determining intermediate, auxiliary data of the chemical shift assignments. The FLYA calculations for this report resulted in 252 ubiquitin structure bundles, obtained with different input data but identical structure calculation and refinement methods. These structures cover the entire range from highly accurate structures to seriously, but not trivially, wrong structures, and thus constitute a valuable database for the substantiation of structure validation methods.

  5. Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design

    NASA Astrophysics Data System (ADS)

    Lerner, Michael G.; Meagher, Kristin L.; Carlson, Heather A.

    2008-10-01

    Use of solvent mapping, based on multiple-copy minimization (MCM) techniques, is common in structure-based drug discovery. The minima of small-molecule probes define locations for complementary interactions within a binding pocket. Here, we present improved methods for MCM. In particular, a Jarvis-Patrick (JP) method is outlined for grouping the final locations of minimized probes into physical clusters. This algorithm has been tested through a study of protein-protein interfaces, showing the process to be robust, deterministic, and fast in the mapping of protein "hot spots." Improvements in the initial placement of probe molecules are also described. A final application to HIV-1 protease shows how our automated technique can be used to partition data too complicated to analyze by hand. These new automated methods may be easily and quickly extended to other protein systems, and our clustering methodology may be readily incorporated into other clustering packages.

  6. Improving the correlation of structural FEA models by the application of automated high density robotized laser Doppler vibrometry

    NASA Astrophysics Data System (ADS)

    Chowanietz, Maximilian; Bhangaonkar, Avinash; Semken, Michael; Cockrill, Martin

    2016-06-01

    Sound has had an intricate relation with the wellbeing of humans since time immemorial. It has the ability to enhance the quality of life immensely when present as music; at the same time, it can degrade its quality when manifested as noise. Hence, understanding its sources and the processes by which it is produced gains acute significance. Although various theories exist with respect to evolution of bells, it is indisputable that they carry millennia of cultural significance, and at least a few centuries of perfection with respect to design, casting and tuning. Despite the science behind its design, the nuances pertaining to founding and tuning have largely been empirical, and conveyed from one generation to the next. Post-production assessment for bells remains largely person-centric and traditional. However, progressive bell manufacturers have started adopting methods such as finite element analysis (FEA) for informing and optimising their future model designs. To establish confidence in the FEA process it is necessary to correlate the virtual model against a physical example. This is achieved by performing an experimental modal analysis (EMA) and comparing the results with those from FEA. Typically to collect the data for an EMA, the vibratory response of the structure is measured with the application of accelerometers. This technique has limitations; principally these are the observer effect and limited geometric resolution. In this paper, 3-dimensional laser Doppler vibrometry (LDV) has been used to measure the vibratory response with no observer effect due to the non-contact nature of the technique; resulting in higher accuracy measurements as the input to the correlation process. The laser heads were mounted on an industrial robot that enables large objects to be measured and extensive data sets to be captured quickly through an automated process. This approach gives previously unobtainable geometric resolution resulting in a higher confidence EMA. This is

  7. Human brain atlas for automated region of interest selection in quantitative susceptibility mapping: application to determine iron content in deep gray matter structures.

    PubMed

    Lim, Issel Anne L; Faria, Andreia V; Li, Xu; Hsu, Johnny T C; Airan, Raag D; Mori, Susumu; van Zijl, Peter C M

    2013-11-15

    The purpose of this paper is to extend the single-subject Eve atlas from Johns Hopkins University, which currently contains diffusion tensor and T1-weighted anatomical maps, by including contrast based on quantitative susceptibility mapping. The new atlas combines a "deep gray matter parcellation map" (DGMPM) derived from a single-subject quantitative susceptibility map with the previously established "white matter parcellation map" (WMPM) from the same subject's T1-weighted and diffusion tensor imaging data into an MNI coordinate map named the "Everything Parcellation Map in Eve Space," also known as the "EvePM." It allows automated segmentation of gray matter and white matter structures. Quantitative susceptibility maps from five healthy male volunteers (30 to 33 years of age) were coregistered to the Eve Atlas with AIR and Large Deformation Diffeomorphic Metric Mapping (LDDMM), and the transformation matrices were applied to the EvePM to produce automated parcellation in subject space. Parcellation accuracy was measured with a kappa analysis for the left and right structures of six deep gray matter regions. For multi-orientation QSM images, the Kappa statistic was 0.85 between automated and manual segmentation, with the inter-rater reproducibility Kappa being 0.89 for the human raters, suggesting "almost perfect" agreement between all segmentation methods. Segmentation seemed slightly more difficult for human raters on single-orientation QSM images, with the Kappa statistic being 0.88 between automated and manual segmentation, and 0.85 and 0.86 between human raters. Overall, this atlas provides a time-efficient tool for automated coregistration and segmentation of quantitative susceptibility data to analyze many regions of interest. These data were used to establish a baseline for normal magnetic susceptibility measurements for over 60 brain structures of 30- to 33-year-old males. Correlating the average susceptibility with age-based iron concentrations in gray

  8. Human brain atlas for automated region of interest selection in quantitative susceptibility mapping: application to determine iron content in deep gray matter structures

    PubMed Central

    Lim, Issel Anne L.; Faria, Andreia V.; Li, Xu; Hsu, Johnny T.C.; Airan, Raag D.; Mori, Susumu; van Zijl, Peter C. M.

    2013-01-01

    The purpose of this paper is to extend the single-subject Eve atlas from Johns Hopkins University, which currently contains diffusion tensor and T1-weighted anatomical maps, by including contrast based on quantitative susceptibility mapping. The new atlas combines a “deep gray matter parcellation map” (DGMPM) derived from a single-subject quantitative susceptibility map with the previously established “white matter parcellation map” (WMPM) from the same subject’s T1-weighted and diffusion tensor imaging data into an MNI coordinate map named the “Everything Parcellation Map in Eve Space,” also known as the “EvePM.” It allows automated segmentation of gray matter and white matter structures. Quantitative susceptibility maps from five healthy male volunteers (30 to 33 years of age) were coregistered to the Eve Atlas with AIR and Large Deformation Diffeomorphic Metric Mapping (LDDMM), and the transformation matrices were applied to the EvePM to produce automated parcellation in subject space. Parcellation accuracy was measured with a kappa analysis for the left and right structures of six deep gray matter regions. For multi-orientation QSM images, the Kappa statistic was 0.85 between automated and manual segmentation, with the inter-rater reproducibility Kappa being 0.89 for the human raters, suggesting “almost perfect” agreement between all segmentation methods. Segmentation seemed slightly more difficult for human raters on single-orientation QSM images, with the Kappa statistic being 0.88 between automated and manual segmentation, and 0.85 and 0.86 between human raters. Overall, this atlas provides a time-efficient tool for automated coregistration and segmentation of quantitative susceptibility data to analyze many regions of interest. These data were used to establish a baseline for normal magnetic susceptibility measurements for over 60 brain structures of 30- to 33-year-old males. Correlating the average susceptibility with age-based iron

  9. Stratigraphic framework of Lower and Upper Cretaceous rocks in central and eastern Montana

    USGS Publications Warehouse

    Condon, Steven M.

    2000-01-01

    This study shows the lithology, thickness, distribution, and correlation of Lower and Upper Cretaceous rocks in central and eastern Montana. The described stratigraphic units range from the Aptian Kootenai Formation (oldest) to the Maastrichtian Hell Creek Formation (youngest). An included text report describes the units, and most formations or members are also represented by isopach maps. Structure contour maps of three horizons are also included. Correlations across the study area are shown on a series of cross sections. All text and illustrations are included as Adobe PDF files.

  10. Office automation.

    PubMed

    Arenson, R L

    1986-03-01

    By now, the term "office automation" should have more meaning for those readers who are not intimately familiar with the subject. Not all of the preceding material pertains to every department or practice, but certainly, word processing and simple telephone management are key items. The size and complexity of the organization will dictate the usefulness of electronic mail and calendar management, and the individual radiologist's personal needs and habits will determine the usefulness of the home computer. Perhaps the most important ingredient for success in the office automation arena relates to the ability to integrate information from various systems in a simple and flexible manner. Unfortunately, this is perhaps the one area that most office automation systems have ignored or handled poorly. In the personal computer world, there has been much emphasis recently on integration of packages such as spreadsheet, database management, word processing, graphics, time management, and communications. This same philosophy of integration has been applied to a few office automation systems, but these are generally vendor-specific and do not allow for a mixture of foreign subsystems. During the next few years, it is likely that a few vendors will emerge as dominant in this integrated office automation field and will stress simplicity and flexibility as major components.

  11. Evolving sequence-stratigraphic concepts: Emphasis on siliciclastic systems tracts

    SciTech Connect

    Brown, L.F. Jr.

    1994-11-01

    During the past five years, rapidly evolving new sequence-stratigraphic concepts have begun to impose significant changes in the application of stratigraphy in petroleum exploration and reservoir development. The growing number and variety of oral and published papers on sequence stratigraphy clearly document this stratigraphic revolution. Not since depositional systems concepts evolved in the 1960s to give rise to seismic stratigraphy in the 1970s has the field of stratigraphy changed so rapidly and so fundamentally. Within the next few years, sequence stratigraphy is destined to play an increasingly important role in the way basins are analyzed, hydrocarbon-play potential is assessed, and prospect and production strategies are devised. Geoscientists worldwide are struggling to keep up with the significance of all of these new ideas and techniques.

  12. SAS program for quantitative stratigraphic correlation by principal components

    USGS Publications Warehouse

    Hohn, M.E.

    1985-01-01

    A SAS program is presented which constructs a composite section of stratigraphic events through principal components analysis. The variables in the analysis are stratigraphic sections and the observational units are range limits of taxa. The program standardizes data in each section, extracts eigenvectors, estimates missing range limits, and computes the composite section from scores of events on the first principal component. Provided is an option of several types of diagnostic plots; these help one to determine conservative range limits or unrealistic estimates of missing values. Inspection of the graphs and eigenvalues allow one to evaluate goodness of fit between the composite and measured data. The program is extended easily to the creation of a rank-order composite. ?? 1985.

  13. The Anthropocene is functionally and stratigraphically distinct from the Holocene.

    PubMed

    Waters, Colin N; Zalasiewicz, Jan; Summerhayes, Colin; Barnosky, Anthony D; Poirier, Clément; Gałuszka, Agnieszka; Cearreta, Alejandro; Edgeworth, Matt; Ellis, Erle C; Ellis, Michael; Jeandel, Catherine; Leinfelder, Reinhold; McNeill, J R; Richter, Daniel deB; Steffen, Will; Syvitski, James; Vidas, Davor; Wagreich, Michael; Williams, Mark; Zhisheng, An; Grinevald, Jacques; Odada, Eric; Oreskes, Naomi; Wolfe, Alexander P

    2016-01-08

    Human activity is leaving a pervasive and persistent signature on Earth. Vigorous debate continues about whether this warrants recognition as a new geologic time unit known as the Anthropocene. We review anthropogenic markers of functional changes in the Earth system through the stratigraphic record. The appearance of manufactured materials in sediments, including aluminum, plastics, and concrete, coincides with global spikes in fallout radionuclides and particulates from fossil fuel combustion. Carbon, nitrogen, and phosphorus cycles have been substantially modified over the past century. Rates of sea-level rise and the extent of human perturbation of the climate system exceed Late Holocene changes. Biotic changes include species invasions worldwide and accelerating rates of extinction. These combined signals render the Anthropocene stratigraphically distinct from the Holocene and earlier epochs. Copyright © 2016, American Association for the Advancement of Science.

  14. Phytoplankton community structure in the North Sea: coupling between remote sensing and automated in situ analysis at the single cell level

    NASA Astrophysics Data System (ADS)

    Thyssen, M.; Alvain, S.; Lefèbvre, A.; Dessailly, D.; Rijkeboer, M.; Guiselin, N.; Creach, V.; Artigas, L.-F.

