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Sample records for automated stratigraphic structural

  1. 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%.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Structural and Stratigraphic Evolution of the Iberia and Newfoundland Rifted Margins: A Quantitative Modeling Approach

    NASA Astrophysics Data System (ADS)

    Mohn, G.; Karner, G. D.; Manatschal, G.; Johnson, C. A.

    2014-12-01

    Rifted margins develop generally through polyphased extensional events leading eventually to break-up. We investigate the spatial and temporal evolution of the Iberia-Newfoundland rifted margin from its Permian post-orogenic stage to early Cretaceous break-up. We have applied Quantitative Basin Analysis to integrate seismic stratigraphic interpretations and drill hole data of representative sections across the Iberia-Newfoundland margins with kinematic models for the thinning of the lithosphere and subsequent isostatic readjustment. Our goal is to predict the distribution of extension and thinning, environments of deposition, crustal structure and subsidence history as functions of space and time. The first sediments deposited on the Iberian continental crust were in response to Permian lithospheric thinning, associated with magmatic underplating and subsequent thermal re-equilibration of the lithosphere. During late Triassic-early Jurassic rifting, a broadly distributed depth-independent lithospheric extension occurred, followed by late Jurassic rifting that increasingly focused with time and became depth-dependent during the early Cretaceous. However, there exists a temporality in the along-strike deformation of the Iberia-Newfoundland margin: significant Valanginian-Hauterivian deformation characterizes the northern Galicia Bank-Flemish Cap while the southern Iberian-Newfoundland region is characterized by Tithonian-early Berriasian extension. Deformation localized with time on both margins leading to late Aptian break-up. To match the distribution and magnitude of subsidence across the profiles requires significant thinning of middle/lower crustal level and subcontinental lithospheric mantle, leading to the formation of the hyper-extended domains. The late-stage deformation of both margins was characterized by a predominantly brittle deformation of the residual continental crust, leading to exhumation of subcontinental mantle and ultimately to seafloor

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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…

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.…

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. 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.

  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. 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.

  16. Structural and stratigraphic evolution of the Iberia and Newfoundland hyper-extended rifted margins: A quantitative modeling approach

    NASA Astrophysics Data System (ADS)

    Mohn, Geoffroy; Karner, Garry; Manatschal, Gianreto; Johnson, Christopher

    2014-05-01

    Rifted margins develop through polyphased extensional events leading eventually to break-up. Of particular interests are the stratigraphic and subsidence evolutions of these polyphased rift events. In this contribution, we investigate the spatial and temporal evolution of the Iberia-Newfoundland rift system from the Permian, post-orogenic development of European crust to early Cretaceous break-up on the continental lithosphere between Iberia and Newfoundland. Based on seismic reflection and refraction and ODP drill data combined with a kinematic and flexural model for the deformation of the lithosphere, we explore the general tectono-stratigraphic evolution of Iberia-Newfoundland rift system and its relationship to repeated lithospheric thinning events. Our results emphasize the kinematic and isostatic interactions engendered by the distinct distribution, amplitude and depth-partitioning of extensional events that allowed the formation of the Iberia-Newfoundland rift system. The initial stratigraphic record is controlled by Permian, post-orogenic topographic erosion, lithospheric thinning, and its subsequent thermal re-equilibration that lead to a regional subsidence characterized by non-marine to marine sedimentation. During late Triassic and early Jurassic time, extensional deformation was characterized by broadly-distributed depth uniform thinning related to minor thinning of the crust. From the Late Jurassic onward, extensional deformation was progressively localized and associated with depth-dependent thinning that finally lead to the formation of hyper-extended domains pre-dating the Late Aptian/Early Albian break-up of the Iberia-Newfoundland continental lithosphere. In particular, extension was diachronous, propagating in severity from south to north - while the southern Iberian margin was undergoing significant thinning in the Tithonian-early Berriasian, the northern margin (i.e., Galicia Bank) had yet to start rifting. Break-up is likewise diachronous

  17. 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.

  18. 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.

  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. 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.

  1. 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

  2. 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

  3. 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.

  4. 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)

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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 =...

  6. 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 =...

  7. 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 =...

  8. 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 =...

  9. 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 =...

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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.

  19. Registration and machine learning-based automated segmentation of subcortical and cerebellar brain structures.

    PubMed

    Powell, Stephanie; Magnotta, Vincent A; Johnson, Hans; Jammalamadaka, Vamsi K; Pierson, Ronald; Andreasen, Nancy C

    2008-01-01

    The large amount of imaging data collected in several ongoing multi-center studies requires automated methods to delineate brain structures of interest. We have previously reported on using artificial neural networks (ANN) to define subcortical brain structures. Here we present several automated segmentation methods using multidimensional registration. A direct comparison between template, probability, artificial neural network (ANN) and support vector machine (SVM)-based automated segmentation methods is presented. Three metrics for each segmentation method are reported in the delineation of subcortical and cerebellar brain regions. Results show that the machine learning methods outperform the template and probability-based methods. Utilization of these automated segmentation methods may be as reliable as manual raters and require no rater intervention.

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  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. 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.

  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. 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

  11. 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.

  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. 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.

  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 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.

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. [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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  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. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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%.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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)

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  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. 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.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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/.

  4. 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

  5. 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

  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. 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…

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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

  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. 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

  19. 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.

  20. 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

  1. 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.

  2. 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.

  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. 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

  5. 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.

  6. 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.

  7. 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:…

  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. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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).

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. Evidence for Cambrian deformation in the Ellsworth-Whitmore Mountains terrane, Antarctica: Stratigraphic and tectonic implications

    NASA Astrophysics Data System (ADS)

    Duebendorfer, Ernest M.; Rees, Margaret N.