    2014-11-01

    Phytoplankton observation in the ocean can be a challenge in oceanography. Accurate estimations of their biomass and dynamics will help to understand ocean ecosystems and refine global climate models. This requires relevant datasets of phytoplankton at a functional level and on a daily and sub meso scale. In order to achieve this, an automated, high frequency, dedicated scanning flow cytometer (SFC, Cytobuoy, NL), has been developed to cover the entire size range of phytoplankton cells whilst simultaneously taking pictures of the largest of them. This cytometer was directly connected to the water inlet of a~pocket Ferry Box during a cruise in the North Sea, 8-12 May 2011 (DYMAPHY project, INTERREG IV A "2 Seas"), in order to identify the phytoplankton community structure of near surface waters (6 m) with a high resolution spacial basis (2.2 ± 1.8 km). Ten groups of cells, distinguished on the basis of their optical pulse shapes, were described (abundance, size estimate, red fluorescence per unit volume). Abundances varied depending on the hydrological status of the traversed waters, reflecting different stages of the North Sea blooming period. Comparisons between several techniques analyzing chlorophyll a and the scanning flow cytometer, using the integrated red fluorescence emitted by each counted cell, showed significant correlations. The community structure observed from the automated flow cytometry was compared with the PHYSAT reflectance anomalies over a daily scale. The number of matchups observed between the SFC automated high frequency in situ sampling and the remote sensing was found to be two to three times better than when using traditional water sampling strategies. Significant differences in the phytoplankton community structure within the two days for which matchups were available, suggest that it is possible to label PHYSAT anomalies not only with dominant groups, but at the level of the community structure.

  15. Paleoclimate controls on stratigraphic repetition of chemical and siliciclastic rocks

    SciTech Connect

    Cecil, C.B. )

    1990-06-01

    Climate is a primary control on sediment flux from continental sources into sedimentary systems. In warm climates, siliciclastic input is greatest under highly seasonal rainfall. Nonseasonal conditions favor formation of end member chemical rocks; perennially wet climates are conductive to coal formation, whereas dry climates produce carbonates and/or evaporites. Stratigraphic repetition of siliciclastic and chemical rocks therefore appears to be related to paleoclimate cycles as well as to transgressive-regressive events and tectonics.

  16. Surface Process Control on Stratigraphic Completeness in Simple Experimental Deltas

    NASA Astrophysics Data System (ADS)

    Hobley, D. E. J.; Tucker, G. E.; Mahon, R. C.; Barnhart, K. R.; Shaw, J.; Liang, M.; Paola, C.; Voller, V. R.

    2015-12-01

    The ability to measure and understand stratigraphic completeness is fundamental to the interpretation of the sedimentary record. It provides the epistemic basis that allows us to predict the preservation potential of input signals to sedimentary systems, and gives us a null hypothesis of sorts against which real stratigraphic sequences can be compared. Stratigraphic completeness essentially sets the resolution of a seismic section. However, despite the importance of stratigraphic completeness, significant gaps remain in our understanding, especially as regards the mechanistic underpinnings of how real geomorphic and transport processes influence completeness. Here we use a suite of reduced complexity numerical models of a delta to investigate what degree of realism in representation of surface processes is required to match measured completeness-timescale relationships in real systems. Target data is drawn from experimental deltas, where input variables are known and well constrained. We explore the extent to which surface processes - in particular, expressed as the spatial restriction of and correlation between loci of erosion and deposition on the delta top and front - control completeness, independent of the forcing parameters of sediment input and base level. We illustrate the importance of data resolution in controlling measured completeness, and demonstrate that these resolution effects can combine with trends driven by process localization on the delta top. We discuss the extent to which these two effects can or cannot be distinguished in real data. We argue that signals of localized erosion on the delta top and localized deposition on the delta front are key drivers of completeness-timescale trends, even for simple Gilbert-style deltas under elementary experimental boundary conditions.

  17. Habitat automation

    NASA Technical Reports Server (NTRS)

    Swab, Rodney E.

    1992-01-01

    A habitat, on either the surface of the Moon or Mars, will be designed and built with the proven technologies of that day. These technologies will be mature and readily available to the habitat designer. We believe an acceleration of the normal pace of automation would allow a habitat to be safer and more easily maintained than would be the case otherwise. This document examines the operation of a habitat and describes elements of that operation which may benefit from an increased use of automation. Research topics within the automation realm are then defined and discussed with respect to the role they can have in the design of the habitat. Problems associated with the integration of advanced technologies into real-world projects at NASA are also addressed.

  18. Subsalt risk reduction using seismic sequence stratigraphic analysis

    SciTech Connect

    Wornardt, W.W. Jr.

    1994-12-31

    Several recent projects involving detailed seismic sequence stratigraphic analysis of existing wells near subsalt prospects in the south additions of the offshore Louisiana area in the Gulf of Mexico have demonstrated the utility of using seismic sequence stratigraphic analysis to reduce risk when drilling subsalt plays. First, the thick section of sedimentary rocks that was though to be above and below the salt was penetrated in the area away from the salt. These sedimentary rocks were accurately dated using maximum flooding surface first occurrence downhole of important bioevent, condensed sections, abundance and diversity histograms, and high-resolution biostratigraphy while the wells were being drilled. Potential reservoir sandstones within specific Vail sequences in these wells were projected using seismic data up to the subsalt and non-subsalt sediment interface. The systems tract above and below the maximum flooding surface and the type of reservoir sandstones that were to be encounterd were predictable based on the paleobathymetry, increase and decrease of fauna and flora, recognition of the bottom-set turbidite, slope fan and basin floor fan condensed sections, and superpositional relationship of the Vail sequences and systems tracts to provide a detailed sequence stratigraphic analysis of the well. Subsequently, wells drilled through the salt could be accurately correlated with Vail sequences and systems tracts in wells that were previously correlated away from the salt layer with seismic reflection profiles.

  19. Subsalt risk reduction using seismic sequence-stratigraphic analysis

    SciTech Connect

    Wornardt, W.W. Jr.

    1994-09-01

    Several recent projects involving detailed seismic-sequence stratigraphic analysis of existing wells near subsalt prospects in the south additions of the offshore Louisiana area in the Gulf of Mexico have demonstrated the utility of using seismic sequence-stratigraphic analysis to reduce risk when drilling subsalt plays. First, the thick section of sediments that was thought to be above and below the salt was penetrated in the area away from the salt. These sediments were accurately dated using maximum flooding surface first occurrence downhole of important bioevent, condensed sections, abundance and diversity histograms, and high-resolution biostratigraphy while the wells were being drilled. Potential reservoir sands within specific Vail sequences in these wells were projected on seismic up to the subsalt and non-subsalt sediment interface. The systems tract above and below the maximum flooding surface and the type of reservoir sands that were to be encountered were predictable based on the paleobathymetry, increase and decrease of fauna and flora abundance, recognition of the bottom-set turbidite, slope fan and basin floor fan condensed sections, and superpositional relationship of the Vail sequences and systems tracts to provide a detailed sequence-stratigraphic analysis of the well in question. Subsequently, the wells drilled through the salt could be accurately correlated with the Vail sequences and systems tracts in wells that were previously correlated with seismic reflection profiles away from the salt layer.

  20. Fully automated protein purification

    PubMed Central

    Camper, DeMarco V.; Viola, Ronald E.

    2009-01-01

    Obtaining highly purified proteins is essential to begin investigating their functional and structural properties. The steps that are typically involved in purifying proteins can include an initial capture, intermediate purification, and a final polishing step. Completing these steps can take several days and require frequent attention to ensure success. Our goal was to design automated protocols that will allow the purification of proteins with minimal operator intervention. Separate methods have been produced and tested that automate the sample loading, column washing, sample elution and peak collection steps for ion-exchange, metal affinity, hydrophobic interaction and gel filtration chromatography. These individual methods are designed to be coupled and run sequentially in any order to achieve a flexible and fully automated protein purification protocol. PMID:19595984

  1. Automated High Throughput Drug Target Crystallography

    SciTech Connect

    Rupp, B

    2005-02-18

    The molecular structures of drug target proteins and receptors form the basis for 'rational' or structure guided drug design. The majority of target structures are experimentally determined by protein X-ray crystallography, which as evolved into a highly automated, high throughput drug discovery and screening tool. Process automation has accelerated tasks from parallel protein expression, fully automated crystallization, and rapid data collection to highly efficient structure determination methods. A thoroughly designed automation technology platform supported by a powerful informatics infrastructure forms the basis for optimal workflow implementation and the data mining and analysis tools to generate new leads from experimental protein drug target structures.

  2. Influence of Holocene stratigraphic architecture on ground surface settlements: A case study from the City of Pisa (Tuscany, Italy)

    NASA Astrophysics Data System (ADS)

    Sarti, Giovanni; Rossi, Veronica; Amorosi, Alessandro

    2012-12-01

    The Holocene stratigraphic architecture of modern coastal and deltaic plains has peculiar characteristics that may influence ground surface settlements. In the Pisa urban area, the inhomogeneous spatial distribution of geotechnically weak layers, typically formed during the mid-late Holocene (highstand) coastal progradation, is inferred to be responsible for urban ground settlement and building damage, as evidenced by the tilt of several surface structures, among which the famous Leaning Tower of Pisa is the most prominent. On the basis of integrated stratigraphic, sedimentological and geotechnical data from a wide georeferenced database, three facies associations with high deformability potential (Units 1-3) are identified in the uppermost 30 m as opposed to depositional facies (Units 4-5) with higher geotechnical strength. Whereas Unit 1 represents a thick, laterally extensive lagoonal clay deposit, the overlying highly deformable units (Units 2-3) show more discontinuous spatial distribution controlled by the Holocene paleohydrographic evolution of the Arno coastal plain. Unit 2, dated between the Neolithic and the Etruscan age (ca. 5000-2000 yr BP), is composed of swamp clays and silty clays recording lagoon infilling due to Arno Delta progradation. Units 3 and 4, which consist of wet levee deposits and stiff floodplain clays, respectively, formed during the subsequent phases of alluvial plain construction started around the Roman age (from ca. 2000 yr BP). Whereas Units 3 and 4 are recorded within the uppermost 5 m, fluvial and distributary channel sands (Unit 5) cut the underlying deltaic-alluvial succession at various stratigraphic levels, down to Unit 1. The spatial distribution of these units gives rise to three, locally juxtaposed, stratigraphic motifs in Pisa underground, reflecting different potential risks for settlement under building loads. We show how lateral changes in stratigraphic architecture account for the irregular spatial distribution of

  3. Sequence stratigraphy and stratigraphic trap potential of the Villeta Formation (Cretaceous), Putumayo Basin, Columbia

    SciTech Connect

    Robertson, H.C.; Cregg, A.; Cleveland, G.

    1996-12-31

    The Villeta Formation, which was deposited in -15 Ma (Cenomanian-Campanian), includes four 3rd-order sequences representing marine shelf, siliciclastic shoreface, and lower coastal-plain environments. Although these environments transgressed landward across the pre-Cretaceous basement during a 2nd-order base-level rise, several brief but important base-level falls and abrupt basinward and downward facies-shifts interrupted this trend. The 3rd-order base-level falls and subsequent transgressions led to the deposition of important hydrocarbon-bearing sandstones in the Villeta Formation. Sequence boundaries record abrupt downward facies shifts and separate black marine shales and deep-shelf limestones below from fluvial to tidally- and wave-influenced shoreface sandstones above. Each of these sands (Arenisca T, U inferior, U superior, and M2) laps out landward and passes upward into transgressive shales and thin highstand limestones. Base-level rise and retrogradation of the shoreline is indicated by upward thinning of transgressive sandstones and upward increase in marine shale. Sandstones thin or downlap basinward into shales. Transgressive deposits dominate the sequences. Highstand progradation of siliciclastic shorelines was minimal and limited by a relatively high accommodation/sediment-supply ratio. Base-level falls, however, allowed shorelines to advance basinward long distances. The stratigraphic geometries of the Villeta sandstones, as indicated by seismic data and well-log correlations, indicate that potentially large stratigraphic traps are present in the Putumayo Basin. Stratigraphic entrapment is indicated by landward onlap of the Villeta sandstones, the presence of shales and tight limestones overlying porous sandstones, and known hydrocarbon accumulations in the sandstones over structural highs.

  4. Sequence stratigraphy and stratigraphic trap potential of the Villeta Formation (Cretaceous), Putumayo Basin, Columbia

    SciTech Connect

    Robertson, H.C. ); Cregg, A.; Cleveland, G. )

    1996-01-01

    The Villeta Formation, which was deposited in -15 Ma (Cenomanian-Campanian), includes four 3rd-order sequences representing marine shelf, siliciclastic shoreface, and lower coastal-plain environments. Although these environments transgressed landward across the pre-Cretaceous basement during a 2nd-order base-level rise, several brief but important base-level falls and abrupt basinward and downward facies-shifts interrupted this trend. The 3rd-order base-level falls and subsequent transgressions led to the deposition of important hydrocarbon-bearing sandstones in the Villeta Formation. Sequence boundaries record abrupt downward facies shifts and separate black marine shales and deep-shelf limestones below from fluvial to tidally- and wave-influenced shoreface sandstones above. Each of these sands (Arenisca T, U inferior, U superior, and M2) laps out landward and passes upward into transgressive shales and thin highstand limestones. Base-level rise and retrogradation of the shoreline is indicated by upward thinning of transgressive sandstones and upward increase in marine shale. Sandstones thin or downlap basinward into shales. Transgressive deposits dominate the sequences. Highstand progradation of siliciclastic shorelines was minimal and limited by a relatively high accommodation/sediment-supply ratio. Base-level falls, however, allowed shorelines to advance basinward long distances. The stratigraphic geometries of the Villeta sandstones, as indicated by seismic data and well-log correlations, indicate that potentially large stratigraphic traps are present in the Putumayo Basin. Stratigraphic entrapment is indicated by landward onlap of the Villeta sandstones, the presence of shales and tight limestones overlying porous sandstones, and known hydrocarbon accumulations in the sandstones over structural highs.

  5. Relation between stratigraphic architecture and multi-scale heterogeneities in carbonate platforms: The Barremian-lower Aptian of the Monts de Vaucluse, SE France

    NASA Astrophysics Data System (ADS)

    Leonide, Philippe; Borgomano, Jean; Masse, Jean-Pierre; Doublet, Stefan

    2012-07-01

    facies variations) and the morphology of the shelf reflect a strong interaction between tectonic (differential subsidence), sediment production and global environmental conditions. At the km-scale, the "Gorges de la Nesque" stratigraphic motif could represent a nested stratigraphic structure within the large-scale model, which could be implemented for up-scaling petrophysical properties from the well to a full-field model. The association of coral facies to the rudist-dominated system in the Provence platform is a very clear proxy of the polarity of the carbonate platform and is critical for subsurface facies-property modeling based on well data. Finally, at the global scale, the stratigraphic architecture and the step-wise drowning events of the Provence platform confirm and document the precursor events associated with environmental perturbations that affected the carbonate factory prior the Oceanic Anoxic Event 1a (OAE1a).

  6. Tectonic and stratigraphic evolution of the Western Alboran Sea basin since the last 25 Myrs

    NASA Astrophysics Data System (ADS)

    Do Couto, Damien; Gorini, Christian; Jolivet, Laurent; Lebret, Noëmie; Augier, Romain; Gumiaux, Charles; D'Acremont, Elia; Ammar, Abdellah; Auxietre, Jean-Luc

    2016-04-01

    The Western Alboran Basin (WAB) formation has always been a matter of debate and was either considered as a backarc or a forearc basin. Based on stratigraphic analysis of high-resolution 2D seismic profiles mostly located offshore Morocco, the tectonic and stratigraphic history of the WAB is clarified. A thick pre-rift sequence is observed beneath the Miocene basin and interpreted as the topmost Malaguide/Ghomaride complex composing the Alboran domain. The structural position of this unit compared with the HP-LT exhumed Alpujarride/Sebtide metamorphic basement, leads us to link the Early Miocene subsidence of the basin with an extensional detachment. Above the Early Miocene, a thick Serravallian sequence marked by siliciclastic deposits is nearly devoid of extensional structures. Its overall landward to basinward onlap geometry indicates that the WAB has behaved as a sag basin during most of its evolution, from the Serravallian to the Late Tortonian. Tectonic reconstructions in map view and cross-section further suggest that the basin has always represented a strongly subsiding topographic low without internal deformation that has migrated westward together with the retreating slab. We propose that the subsidence of the WAB was controlled by the pull of the dipping subducting lithosphere explaining the large thickness (10 km) of the mostly undeformed sedimentary infill.

  7. Tectonic and stratigraphic evolution of the Western Alboran Sea Basin in the last 25 Myrs

    NASA Astrophysics Data System (ADS)

    Do Couto, Damien; Gorini, Christian; Jolivet, Laurent; Lebret, Noëmie; Augier, Romain; Gumiaux, Charles; d'Acremont, Elia; Ammar, Abdellah; Jabour, Haddou; Auxietre, Jean-Luc

    2016-05-01

    The Western Alboran Basin (WAB) formation has always been the subject of debate and considered either as a back-arc or a forearc basin. Stratigraphic analyses of high-resolution 2D seismic profiles mostly located offshore Morocco, enabled us to clarify the tectonic and stratigraphic history of the WAB. The thick pre-rift sequence located beneath the Miocene basin is interpreted as the topmost Malaguide/Ghomaride complex composing the Alboran domain. The structural position of this unit compared with the HP-LT exhumed Alpujarride/Sebtide metamorphic basement, leads us to link the Early Miocene subsidence of the basin with an extensional detachment. Above the Early Miocene, a thick Serravallian sequence marked by siliciclastic deposits is nearly devoid of extensional structures. Its overall landward to basinward onlap geometry indicates that the WAB has behaved as a sag basin during most of its evolution from the Serravallian to the late Tortonian. Tectonic reconstructions in map view and in cross section further suggest that the basin has always represented a strongly subsiding topographic low without internal deformation that migrated westward together with the retreating slab. We propose that the subsidence of the WAB was controlled by the pull of the dipping subducting lithosphere hence explaining the considerable thickness (10 km) of the mostly undeformed sedimentary infill.

  8. Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX.

    PubMed

    Bell, Jeffrey A; Ho, Kenneth L; Farid, Ramy

    2012-08-01

    All-atom models are essential for many applications in molecular modeling and computational chemistry. Nonbonded atomic contacts much closer than the sum of the van der Waals radii of the two atoms (clashes) are commonly observed in such models derived from protein crystal structures. A set of 94 recently deposited protein structures in the resolution range 1.5-2.8 Å were analyzed for clashes by the addition of all H atoms to the models followed by optimization and energy minimization of the positions of just these H atoms. The results were compared with the same set of structures after automated all-atom refinement with PrimeX and with nonbonded contacts in protein crystal structures at a resolution equal to or better than 0.9 Å. The additional PrimeX refinement produced structures with reasonable summary geometric statistics and similar R(free) values to the original structures. The frequency of clashes at less than 0.8 times the sum of van der Waals radii was reduced over fourfold compared with that found in the original structures, to a level approaching that found in the ultrahigh-resolution structures. Moreover, severe clashes at less than or equal to 0.7 times the sum of atomic radii were reduced 15-fold. All-atom refinement with PrimeX produced improved crystal structure models with respect to nonbonded contacts and yielded changes in structural details that dramatically impacted on the interpretation of some protein-ligand interactions.

  9. Automating Finance

    ERIC Educational Resources Information Center

    Moore, John

    2007-01-01

    In past years, higher education's financial management side has been riddled with manual processes and aging mainframe applications. This article discusses schools which had taken advantage of an array of technologies that automate billing, payment processing, and refund processing in the case of overpayment. The investments are well worth it:…

  10. Sedimentary Processes and Stratigraphic Responses in a Tectonically Driven Basin: Northern California Continental Shelf and Upper Slope

    DTIC Science & Technology

    2003-09-30

    significant right-lateral offset across that structure. 4. Anticlinal folding in the Little Salmon Fault Zone (LSFZ) ended on the shelf ~700 ka, but...northern California. In: Carver, G.A. and Aalto, K.R. (eds.), Field guide to the late Cenozoic subduction , tectonics, and sedimentation of northern...Stratigraphic development. Geological Society of America Bulletin, 114: 178-191. McCrory, P.A., 1995, Evolution of a trench-slope basin within the Cascadia

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

    NASA Astrophysics Data System (ADS)

    Dominici, Stefano; Benvenuti, Marco; Danise, Silvia

    2015-04-01

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

  12. Structure_threader: An improved method for automation and parallelization of programs structure, fastStructure and MavericK on multicore CPU systems.

    PubMed

    Pina-Martins, Francisco; Silva, Diogo N; Fino, Joana; Paulo, Octávio S

    2017-08-04

    Structure_threader is a program to parallelize multiple runs of genetic clustering software that does not make use of multithreading technology (structure, fastStructure and MavericK) on multicore computers. Our approach was benchmarked across multiple systems and displayed great speed improvements relative to the single-threaded implementation, scaling very close to linearly with the number of physical cores used. Structure_threader was compared to previous software written for the same task-ParallelStructure and StrAuto and was proven to be the faster (up to 25% faster) wrapper under all tested scenarios. Furthermore, Structure_threader can perform several automatic and convenient operations, assisting the user in assessing the most biologically likely value of 'K' via implementations such as the "Evanno," or "Thermodynamic Integration" tests and automatically draw the "meanQ" plots (static or interactive) for each value of K (or even combined plots). Structure_threader is written in python 3 and licensed under the GPLv3. It can be downloaded free of charge at https://github.com/StuntsPT/Structure_threader. © 2017 John Wiley & Sons Ltd.

  13. SU-C-9A-02: Structured Noise Index as An Automated Quality Control for Nuclear Medicine: A Two Year Experience

    SciTech Connect

    Nelson, J; Christianson, O; Samei, E

    2014-06-01

    Purpose: Flood-field uniformity evaluation is an essential element in the assessment of nuclear medicine (NM) gamma cameras. It serves as the central element of the quality control (QC) program, acquired and analyzed on a daily basis prior to clinical imaging. Uniformity images are traditionally analyzed using pixel value-based metrics which often fail to capture subtle structure and patterns caused by changes in gamma camera performance requiring additional visual inspection which is subjective and time demanding. The goal of this project was to develop and implement a robust QC metrology for NM that is effective in identifying non-uniformity issues, reporting issues in a timely manner for efficient correction prior to clinical involvement, all incorporated into an automated effortless workflow, and to characterize the program over a two year period. Methods: A new quantitative uniformity analysis metric was developed based on 2D noise power spectrum metrology and confirmed based on expert observer visual analysis. The metric, termed Structured Noise Index (SNI) was then integrated into an automated program to analyze, archive, and report on daily NM QC uniformity images. The effectiveness of the program was evaluated over a period of 2 years. Results: The SNI metric successfully identified visually apparent non-uniformities overlooked by the pixel valuebased analysis methods. Implementation of the program has resulted in nonuniformity identification in about 12% of daily flood images. In addition, due to the vigilance of staff response, the percentage of days exceeding trigger value shows a decline over time. Conclusion: The SNI provides a robust quantification of the NM performance of gamma camera uniformity. It operates seamlessly across a fleet of multiple camera models. The automated process provides effective workflow within the NM spectra between physicist, technologist, and clinical engineer. The reliability of this process has made it the preferred

  14. Vombat: an open source proof-of-concept for the use of Digital outcrop models as reference frame for stratigraphic observations

    NASA Astrophysics Data System (ADS)

    Penasa, Luca; Franceschi, Marco; Preto, Nereo; Girardeau-Montaut, Daniel

    2015-04-01

    Three-dimensional Virtual Outcrop Models (VOMs), often produced using terrestrial laser scanning or photogrammetry, have become popular in the Geosciences. The main feature of a VOM is that it allows for a quantification of the 3D geometry and/or distribution of geologic features that range from rock properties to structural elements. This actually generated much of the interest in VOMs by the oil and gas industry. The potential importance of a VOM in stratigraphy, however, does not seems completely disclosed yet. Indeed outcrops are the primary sources of data for a number of stratigraphic studies (e.g. palaeontology, sedimentology, cyclostratigraphy, geochemistry...). All the observations are typically reported on stratigraphic logs which constitute an idealized representation of the stratigraphic series, drawn by the researcher on the basis of the features that has to be highlighted. The observations are localized by means of manual measurements and a certain amount of subjectivity in log drawing is involved. These facts can prevent the log from being properly pinned to the real outcrop. Moreover, the integration of stratigraphic logs made by different researchers studying the same outcrop may be difficult. The exposure conditions of outcrops can change through time, to the point that they can become unaccessible or even be destroyed. In such a case, linking the stratigraphic log to its physical counterpart becomes impossible. This can be particularly relevant when a classical outcrop or even a GSSP is considered. A VOM may prove useful to tackle these issues, by providing a more objective stratigraphic reference for measurements and by preserving an outcrop through time as a visual representation, thus permitting reference and accurate comparison between observations made through time. Finally, a VOM itself may contain relevant stratigraphic information (e.g. scalar fields associated with the point cloud as intensity, rgb data or hyperspectral information from

  15. Fossil preservation and the stratigraphic ranges of taxa

    NASA Technical Reports Server (NTRS)

    Foote, M.; Raup, D. M.

    1996-01-01

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

  16. Punctuated Stratigraphic Appearance of Cold-Water Coral Reefs

    NASA Astrophysics Data System (ADS)

    Eberli, G. P.; Correa, T.; Massaferro, J. L.

    2008-05-01

    Existing and new data acquired with an AUV document a high abundance of cold-water coral mounds in the bottom of the Straits of Florida (SoF). These mounds display a large variability of shapes and heights. The abundance and variability encountered in these and modern cold-water coral mounds elsewhere is in stark contrast to lack of reported ancient cold-water coral reefs. Furthermore, the stratigraphic distribution suggests that cold-water corals punctuate the stratigraphic record with times of bloom and times of near complete absence. In the Florida Bahamas region, for example, the stratigraphic distribution is non-uniform. Preliminary age dating of the modern coral mounds produce ages of a few hundred to 1300 years for corals at the surface of the mounds. Sub-bottom profiles and seismic data across the investigated mound fields reveal that the "modern" mounds root in Pleistocene strata but are absent in the Pliocene strata below. Cores taken during ODP Legs 101 and 166 in the SoF confirm the punctuated appearance as deep-water coral rubble was penetrated only in the Pleistocene and in the upper Oligocene strata. The vast occurrence of Oligocene cold-water coral mounds is also visible on a 2-D seismic line in the northern SoF and on a 3-D seismic survey in the southwestern portion of the SoF. In this latter data set a mid-Miocene and the base of Tertiary seismic horizon also image mounded features. These spikes in reef development indicate that environmental conditions were only occasionally favorable for reef growth. The punctuated appearance is surprising as the core and seismic data document continuous current activity since the late Miocene in the SoF. We speculate that the "modern" bloom of cold-water coral reefs in the Pleistocene coincides with the onset of the large barrier reef systems in the Australia and Belize.

  17. Sedimentary fill and stratigraphic traps of Porcupine basin, offshore Ireland

    SciTech Connect

    Macurda, D.B. Jr.

    1986-05-01

    The Porcupine basin, off the southwest coast of Ireland, is a triangular north-south re-entrant into the present-day continental shelf. This aulacogen was formed in the Jurassic during the opening of the North Atlantic. A seismic stratigraphic investigation of the southern part of the basin has shown the complex evolution of the sedimentary fill from shallow to deep water facies, resulting in several stratigraphic traps. The central axis of the basin is dominated by a volcanic ridge. Part of the early sedimentary fill was intermittently covered by volcanic flows. The final stage of thin initial siliciclastic infill was the development of an extensive alluvial fan or fan-delta complex along the eastern basin margin. Aerially extensive carbonate sedimentation occurred during the Cretaceous, including a north-south reef tract more than 20 km wide in the eastern part of the basin. Increased subsidence resulted in the deposition of deep water siliciclastics in the Tertiary. The most prominent of these is a series of lower Tertiary submarine fans that were sourced from the western, northern, and eastern margins of the aulacogen. The early portions of the fans correlate well basin-wide; their later history is much more complex, with younger lobes up to 25 km wide developing south of their precursors. Subsequent onlap fill deposits provide an excellent seal. Sedimentation in the late Tertiary has included both high-energy and low-energy deep water deposits. The complex fill of the aulacogen has set up several stratigraphic plays, including carbonate reefs, alluvial fans of fan deltas, and submarine fans. Seismic amplitude anomalies in the latter suggest the heat flow has been sufficient to generate hydrocarbons to fill some of the traps.

  18. Measuring the Stratigraphic Filter in Ancient Deltaic Deposits

    NASA Astrophysics Data System (ADS)

    Trampush, S. M.; Hajek, E. A.

    2014-12-01

    Internal or autogenic sedimentary-system dynamics act as a filter that can dampen or obliterate signals of environmental perturbations, such as changes in climate and tectonics. Additionally, the transfer of material into the sedimentary archive can further degrade environmental signals. Presently we have a poor understanding of the rates, scales, and types of sedimentary processes that influence the stratigraphic filter in natural systems. A set of statistical tools has been developed for estimating the spatial and temporal scales over which the sedimentary filter operates from preserved stratigraphy. These tools, such as the compensation index, have been applied to experimental data and numerical models, with only limited use on outcrop data. Experimental datasets commonly have several orders of magnitude more data than even the most well exposed ancient outcrops; consequently, the ability to confidently use tools in natural systems is limited. Here we present an evaluation of the suitability of the compensation index for measuring and interpreting sedimentary outcrops. In order to constrain uncertainty due to data-set-size limitations, we model the degree to which measurement error, small data sets, and incomplete sampling influence attempts to quantify stratigraphic architecture. We demonstrate the potential for measuring the stratigraphic filter in ancient deposits by evaluating well-exposed deltaic deposits in the Cretaceous Western Interior Seaway that have been interpreted as having different degrees of to wave, tide, and river influence. Ultimately our results underscore how powerful quantitative tools developed in experimental and model datasets must be applied and interpreted with care in ancient deposits where data availability is limited.

  19. Fossil preservation and the stratigraphic ranges of taxa

    NASA Technical Reports Server (NTRS)

    Foote, M.; Raup, D. M.

    1996-01-01

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

  20. Preliminary Stratigraphic Basis for Geologic Mapping of Venus

    NASA Technical Reports Server (NTRS)

    Basilevsky, A. T.; Head, J. W.

    1993-01-01

    The age relations between geologic formations have been studied at 36 1000x1000 km areas centered at the dark paraboloid craters. The geologic setting in all these sites could be characterized using only 16 types of features and terrains (units). These units form a basic stratigraphic sequence (from older to younger: (1) Tessera (Tt); (2-3) Densely fractured terrains associated with coronae (COdf) and in the form of remnants among plains (Pdf); (4) Fractured and ridged plains (Pfr); (5) Plains with wrinkle ridges (Pwr); (6-7) Smooth and lobate plains (Ps/Pl); and (8) Rift-associated fractures (Fra). The stratigraphic position of the other units is determined by their relation with the units of the basic sequence: (9) Ridge bells (RB), contemporary with Pfr; (10-11) Ridges of coronae and arachnoids annuli (COar/Aar), contemporary with wrinkle ridges of Pwr; (12) Fractures of coronae annuli (COaf) disrupt Pwr and Ps/Pl; (13) Fractures (F) disrupt Pwr or younger units; (14) Craters with associated dark paraboloids (Cdp), which are on top of all volcanic and tectonic units except the youngest episodes of rift-associated fracturing and volcanism; (15-16) Surficial streaks (Ss) and surficial patches (Sp) are approximately contemporary with Cdp. These units may be used as a tentative basis for the geologic mapping of Venus including VMAP. This mapping should test the stratigraphy and answer the question of whether this stratigraphic sequence corresponds to geologic events which were generally synchronous all around the planet or whether the sequence is simply a typical sequence of events which occurred in different places at diffferent times.

  1. Gulf Coast stratigraphic traps in the Lower Cretaceous carbonates

    SciTech Connect

    Sams, R.H.

    1981-09-01

    Prolific oil and gas production is being obtained from carbonate patch reef reservoirs within Lower Cretaceous formations along the Gulf Coast from Florida to Mexico. Many of these reservoirs are trapped stratigraphically where facies changes within a formation or patch reef unit establish an up-dip permeability barrier. Illustrations of such traps are given from the literature for oil and gas fields in Florida, Mississippi, Louisiana, and E. Texas. A geologic model is presented which provides the explorationist with an actual drilling target suitable to a multiple well exploratory program. 18 references.

  2. The effect of stratigraphic uncertainty on repository performance

    SciTech Connect

    Wilson, M.L.; Robey, T.H.

    1994-08-01

    One source of uncertainty in calculating radionuclide releases from a potential radioactive-waste at Yucca Mountain, Nevada, is uncertainty in the unsaturated-zone stratigraphy. Uncertainty stratigraphy results from sparse drillhole data; possible variations in stratigraphy are modeled using the geostatistical method of indicator simulation. One-dimensional stratigraphic columns are generated and used for calculations of groundwater flow and radionuclide transport. There are indications of a dependence of release on hydrogeologic-unit thicknesses, but the resulting variation in release is smaller than variations produced by other sources of uncertainty.

  3. Laser induced breakdown spectroscopy stratigraphic characterization of multilayered painted surfaces

    NASA Astrophysics Data System (ADS)

    Staicu, A.; Apostol, I.; Pascu, A.; Iordache, I.; Damian, V.; Pascu, M. L.

    2012-08-01

    Laser spectroscopy techniques are modern and competitive methods for elemental analysis. Laser induced breakdown spectroscopy (LIBS), due to its advantages as minimally invasive method that provides real time monitoring and selectivity, is a suitable tool to analyze sample composition. Based on the known emission spectra of heavy metals such as Pb, Zn, Au, Ca, a stratigraphic study regarding the identification of the painting layers content of different mock-up samples was performed. LIBS was used to monitor the laser induced stepwise selective removal of the painting layers and to analyze their composition. The obtained LIBS spectra were correlated with profilometric measurements.

  4. Variations in depositional systems of the Micocene Oficina Formation in the Cerro Negro area using a sequence stratigraphic analysis: Application to siliciclastic exploration

    SciTech Connect

    Rodriguez, A. )

    1991-03-01

    The Cerro Negro oil-sands area is located in eastern Venezuela. Although the Oficina Formation is the major oil-producing formation in this region, until now no attempt has been made to analyze and produce a sedimentological model for these sediments using modern sedimentological sequence stratigraphic techniques in which variations in depositional styles could be documented. Seven continuously cored wells penetrating the Oficina Formation provide the 1955.9 m (6417 ft) of cored section employed in this study. The sedimentological information gathered during analysis of the cored sedimentary sections comes from the study of lithology, trace fossils and bioturbation structures, abundant shell fragments, clay mineralogical assemblages, and microfaunal data. This information provides a basis for recognizing 13 facies as representative of the cored sedimentary intervals and leads one to divide the sedimentary section into four genetically related facies assemblages or stratigraphic units. This interpretation is supported by computer-drawn isopach maps of selected sands within each stratigraphic unit, sand percentage, and sand isolith maps of individual stratigraphic units. This deltaic to shallow-marine facies model proposed for Cerro Negro predicts that sand bodies should have different trends, thicknesses, and distribution, depending upon the stratigraphic unit in which they were formed. Therefore, the model can be used as a guide in exploration studies of this and other areas having similar geological characteristics to those of Cerro Negro.

  5. Student learning and understanding of sequence stratigraphic principles

    NASA Astrophysics Data System (ADS)

    Herrera, Juan Sebastian

    Research in geoscience education addressing students' conceptions of geological subjects has concentrated in topics such as geological time, plate tectonics, and problem solving in the field, mostly in K-12 and entry level college scenarios. Science education research addressing learning of sedimentary systems in advance undergraduates is rather limited. Therefore, this dissertation contributed to filling that research gap and explored students' narratives when explaining geological processes associated with the interaction between sediment deposition and sea level fluctuations. The purpose of the present study was to identify the common conceptions and alternative conceptions held by students when learning the basics of the sub discipline known as sequence stratigraphy - which concepts students were familiar and easily identified, and which ones they had more difficulty with. In addition, we mapped the cognitive models that underlie those conceptions by analyzing students' gestures and conceptual metaphors used in their explanations. This research also investigated the interaction between geoscientific visual displays and student gesturing in a specific learning context. In this research, an in-depth assessment of 27 students' ideas of the basic principles of sequence stratigraphy was completed. Participants were enrolled in advanced undergraduate stratigraphy courses at three research-intensive universities in Midwest U.S. Data collection methods included semi-structured interviews, spatial visualization tests, and lab assignments. Results indicated that students poorly integrated temporal and spatial scales in their sequence stratigraphic models, and that many alternative conceptions were more deeply rooted than others, especially those related to eustasy and base level. In order to better understand the depth of these conceptions, we aligned the analysis of gesture with the theory of conceptual metaphor to recognize the use of mental models known as image

  6. Prediction of the three-dimensional structures of the biotinylated domain from yeast pyruvate carboxylase and of the lipoylated H-protein from the pea leaf glycine cleavage system: a new automated method for the prediction of protein tertiary structure.

    PubMed Central

    Brocklehurst, S. M.; Perham, R. N.

    1993-01-01

    A new, automated, knowledge-based method for the construction of three-dimensional models of proteins is described. Geometric restraints on target structures are calculated from a consideration of homologous template structures and the wider knowledge base of unrelated protein structures. Three-dimensional structures are calculated from initial partly folded states by high-temperature molecular dynamics simulations followed slow cooling of the system (simulated annealing) using nonphysical potentials. Three-dimensional models for the biotinylated domain from the pyruvate carboxylase of yeast and the lipoylated H-protein from the glycine cleavage system of pea leaf were constructed, based on the known structures of two lipoylated domains of 2-oxo acid dehydrogenase multienzyme complexes. Despite their weak sequence similarity, the three proteins are predicted to have similar three-dimensional structures, representative of a new protein module. Implications for the mechanisms of posttranslational modification of these proteins and their catalytic function are discussed. PMID:8518734

  7. Preservation of lunar core samples - Preparation and interpretation of three-dimensional stratigraphic sections

    NASA Technical Reports Server (NTRS)

    Fryxell, R.; Heiken, G.

    1974-01-01

    Preservation and analysis of core samples collected from the lunar regolith are discussed. The objectives of core sampling are described together with the core-sampling equipment used in the Apollo program. The effects of disaggregation in core samples are summarized, and ways to preserve the stratigraphy in these samples are reviewed, particularly partial impregnation of samples with polybutyl methacrylate. It is shown that stratigraphic sections preserved in this way reveal individual fragments of the regolith in their original positions, primary and secondary depositional structures related to lunar processes, and the nature and extent of deformations caused by sampling equipment. It is concluded that since the core sedimentary structures indicate complex three-dimensional variations in the regolith, quantitative models of regolith evolution must allow for distinctive local histories as well as irregular reworking and deposition events due to impact processes.

  8. Numerical analysis of stiffened shells of revolution. Volume 3: Users' manual for STARS-2B, 2V, shell theory automated for rotational structures, 2 (buckling, vibrations), digital computer programs

    NASA Technical Reports Server (NTRS)

    Svalbonas, V.

    1973-01-01

    The User's manual for the shell theory automated for rotational structures (STARS) 2B and 2V (buckling, vibrations) is presented. Several features of the program are: (1) arbitrary branching of the shell meridians, (2) arbitrary boundary conditions, (3) minimum input requirements to describe a complex, practical shell of revolution structure, and (4) accurate analysis capability using a minimum number of degrees of freedom.

  9. Developing a Graphical User Interface to Automate the Estimation and Prediction of Risk Values for Flood Protective Structures using Artificial Neural Network

    NASA Astrophysics Data System (ADS)

    Hasan, M.; Helal, A.; Gabr, M.

    2014-12-01

    In this project, we focus on providing a computer-automated platform for a better assessment of the potential failures and retrofit measures of flood-protecting earth structures, e.g., dams and levees. Such structures play an important role during extreme flooding events as well as during normal operating conditions. Furthermore, they are part of other civil infrastructures such as water storage and hydropower generation. Hence, there is a clear need for accurate evaluation of stability and functionality levels during their service lifetime so that the rehabilitation and maintenance costs are effectively guided. Among condition assessment approaches based on the factor of safety, the limit states (LS) approach utilizes numerical modeling to quantify the probability of potential failures. The parameters for LS numerical modeling include i) geometry and side slopes of the embankment, ii) loading conditions in terms of rate of rising and duration of high water levels in the reservoir, and iii) cycles of rising and falling water levels simulating the effect of consecutive storms throughout the service life of the structure. Sample data regarding the correlations of these parameters are available through previous research studies. We have unified these criteria and extended the risk assessment in term of loss of life through the implementation of a graphical user interface to automate input parameters that divides data into training and testing sets, and then feeds them into Artificial Neural Network (ANN) tool through MATLAB programming. The ANN modeling allows us to predict risk values of flood protective structures based on user feedback quickly and easily. In future, we expect to fine-tune the software by adding extensive data on variations of parameters.

  10. Digital tabulation of stratigraphic data from oil and gas wells in the Santa Maria Basin and surrounding areas, central California coast

    USGS Publications Warehouse

    Sweetkind, Donald S.; Tennyson, Marilyn E.; Langenheim, V.E.; Shumaker, Lauren E.

    2010-01-01

    Stratigraphic information from 694 oil and gas exploration wells from the onshore Santa Maria basin and surrounding areas are herein compiled in digital form from reports that were released originally in paper form. The Santa Maria basin is located within the southwesternmost part of the Coast Ranges and north of the western Transverse Ranges on the central California coast. Knowledge of the location and elevation of stratigraphic tops of formations throughout the basin is a first step toward understanding depositional trends and the structural evolution of the basin through time.

  11. 3-D Numerical Stratigraphic Forward Modeling of Rifts

    NASA Astrophysics Data System (ADS)

    Lovely, P. J.; Harris, A.; Baumgardner, S. E.; Engelder, T.; Sun, T.; Lyons, R. P.; Granjeon, D.

    2016-12-01

    Continental rifts are of great interest and relevance to scientists and the general public because they contain numerous depositional environments at relatively compressed spatiotemporal scales, continuous climate records, and hydrocarbon resources. The interaction of climate, sediment routing, and tectonism controls the distribution and continuity of the depositional environments, but these relationships are nonlinear and complex. Conceptual stratigraphic models provide useful insight into facies distribution but are typically qualitative and may not capture the full range of geologically plausible scenarios generated by these interactions. Here, we use a numerical forward stratigraphic model to demonstrate that a deterministic, nonlinear diffusion-based sediment transport model can approximate key tectonostratigraphic processes interpreted from continental rift systems. The sediment transport model acts upon a simple elastic tectonic model that approximates appropriate distributions of subsidence and uplift associated with a schematic fault architecture typical of early stage continental rifting. Comparison of model results to observations of outcrops and the subsurface demonstrates the model's ability to reproduce key tectonostratigraphic features. We also show that such a model may be used to analyze the sensitivity of sand distributions to base-level, sediment, and water flux changes. We present an example analysis with a suite of metrics such as sand thickness, net-to-gross, and mass extraction methods that quantitatively describe the deposits that result from various inputs. This simple sensitivity analysis can be conducted by academic and industry groups to better characterize facies distribution or quantify uncertainties associated with continental rifts.

  12. Subsidence and stratigraphic modeling of the US Atlantic margin

    SciTech Connect

    Steckler, M.S.; Watts, A.B.; Thorne, J.A.

    1985-01-01

    The deep offshore basins of the US Atlantic margin show an exponential subsidence consistent with lithospheric extension followed by cooling. In the Baltimore Canyon Trough, extension reaches ..beta.. approx. =4. The resultant deep burial and inaccessibility of the syn-rift sediment preclude a detailed understanding of the rifting history. On the other hand, the general similarity of predicted subsidence for all rifting models during the later post-rift period allows a detailed reconstruction of the paleobathymetry and an evaluation of the nature of the control of the stratigraphic record. Layer by layer backstripping indicates that there has been no major erosional retreat of the Early Cretaceous shelf edge. The change in position of the shelf edge following the termination of the Jurassic-Early Cretaceous reef, was accomplished by a gentle sagging and sediment supply variations. Stratigraphic modeling reveals the primary factors affecting the post-rift development of the shelf. These are the presence of a broad thermal uplift during the Jurassic at the site of the present coastal plain, increasing flexural rigidity of the lithosphere creating the coastal plain wedge, and a moderate (150-200 m) sea level fall since the Late Cretaceous in order to match the observed thicknesses and coastal onlap-offlap patterns during the Cenozoic.

  13. Stratigraphic mapping of hydrated phases in Western Ius Chasma, Mars

    NASA Astrophysics Data System (ADS)

    Cull, S.; McGuire, P. C.; Gross, C.; Dumke, A.

    2013-12-01

    Recent mapping with the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) and Observatoire pour la Minéralogie, l'Eau, les Glaces et l'Activité (OMEGA) has revealed a wide range of hydrated minerals throughout Valles Marineris. Noctis Labyrinthus has interbedded polyhydrated and monohydrated sulfates, with occasional beds of nontronite (Weitz et al. 2010, Thollot et al. 2012). Tithonium Chasma has interbedded poly- and monohydrated sulfates (Murchie et al. 2012); Juventae has poly- and monohydrated sulfates and an anhydrous ferric hydroxysulfate-bearing material (Bishop et al. 2009); and Melas and Eastern Candor contain layers of poly- and monohydrated sulfates (e.g., Roach et al. 2009). Though each chasm displays its own mineralogy, in general, the eastern valles tend to be dominated by layered sequences with sulfates; whereas, the far western valles (Noctis Labyrinthus) has far more mineral phases, possibly due to a wider variety of past environments or processes affecting the area. Ius Chasma, which is situated between Noctis Labyrinthus and the eastern valles and chasmata, also displays a complex mineralogy, with polyhydrated sulfates, Fe/Mg smectites, hydrated silica, and kieserite (e.g. Roach et al. 2010). Here, we present mapping of recently acquired CRISM observations over Ius Chasma, combining the recent CRISM cubes with topographic terrains produced using High Resolution Stereo Camera (HRSC) data from the Mars Express spacecraft. Stratigraphic columns are produced along the length of Ius Chasma, and compared to stratigraphic columns produced throughout the Valles Marineris

  14. Automated RTOP Management System

    NASA Technical Reports Server (NTRS)

    Hayes, P.

    1984-01-01

    The structure of NASA's Office of Aeronautics and Space Technology electronic information system network from 1983 to 1985 is illustrated. The RTOP automated system takes advantage of existing hardware, software, and expertise, and provides: (1) computerized cover sheet and resources forms; (2) electronic signature and transmission; (3) a data-based information system; (4) graphics; (5) intercenter communications; (6) management information; and (7) text editing. The system is coordinated with Headquarters efforts in codes R,E, and T.

  15. Accuracy and Reliability of Automated Gray Matter Segmentation Pathways on Real and Simulated Structural Magnetic Resonance Images of the Human Brain

    PubMed Central

    Eggert, Lucas D.; Sommer, Jens; Jansen, Andreas; Kircher, Tilo; Konrad, Carsten

    2012-01-01

    Automated gray matter segmentation of magnetic resonance imaging data is essential for morphometric analyses of the brain, particularly when large sample sizes are investigated. However, although detection of small structural brain differences may fundamentally depend on the method used, both accuracy and reliability of different automated segmentation algorithms have rarely been compared. Here, performance of the segmentation algorithms provided by SPM8, VBM8, FSL and FreeSurfer was quantified on simulated and real magnetic resonance imaging data. First, accuracy was assessed by comparing segmentations of twenty simulated and 18 real T1 images with corresponding ground truth images. Second, reliability was determined in ten T1 images from the same subject and in ten T1 images of different subjects scanned twice. Third, the impact of preprocessing steps on segmentation accuracy was investigated. VBM8 showed a very high accuracy and a very high reliability. FSL achieved the highest accuracy but demonstrated poor reliability and FreeSurfer showed the lowest accuracy, but high reliability. An universally valid recommendation on how to implement morphometric analyses is not warranted due to the vast number of scanning and analysis parameters. However, our analysis suggests that researchers can optimize their individual processing procedures with respect to final segmentation quality and exemplifies adequate performance criteria. PMID:23028771

  16. Accuracy and reliability of automated gray matter segmentation pathways on real and simulated structural magnetic resonance images of the human brain.

    PubMed

    Eggert, Lucas D; Sommer, Jens; Jansen, Andreas; Kircher, Tilo; Konrad, Carsten

    2012-01-01

    Automated gray matter segmentation of magnetic resonance imaging data is essential for morphometric analyses of the brain, particularly when large sample sizes are investigated. However, although detection of small structural brain differences may fundamentally depend on the method used, both accuracy and reliability of different automated segmentation algorithms have rarely been compared. Here, performance of the segmentation algorithms provided by SPM8, VBM8, FSL and FreeSurfer was quantified on simulated and real magnetic resonance imaging data. First, accuracy was assessed by comparing segmentations of twenty simulated and 18 real T1 images with corresponding ground truth images. Second, reliability was determined in ten T1 images from the same subject and in ten T1 images of different subjects scanned twice. Third, the impact of preprocessing steps on segmentation accuracy was investigated. VBM8 showed a very high accuracy and a very high reliability. FSL achieved the highest accuracy but demonstrated poor reliability and FreeSurfer showed the lowest accuracy, but high reliability. An universally valid recommendation on how to implement morphometric analyses is not warranted due to the vast number of scanning and analysis parameters. However, our analysis suggests that researchers can optimize their individual processing procedures with respect to final segmentation quality and exemplifies adequate performance criteria.

  17. Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX

    PubMed Central

    Bell, Jeffrey A.; Ho, Kenneth L.; Farid, Ramy

    2012-01-01

    All-atom models are essential for many applications in molecular modeling and computational chemistry. Non­bonded atomic contacts much closer than the sum of the van der Waals radii of the two atoms (clashes) are commonly observed in such models derived from protein crystal structures. A set of 94 recently deposited protein structures in the resolution range 1.5–2.8 Å were analyzed for clashes by the addition of all H atoms to the models followed by optimization and energy minimization of the positions of just these H atoms. The results were compared with the same set of structures after automated all-atom refinement with PrimeX and with nonbonded contacts in protein crystal structures at a resolution equal to or better than 0.9 Å. The additional PrimeX refinement produced structures with reasonable summary geometric statistics and similar R free values to the original structures. The frequency of clashes at less than 0.8 times the sum of van der Waals radii was reduced over fourfold compared with that found in the original structures, to a level approaching that found in the ultrahigh-resolution structures. Moreover, severe clashes at less than or equal to 0.7 times the sum of atomic radii were reduced 15-­fold. All-atom refinement with PrimeX produced improved crystal structure models with respect to nonbonded contacts and yielded changes in structural details that dramatically impacted on the interpretation of some protein–ligand interactions. PMID:22868759

  18. Three-dimensional structure of lipid vesicles embedded in vitreous ice and investigated by automated electron tomography.

    PubMed

    Dierksen, K; Typke, D; Hegerl, R; Walz, J; Sackmann, E; Baumeister, W

    1995-04-01

    Automated electron tomography is shown to be a suitable means to visualize the shape of phospholipid vesicles embedded in vitrified ice. With a slow-scan charge-coupled device camera as a recording device, the cumulative electron dose needed to record a data set of 60 projections at a magnification of 20,000X can be kept as low as 15 e-/A2 (or 1500 electrons/nm2). The membrane of the three-dimensionally reconstructed vesicles is clearly visible in two-dimensional sections through the three-dimensionally reconstructed volume. Some edges indicating a polygonal shape of the vesicles, frozen from the gel phase, are also clearly recognized. Because of the presently limited tilt angle range (+/- 60 degrees), the upper and lower "caps" of the vesicles (representing about 35% of the surface of the ellipsoidal particles) remain invisible in the three-dimensional reconstruction.

  19. North American Commission on Stratigraphic Nomenclature Report 12 – Revision of article 37, lithodemic units, of the North American Stratigraphic Code

    USGS Publications Warehouse

    Easton, Robert M.; Edwards, Lucy E.; Orndorff, Randall C.; Duguet, Manuel; Ferrusquia-Villafranca, Ismael

    2017-01-01

    At the 71st Annual Meeting of the North American Commission on Stratigraphic Nomenclature, 26 September, 2016, in Denver, Colorado, the Commission voted unanimously to accept the revision of Article 37 of the North American Stratigraphic Code (North American Commission on Stratigraphic Nomenclature, 2005), printed below. It replaces all older versions of this Article. An application for this revision (Easton et al. 2015) was published in Stratigraphy more than one year prior to the meeting; thus, the vote on this application for revision follows Article 21 of the Code.

  20. H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.

    PubMed

    Anandakrishnan, Ramu; Aguilar, Boris; Onufriev, Alexey V

    2012-07-01

    The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ (http://biophysics.cs.vt.edu/) is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.

  1. Triassic-Jurassic sediments and multiple volcanic events in North Victoria Land, Antarctica: A revised stratigraphic model

    USGS Publications Warehouse

    Schöner, R.; Viereck-Goette, L.; Schneider, J.; Bomfleur, B.

    2007-01-01

    Field investigations in North Victoria Land, Antarctica during GANOVEX IX (2005/2006) allow the revision of the Triassic-Jurassic stratigraphy of ~300 m thick continental deposits in between the crystalline basement and the Kirkpatrick lava flows of the Ferrar Group. The lower stratigraphic unit (Section Peak Formation) is characterised by braided river-type quartzose sandstone deposits with intercalations of shale and coal occurring at the top. It is overlain by a homogeneous unit of reworked tuffs composed of fine-grained silicic shards, quartz and feldspar (new name: "Shafer Peak Formation"). These deposits can be correlated with parts of the Hanson Formation in the Central Transantarctic Mountains and require a distal yet unknown source of massive silicic volcanism. Clastic products of mafic volcanic eruptions, formerly described as a separate stratigraphic formation (Exposure Hill Formation), occur within local diatreme structures as well as intercalated at various stratigraphic levels within the sedimentary succession. These dominantly hydroclastic eruptions are the first subaerial expression of Ferrar magmatism. The initial Kirkpatrick lavas/pillow lavas were generated from local eruptive centres and again may be overlain by thin sediments, which are covered by the thick plateau lava succession known throughout the Transantarctic Mountain Range.

  2. Stratigraphic positioning of the Lower Cretaceous conglomerates, Wind River basin, Wyoming and implications for possible hydrocarbon traps

    SciTech Connect

    Furer, L.C.; Kvale, E.P. ); May, M.T.; Suttner, L.J. )

    1991-03-01

    Most previous outcrop and subsurfaces studies of the Lower Cretaceous conglomerates and conglomeratic sandstones in Wyoming have assumed a time equivalency for these deposits. The conglomerates have been utilized to identify the Jurassic-Cretaceous boundary and interpret tectonic conditions within the Sevier foreland basin. However, the authors integrated subsurface-outcrop correlations show that the conglomerates occur at distinctly different stratigraphic levels, thus invalidating their use in marking the Jurassic-Cretaceous boundary and complicating interpretations of their tectonic significance. A chert-bearing conglomerate occurs at the base of the Cloverly Formation over the entire western flank of the Wind River basin except within a 30 km Cloverly outcrop belt near Lander. The zero edge of this unit lies just east of Muskrat field where it may be a facies equivalent with what has previously been interpreted as the Upper Jurassic Morrison Formation. In contrast, in the eastern quarter of the Wind River basin, a thick chert-bearing conglomerate occurs in the upper part of the Cloverly Formation. This conglomerate may be the time-stratigraphic equivalent to the transitional marine 'Rusty beds' present in the western margin of the basin. In both areas, the conglomerates and conglomeratic sandstones are encased in thick mudstones. Paleocurrent data suggest different source areas for the eastern and western conglomerates. The basal conglomerate was derived from the southwest, whereas the younger, eastern conglomerate was derived from the south. Their areal distributions have been useful in suggesting areas of potential structural-stratigraphic hydrocarbon plays.

  3. Venusian extended ejecta deposits as time-stratigraphic markers

    NASA Technical Reports Server (NTRS)

    Izenberg, Noam R.

    1992-01-01

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

  4. Venusian extended ejecta deposits as time-stratigraphic markers

    NASA Astrophysics Data System (ADS)

    Izenberg, Noam R.

    1992-12-01

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

  5. OWL representation of the geologic timescale implementing stratigraphic best practice

    NASA Astrophysics Data System (ADS)

    Cox, S. J.

    2011-12-01

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

  6. Stratigraphic variations in the Carboniferous section across the Arkansas-Oklahoma State Line Arch

    NASA Astrophysics Data System (ADS)

    Engelhardt, Tyler D.

    The State Line Arch is represented by a structural high that trends through the study area in a loose alignment with the Arkansas-Oklahoma state line. Evidence of the arch extending further to the north includes a structural high and stratigraphic variation at an outcrop on Highway 59 near Evansville Mountain in Crawford County, Arkansas. The exact timing of the formation of the arch remains undetermined, but upper Devonian thinning at the top of the arch indicates the structure is pre-Mississippian. The reason for the development of the arch is poorly understood, but evidence linking Mississippian-aged Waulsortian mounds to Precambrian Spavinaw granite structures of northeastern Oklahoma and southwestern Missouri suggests Precambrian basement structures may extend into the study area. The structural nature of the arch provided an environment favorable to carbonate build-up during deposition of the Mississippian interval. A previously unidentified limestone unit measuring 175 feet thick likely represents the transgressive phase of a transgressive-regressive sequence responsible for the deposition of the Mayes Group of northeastern Oklahoma. Growth on the downthrown side of the Muldrow-Mulberry Fault system may indicate earlier movement than previous studies have suggested on the east-west trending normal faults of the Arkoma Basin. A possible roll-over anticline structure may exist to the south of the Muldrow-Mulberry fault system.

  7. Beyond the Twilight Zone: automated prediction of structural properties of proteins by recursive neural networks and remote homology information.

    PubMed

    Mooney, Catherine; Pollastri, Gianluca

    2009-10-01

    The prediction of 1D structural properties of proteins is an important step toward the prediction of protein structure and function, not only in the ab initio case but also when homology information to known structures is available. Despite this the vast majority of 1D predictors do not incorporate homology information into the prediction process. We develop a novel structural alignment method, SAMD, which we use to build alignments of putative remote homologues that we compress into templates of structural frequency profiles. We use these templates as additional input to ensembles of recursive neural networks, which we specialise for the prediction of query sequences that show only remote homology to any Protein Data Bank structure. We predict four 1D structural properties - secondary structure, relative solvent accessibility, backbone structural motifs, and contact density. Secondary structure prediction accuracy, tested by five-fold cross-validation on a large set of proteins allowing less than 25% sequence identity between training and test set and query sequences and templates, exceeds 82%, outperforming its ab initio counterpart, other state-of-the-art secondary structure predictors (Jpred 3 and PSIPRED) and two other systems based on PSI-BLAST and COMPASS templates. We show that structural information from homologues improves prediction accuracy well beyond the Twilight Zone of sequence similarity, even below 5% sequence identity, for all four structural properties. Significant improvement over the extraction of structural information directly from PDB templates suggests that the combination of sequence and template information is more informative than templates alone.

  8. Stratigraphic sections of the Phosphoria formation 1953 and 1954

    USGS Publications Warehouse

    Swanson, R.W.; Carswell, L.D.; Sheldon, R.P.; Cheney, T.M.

    1955-01-01

    Since 1947, the U.S. Geological Survey has measured and sampled phosphatic parts of the Permian Phosphoria formation and its partial stratigraphic correlatives at many localities in Montana, Idaho, Wyoming, and Utah.  Preliminary data on the thickness of the beds and their composition at localities sampled prior to 1952 have been issued already in TEI-183, 184, 185, 186, 187, 188, 360, 361, 362, 363, 364, 365, 375, 376, 377, and 378. This report presents similar data on the localitites sampled in 1953 and 1954 (figs. 1, 2, and 3).  The field and laboratory procedures adopted in these investigations are described in a previous report (McKelvey and others 1953a).

  9. Drilling rate for the Cerro Prieto stratigraphic sequence

    SciTech Connect

    Prian C, R.

    1981-01-01

    Drilling practice at the field has been modified in several ways as better information is being obtained. The stratigraphic sequence of the area is made up of three sedimentary rock units of deltaic origin having different densities. These units have been named non-consolidated, semi-consolidated, and consolidated rocks; the thermal reservoirs are located in the latter. To investigate how the drilling rates are affected by the three rock units, plots of drilling advance versus time were made for a large number of wells. A typical plot is shown and drilling rates are practically constant in three different zones; that is, the drilling rate has only two breaks or changes in slope.

  10. Mars Tharsis region - Volcanotectonic events in the stratigraphic record

    NASA Technical Reports Server (NTRS)

    Scott, D. H.; Tanaka, K. L.

    1980-01-01

    It is pointed out that the most recent volcanism and much of the oldest tectonic activity on Mars have apparently occurred within the Tharsis region. Detailed geologic mapping from Viking images has provided new information on the evolutionary history of the region. The eruptive sequence and areal extent of lava flows in the Tharsis region have been defined by stratigraphic studies and crater counts made on individual flow units. Faults and fractures transecting these units provide a record of changing tectonic intensity during the period of high volcanic activity. Volcanism began with the resurfacing of basement rocks early in the history of the region and continued without large interruptions through nine major eruptive episodes. Volcanic centers shifted from place to place but resurgent activity occurred at several volcanoes. Volcanism culminated during the foration of large shield volcanoes along Tharsis Montes and thereafter appears to have gradually declined.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  12. Automated campaign system

    NASA Astrophysics Data System (ADS)

    Vondran, Gary; Chao, Hui; Lin, Xiaofan; Beyer, Dirk; Joshi, Parag; Atkins, Brian; Obrador, Pere

    2006-02-01

    To run a targeted campaign involves coordination and management across numerous organizations and complex process flows. Everything from market analytics on customer databases, acquiring content and images, composing the materials, meeting the sponsoring enterprise brand standards, driving through production and fulfillment, and evaluating results; all processes are currently performed by experienced highly trained staff. Presented is a developed solution that not only brings together technologies that automate each process, but also automates the entire flow so that a novice user could easily run a successful campaign from their desktop. This paper presents the technologies, structure, and process flows used to bring this system together. Highlighted will be how the complexity of running a targeted campaign is hidden from the user through technologies, all while providing the benefits of a professionally managed campaign.

  13. The automation of science.

    PubMed

    King, Ross D; Rowland, Jem; Oliver, Stephen G; Young, Michael; Aubrey, Wayne; Byrne, Emma; Liakata, Maria; Markham, Magdalena; Pir, Pinar; Soldatova, Larisa N; Sparkes, Andrew; Whelan, Kenneth E; Clare, Amanda

    2009-04-03

    The basis of science is the hypothetico-deductive method and the recording of experiments in sufficient detail to enable reproducibility. We report the development of Robot Scientist "Adam," which advances the automation of both. Adam has autonomously generated functional genomics hypotheses about the yeast Saccharomyces cerevisiae and experimentally tested these hypotheses by using laboratory automation. We have confirmed Adam's conclusions through manual experiments. To describe Adam's research, we have developed an ontology and logical language. The resulting formalization involves over 10,000 different research units in a nested treelike structure, 10 levels deep, that relates the 6.6 million biomass measurements to their logical description. This formalization describes how a machine contributed to scientific knowledge.

  14. FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms

    PubMed Central

    Kaltdorf, Kristin Verena; Schulze, Katja; Helmprobst, Frederik; Kollmannsberger, Philip; Stigloher, Christian

    2017-01-01

    Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i) in embryonic Danio rerio 4 and 8 days past fertilization (dpf) and (ii) to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ) wild-type and its septin mutant (unc-59(e261)). We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models. We confirm the functionality of our macro by applying our 3D ART VeSElecT on zebrafish NMJ showing smaller vesicles in 8 dpf embryos then 4 dpf, which was validated by manual reconstruction of the vesicle pool. Furthermore, we analyze the impact of C. elegans septin mutant unc-59(e261) on vesicle pool formation and vesicle size. Automated vesicle registration and characterization was implemented in Fiji as two macros (registration and measurement). This flexible arrangement allows in particular reducing false positives by an optional manual revision step. Preprocessing and contrast enhancement work on image-stacks of 1nm/pixel in x and y direction. Semi-automated cell selection was integrated. 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Results are collected in color using the RoiManager plugin including the possibility of manual removal of non-matching confounder vesicles. Detailed evaluation considered performance (detected vesicles) and specificity (true vesicles) as well as precision and recall. We furthermore show gain in segmentation and morphological filtering compared to learning based methods and a large time gain compared to manual segmentation. 3D ART VeSElecT shows small error rates and its speed gain can be up to 68 times faster in comparison to manual annotation

  15. Forward stratigraphic modeling of the Permian of the Delaware Basin

    SciTech Connect

    Qiucheng, Ye; Kerans, C.; Bowman, S. )

    1996-01-01

    Permian platform-to-basin strata of the Delaware Basin In west Texas and New Mexico represent one of the world's most complete, best studied, and most hydrocarbon productive records of this geologic period in the world. This superb marriage of a refined stratigraphic framework and active exploration provided impetus to develop a forward stratigraphic model of this section to better predict the distribution of reservoir and seal relationships. The approximately 30 m.y. interval modeled is composed of 2 km of platform strata and 3 km of basinal strata divided into 8 composite sequences (average 3 m.y. duration) and 45 high-frequency sequences (400 ky m.y. duration). A 130 km dip section through the basin margin Guadalupe/Deleware Mountain outcrop is inversely modeled to derive local tectonic subsidence and a sea level curve for the Permian. In this process, the highest and lowest shoreline positions of each sequence are interpreted based on facies description which are assumed to approximate the highest and lowest relative sea level. A eustatic sea level curve is calculated by restoring these shoreline positions and removing local tectonic subsidence using a polynomial fit to the derived relative sea level curve. The quantitatively constrained curve for the Permian contains 2nd, 3rd, and 4th order 180m. This quantitatively constrained accommodation history (calculated eustatic curve and subsidence history) are input into the PHIL forward modeling program. Model variables of sediment supply are depositional system are adjusted to match known outcrop relations. The resulting model is potentially capable of predicting stratigraphy elsewhere in the basin using only subsidence history data from the inverse model.

  16. Forward stratigraphic modeling of the Permian of the Delaware Basin

    SciTech Connect

    Qiucheng, Ye; Kerans, C.; Bowman, S.

    1996-12-31

    Permian platform-to-basin strata of the Delaware Basin In west Texas and New Mexico represent one of the world`s most complete, best studied, and most hydrocarbon productive records of this geologic period in the world. This superb marriage of a refined stratigraphic framework and active exploration provided impetus to develop a forward stratigraphic model of this section to better predict the distribution of reservoir and seal relationships. The approximately 30 m.y. interval modeled is composed of 2 km of platform strata and 3 km of basinal strata divided into 8 composite sequences (average 3 m.y. duration) and 45 high-frequency sequences (400 ky m.y. duration). A 130 km dip section through the basin margin Guadalupe/Deleware Mountain outcrop is inversely modeled to derive local tectonic subsidence and a sea level curve for the Permian. In this process, the highest and lowest shoreline positions of each sequence are interpreted based on facies description which are assumed to approximate the highest and lowest relative sea level. A eustatic sea level curve is calculated by restoring these shoreline positions and removing local tectonic subsidence using a polynomial fit to the derived relative sea level curve. The quantitatively constrained curve for the Permian contains 2nd, 3rd, and 4th order 180m. This quantitatively constrained accommodation history (calculated eustatic curve and subsidence history) are input into the PHIL forward modeling program. Model variables of sediment supply are depositional system are adjusted to match known outcrop relations. The resulting model is potentially capable of predicting stratigraphy elsewhere in the basin using only subsidence history data from the inverse model.

  17. Searching for stratigraphic traps in the Neuquen basin of Argentina

    SciTech Connect

    Blangy, J.P.; Follis, M.; Tavella, G.; Wright, C.

    1996-08-01

    Amoco Argentina oil Company secured a farm-in from YPF (50-50 partnership) over the blocks CN-VIII and ON-IX in the Neuquen basin of Argentina. Primary reservoir horizons are Late Jurassic and Early Cretaceous eolian sands. The petrophysical properties of these dunal sands contrast-sometimes sharply-with those of the silts and shales of similar age in the immediate area. Initial evaluation of the blocks had recognized stratigraphic potential associated with the dunal facies, especially in the CN-VIII block. The presence of reservoir quality Avile sands (Barremian age, 18-20% porosity) was mapped on the CN-VIII block directly from older vintage seismic. (1) Seismic Acquisition: Amoco shot approximately 400 km of high resolution 120-fold seismic in late 1994 to high-grade those leads identified on the old seismic. The CN-VIII block is partially covered by basalts of varying thickness. The Amoco survey resulted in an improved penetration through the basalts; it also had a much higher frequency content and yielded superior bed resolution than any previous survey in the area. (2) Seismic Processing and Modeling: Amoco reprocessed inhouse several key lines over producing fields in the immediate area and approximately 200 km of seismic from the 1994 survey in the CN-VIll block for detailed amplitude analysis. Seismic amplitude models [including (1) 2-D stratigraphic pinchout models describing the presence of porous sand lenses, and (2) AVO models] tie the 1994 data very well. (3) Integrated Seismic Interpretation and Reduction of Technical RISK: The integration of various disciplines (Petrophysics, Geophysics, Geology, and Engineering) resulted in the calibration/ranking of seismic responses observed over the CN-VIII area, thus substantially reducing the RISK on trap definition, reservoir quality, seal, and product associated with the early leads.

  18. Cenozoic stratigraphic evolution, North Sea and Labrador Sea

    SciTech Connect

    Gradstein, F.M.; Grant, A.C.; Mudford, B.S. ); Berggren, W.A. ); Kaminski, M.A. ); D'Lorio, M.A. ); Cloetingh, S. ); Griffiths, C.M. )

    1990-05-01

    The authors are studying Cenozoic correlation patterns, burial trends, and subsidence history of the Central North Sea, Labrador, and Orphan basins. The authors objectives are (1) to detail intraregional mid-high latitude biozonations using noise filtering and probabilistic zonation techniques; (2) to detail paleobathymetric trends from basin margins to centers; (3) to apply this knowledge to model basin evolution, in the perspective of the evolving North Atlantic Ocean; (4) to evaluate causes for the occurrence of major hiatuses and rapid changes of subsidence; and (5) to relate rapid changes in sedimentation in the last few millions of years to model observed undercompaction trends. Cenozoic microfossil assemblages in these basins are similar, related to similarities in sedimentary and paleoeceanographic conditions. In more basinal wells, flysch-type agglutinated foraminiferal assemblages occur, also known from Carpathians, Trinidad, and Moroccan foredeeps. Over 90% of agglutinated taxa are common between these basins, although local stratigraphic ranges vary sufficiently to rely on the concept of average ranges, rather than total ones for correlations. Cenozoic stratigraphic resolution in the North Sea and Labrador basins generally is in 3-5-Ma units. and paleobathymetric zonations define a minimum of five niches, from inner shelf to middle slope regimes. Significant hiatuses occurred in the late Eocene through the Miocene, particularly in northern Labrador and northern North Sea. Subsidence in the Labrador/Grand Banks passive margin half grabens was strongly influenced by Labrador Sea opening between anomalies 34 (Campanian) and 13 (early Oligocene), when subsidence exceeded sedimentation and bathyal conditions prevailed along the margin. Thermally induced subsidence in the central North Sea grabens was considerable in the late Paleocene, when the Norwegian Sea started to open.

  19. The Stratigraphic Expression of Formative Processes in Channels

    NASA Astrophysics Data System (ADS)

    Hubbard, S. M.; Covault, J. A.; Fildani, A.; Romans, B.

    2014-12-01

    The stratigraphic record of sinuous fluvial and deep sea channel deposits contains a wealth of information about formative sedimentary processes. For fluvial systems, deposits are considered in the context of processes observed in rivers, with the point bar facies model, as an example, representing a well-established linkage between process and product. A direct link has not been achieved in the deep sea as direct monitoring of coarse-grained sediment transport is challenging, exacerbated by the sporadic and infrequent nature of flows. Until a method for direct observation is developed and widely applied, the stratigraphic record of sediment transfer in the deep sea provides a critical perspective and unique insight into processes that shape not only ancient basin margin slopes, but also the present day seascape. Despite the obvious similarity in sinuous planforms of open, single thread fluvial and deep sea channels, outcrop characteristics, validated in many instances by experimental and theoretical work, indicate different processes. Meandering fluvial systems are most commonly represented by deposits that reflect point bar migration, a process whereby bank erosion and bar growth are genetically linked. At the bed scale, cross-stratification reflects bedload sediment transport and deposition by traction sedimentation. Single thread deep sea channel-fill strata are commonly characterized by sandstone-filled channelform bodies, which reflect both traction and suspension sedimentation. Heterolithic thin beds and cross-stratification can be locally preserved above channel bases and against channel margins, but the majority of depositional thickness comprises tabular sandstone turbidites that bi-directionally lap onto channel edges. The stratal record indicates a distinction between phases of channel maintenance (e.g., erosion, sediment bypass) and phases of substantial infilling with coarse-grained sediment - they are not contemporaneous. This is a key departure from

  20. Chemical Contaminants as Stratigraphic Markers for the Anthropocene

    NASA Astrophysics Data System (ADS)

    Kruge, M. A.

    2012-12-01

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

  1. Automated discovery of structural features of the optic nerve head on the basis of image and genetic data

    NASA Astrophysics Data System (ADS)

    Christopher, Mark; Tang, Li; Fingert, John H.; Scheetz, Todd E.; Abramoff, Michael D.

    2014-03-01

    Evaluation of optic nerve head (ONH) structure is a commonly used clinical technique for both diagnosis and monitoring of glaucoma. Glaucoma is associated with characteristic changes in the structure of the ONH. We present a method for computationally identifying ONH structural features using both imaging and genetic data from a large cohort of participants at risk for primary open angle glaucoma (POAG). Using 1054 participants from the Ocular Hypertension Treatment Study, ONH structure was measured by application of a stereo correspondence algorithm to stereo fundus images. In addition, the genotypes of several known POAG genetic risk factors were considered for each participant. ONH structural features were discovered using both a principal component analysis approach to identify the major modes of variance within structural measurements and a linear discriminant analysis approach to capture the relationship between genetic risk factors and ONH structure. The identified ONH structural features were evaluated based on the strength of their associations with genotype and development of POAG by the end of the OHTS study. ONH structural features with strong associations with genotype were identified for each of the genetic loci considered. Several identified ONH structural features were significantly associated (p < 0.05) with the development of POAG after Bonferroni correction. Further, incorporation of genetic risk status was found to substantially increase performance of early POAG prediction. These results suggest incorporating both imaging and genetic data into ONH structural modeling significantly improves the ability to explain POAG-related changes to ONH structure.

  2. Structure tensor based automated detection of macular edema and central serous retinopathy using optical coherence tomography images.

    PubMed

    Hassan, Bilal; Raja, Gulistan; Hassan, Taimur; Usman Akram, M

    2016-04-01

    Macular edema (ME) and central serous retinopathy (CSR) are two macular diseases that affect the central vision of a person if they are left untreated. Optical coherence tomography (OCT) imaging is the latest eye examination technique that shows a cross-sectional region of the retinal layers and that can be used to detect many retinal disorders in an early stage. Many researchers have done clinical studies on ME and CSR and reported significant findings in macular OCT scans. However, this paper proposes an automated method for the classification of ME and CSR from OCT images using a support vector machine (SVM) classifier. Five distinct features (three based on the thickness profiles of the sub-retinal layers and two based on cyst fluids within the sub-retinal layers) are extracted from 30 labeled images (10 ME, 10 CSR, and 10 healthy), and SVM is trained on these. We applied our proposed algorithm on 90 time-domain OCT (TD-OCT) images (30 ME, 30 CSR, 30 healthy) of 73 patients. Our algorithm correctly classified 88 out of 90 subjects with accuracy, sensitivity, and specificity of 97.77%, 100%, and 93.33%, respectively.

  3. Hydraulically-distinct, Stratigraphic Horizons in the Southern Margin of the Utopia Impact Basin, Mars.

    NASA Astrophysics Data System (ADS)

    Skinner, J. A.

    2005-12-01

    The southern Utopia boundary plain may have formed due to pre-Hesperian detrital aggradations in the annular rings of the Early Noachian-age Utopia multi-ring impact structure. These ring-basin sequences likely controlled the location and intensity of Hesperian-age resurfacing in the boundary plain. Previous researchers delineated stratigraphic horizons in other regions based on model calculations, wall-rock exposures, and terrestrial analogs. Here, I extrapolate and expand these models by proposing that the southern Utopia ring-basin sequences are uniquely composed of three hydraulically-distinct stratigraphic zones, as follows: (1) a fractured zone that contains >7-km-thick, deeply-buried, intensely-fractured, primordial basement rocks with moderate bulk permeability and a low percentage of compactable, interconnected pore-space; (2) an ejecta zone that contains <2-km of poorly-sorted, poorly-consolidated, impact-related material with low bulk permeability and a moderate percentage of compactable, poorly-connected pore-space; and (3) a detrital zone that constitutes a <1-km-thick zone of mechanically- and chemically-weathered erosional by-products. Detrital zone materials are moderately- to well-sorted, weakly-consolidated, and characteristically fine in the upward direction, decreasing in percentage of well-connected pore-space from >25% to <1% from bottom to top, with equivalent decreasing values of permeability. Hesperian-age soft-sediment and related landforms unique to the southern Utopia boundary plain allude to the presence of buried mechanical weaknesses and significant reservoirs of volatile-rich strata available for mobilization and diapir-like ascent. The above stratigraphic model has distinctly-layered hydraulic and mechanical properties where pore-fluids would migrate primarily in the lower extremities of the detrital zone and in the fractured zone, each separated by the low-permeability, high-porosity, mechanically-weak, ejecta zone aquitard

  4. Offshore Stratigraphic Controls on Salt-Water Intrusion in Los Angeles Area Coastal Aquifers

    NASA Astrophysics Data System (ADS)

    Edwards, B. D.; Ponti, D. J.; Ehman, K. D.; Tinsley, J. C.; Reichard, E. G.

    2002-12-01

    Ground water is a major component of the water supply for the ~10 million residents of Los Angeles County. Ground water pumping, linked to population growth since the early 1900's, caused water levels to decline, reversed seaward hydraulic gradients in some coastal aquifers, and resulted in salt water intrusion. United States Geological Survey geologists and hydrologists are working cooperatively with local water agencies to (1) understand and model the process of salt-water intrusion in this siliciclastic, structurally complex basin, and (2) identify potential pathways for the salt-water intrusion. We collected over 2000 trackline-km of single- and multi-channel intermediate- and high-resolution seismic-reflection profiles (60 to 5000 Hz) from the Los Angeles/Long Beach Harbor complex and the adjacent San Pedro shelf to develop a 3-dimensional stratigraphic model of the coastal aquifer system. These data define stratal geometries, paleo-channels, and fault traces in the offshore that are potential pathways of salt-water intrusion. The offshore seismic-reflection profiles correlate with onshore geophysical and borehole data collected from four nearby drill sites that were cored continuously to depths ranging to 400 meters. These core holes provide detailed 1-dimensional reference sections that furnish stratigraphic, age, and facies control for the seismic-reflection profiles. The coastal aquifer system is described using sequence stratigraphic concepts as units deposited during eustatic sea level fluctuations during the Pleistocene to Recent. Seismic-reflection profiles identify sequence boundaries, and hence aquifer and aquitard units, by the truncation and onlap of reflectors. If and where the sequences crop out on the sea floor provides a potential pathway for intrusion. The youngest unit, the Gaspur aquifer, is intruded with salt water and consists of at least two flat-lying sequences, each marked by basal gravelly sands deposited by the ancestral Los Angeles

  5. Influence of water and sediment supply on the stratigraphic record of alluvial fans and deltas: Process controls on stratigraphic completeness

    NASA Astrophysics Data System (ADS)

    Straub, Kyle M.; Esposito, Christopher R.

    2013-06-01

    contains the most complete record of information necessary to quantitatively reconstruct paleolandscape dynamics, but this record contains significant gaps over a range of time and space scales. These gaps result from stasis on geomorphic surfaces and erosional events that remove previously deposited sediment. Building on earlier statistical studies, we examine stratigraphic completeness in three laboratory experiments where the topography of aggrading deltas was monitored at high temporal and spatial scales. The three experiments cover unique combinations in the absolute magnitudes of sediment and water discharge in addition to generation of accommodation space through base-level rise. This analysis centers on three time scales: (1) the time at which a record is discretized (t), (2) the time necessary to build a deposit with mean thickness equivalent to the maximum roughness on a surface (Tc), and (3) the time necessary for channelized flow to migrate over all locations in a basin (Tch). These time scales incorporate information pertaining to the time-variant topography of actively changing surfaces, kinematics by which the surfaces are changing, and net deposition rate. We find that stratigraphic completeness increases as a function of t/Tc but decreases as a function of Tc/Tch over the parameter space covered in the experiments. Our results suggest that environmental signals disconnected from a sediment routing system are best preserved in systems with low Tc values. Nondimensionalizing t by Tc, however, shows that preservation of information characterizing system morphodynamics is best preserved in stratigraphy constructed by systems with low water to sediment flux ratios.

  6. Elucidating structural order and disorder phenomena in mullite-type Al4B2O9 by automated electron diffraction tomography

    NASA Astrophysics Data System (ADS)

    Zhao, Haishuang; Krysiak, Yaşar; Hoffmann, Kristin; Barton, Bastian; Molina-Luna, Leopoldo; Neder, Reinhard B.; Kleebe, Hans-Joachim; Gesing, Thorsten M.; Schneider, Hartmut; Fischer, Reinhard X.; Kolb, Ute

    2017-05-01

    The crystal structure and disorder phenomena of Al4B2O9, an aluminum borate from the mullite-type family, were studied using automated diffraction tomography (ADT), a recently established method for collection and analysis of electron diffraction data. Al4B2O9, prepared by sol-gel approach, crystallizes in the monoclinic space group C2/m. The ab initio structure determination based on three-dimensional electron diffraction data from single ordered crystals reveals that edge-connected AlO6 octahedra expanding along the b axis constitute the backbone. The ordered structure (A) was confirmed by TEM and HAADF-STEM images. Furthermore, disordered crystals with diffuse scattering along the b axis are observed. Analysis of the modulation pattern implies a mean superstructure (AAB) with a threefold b axis, where B corresponds to an A layer shifted by ½a and ½c. Diffraction patterns simulated for the AAB sequence including additional stacking disorder are in good agreement with experimental electron diffraction patterns.

  7. Stratigraphic evidence for Devonian tectonism on lineaments at Allegheny Front, West Virginia; supporting material

    USGS Publications Warehouse

    Wheeler, R.L.

    1983-01-01

    At the Allegheny Front in northeastern West Virginia, five large structural lineaments trend northwesterly to westerly across the structural grain. This paper concludes that two and perhaps three of them separated structures that were active in Devonian time. Along strike over about 200 km of the Front, J. M. Dennison and coworkers recognized and mapped numerous, mostly thin, shale, siltstone, sandstone, and limestone units in 18 measured sections between the Early Devonian Oriskany Sandstone and the Late Devonian Hampshire Formation. Many of these units terminate in intervals between measured sections. Nonparametric statistical analysis reveals that significant numbers of stratigraphic terminations occur in and between intervals in which three of the five lineaments intersect the Front. The Petersburg and Fairmont-Rowlesburg and perhaps the Bartow lineaments were loci of structural control over topography, bathymetry, or both, and of structural influence on patterns of influx and dispersal of clastic sediment. It is not clear whether this pre-Alleghany activity reflects intermittent motion (1) on a strike-transverse basement fault, as occurred under similar lineaments in Pennsylvania and Alabama, or (2) between Paleozoic thrust masses advancing somewhat independently of each other. However, if the Petersburg lineament formed over a basement fault, it cannot still overlie it because the rocks containing the lineament have been detached and transported too far to the northwest. Of the five lineaments considered, the one most likely to have formed over and to still overlie a basement fault is the Parsons lineament, especially in its northwestern portion in the eastern Plateau province.

  8. Mechanical Alteration And Contamination Issues In Automated Subsurface Sample Acquisition And Handling

    NASA Astrophysics Data System (ADS)

    Glass, B. J.; Cannon, H.; Bonaccorsi, R.; Zacny, K.

    20