    1998-01-01

    The Ellsworth-Whitmore Mountains terrane is a large geologically and geophysically defined crustal block that lies between the Transantarctic Mountains and West Antarctica. The Cambrian position of the terrane is controversial, with many workers placing it between East Antarctica and southern Africa and distant from Cambrian orogenic belts. We present structural and stratigraphic evidence for Cambrian deformation in the Heritage Range, Ellsworth Mountains. From our revised stratigraphy and structural history of the Heritage Range, we propose that the Ellsworth-Whitmore Mountains block was located within the belt of Pan-African deformation, within the Late Cambrian continental arc, and was part of a collage of allochthonous terranes that included the Queen Maud terrane and probably the Bowers terrane of Antarctica. These terranes were situated outboard of Coats Land in the Cambrian and were subsequently translated and accreted to East Antarctica, probably during early Paleozoic time.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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

  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. 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

  7. 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.

  8. 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.

  9. 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.

  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. 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).

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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

  19. 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.

    2006-12-01

    order to obtain cores and ice profiles at the drilling site. In the course of DAME drilling automation testing, the drilling-induced temperature gradients and their effects on encountered subsurface permafrost and ice layers were observed while drilling in frozen impact breccia at Haughton Crater. In repeated tests of robotic core removal processing and handling in the MARTE project, including field tests, cross-contamination issues arose between successive cores and samples, and procedures and metrics were developed for minimizing the cross-contamination. The MARTE core processing cross-contamination aspects were tested by analyzing a set of pristine samples (those stratigraphically known) vs. cuttings (loose clays) or artifacts from the robotic drilling (indurated clay layers). MARTE ground truth drilling, in parallel with the automated tests, provided control information on the discontinuity/continuity of the stratigraphic record (i.e., texture, color and structure of loose and consolidated materials).

  20. Structure-Function Modeling of Optical Coherence Tomography and Standard Automated Perimetry in the Retina of Patients with Autosomal Dominant Retinitis Pigmentosa

    PubMed Central

    Smith, Travis B.; Parker, Maria; Steinkamp, Peter N.; Weleber, Richard G.; Smith, Ning; Wilson, David J.

    2016-01-01

    Purpose To assess relationships between structural and functional biomarkers, including new topographic measures of visual field sensitivity, in patients with autosomal dominant retinitis pigmentosa. Methods Spectral domain optical coherence tomography line scans and hill of vision (HOV) sensitivity surfaces from full-field standard automated perimetry were semi-automatically aligned for 60 eyes of 35 patients. Structural biomarkers were extracted from outer retina b-scans along horizontal and vertical midlines. Functional biomarkers were extracted from local sensitivity profiles along the b-scans and from the full visual field. These included topographic measures of functional transition such as the contour of most rapid sensitivity decline around the HOV, herein called HOV slope for convenience. Biomarker relationships were assessed pairwise by coefficients of determination (R2) from mixed-effects analysis with automatic model selection. Results Structure-function relationships were accurately modeled (conditional R2>0.8 in most cases). The best-fit relationship models and correlation patterns for horizontally oriented biomarkers were different than vertically oriented ones. The structural biomarker with the largest number of significant functional correlates was the ellipsoid zone (EZ) width, followed by the total photoreceptor layer thickness. The strongest correlation observed was between EZ width and HOV slope distance (marginal R2 = 0.85, p<10−10). The mean sensitivity defect at the EZ edge was 7.6 dB. Among all functional biomarkers, the HOV slope mean value, HOV slope mean distance, and maximum sensitivity along the b-scan had the largest number of significant structural correlates. Conclusions Topographic slope metrics show promise as functional biomarkers relevant to the transition zone. EZ width is strongly associated with the location of most rapid HOV decline. PMID:26845445

  1. 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

  2. Automated 3D architecture reconstruction from photogrammetric structure-and-motion: A case study of the One Pilla pagoda, Hanoi, Vienam

    NASA Astrophysics Data System (ADS)

    To, T.; Nguyen, D.; Tran, G.

    2015-04-01

    Heritage system of Vietnam has decline because of poor-conventional condition. For sustainable development, it is required a firmly control, space planning organization, and reasonable investment. Moreover, in the field of Cultural Heritage, the use of automated photogrammetric systems, based on Structure from Motion techniques (SfM), is widely used. With the potential of high-resolution, low-cost, large field of view, easiness, rapidity and completeness, the derivation of 3D metric information from Structure-and- Motion images is receiving great attention. In addition, heritage objects in form of 3D physical models are recorded not only for documentation issues, but also for historical interpretation, restoration, cultural and educational purposes. The study suggests the archaeological documentation of the "One Pilla" pagoda placed in Hanoi capital, Vietnam. The data acquired through digital camera Cannon EOS 550D, CMOS APS-C sensor 22.3 x 14.9 mm. Camera calibration and orientation were carried out by VisualSFM, CMPMVS (Multi-View Reconstruction) and SURE (Photogrammetric Surface Reconstruction from Imagery) software. The final result represents a scaled 3D model of the One Pilla Pagoda and displayed different views in MeshLab software.

  3. Automated three-dimensional registration and volume rebuilding for wide-field angiographic and structural optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Zang, Pengxiao; Liu, Gangjun; Zhang, Miao; Wang, Jie; Hwang, Thomas S.; Wilson, David J.; Huang, David; Li, Dengwang; Jia, Yali

    2017-02-01

    We propose a three-dimensional (3-D) registration method to correct motion artifacts and construct the volume structure for angiographic and structural optical coherence tomography (OCT). This algorithm is particularly suitable for the nonorthogonal wide-field OCT scan acquired by a ultrahigh-speed swept-source system (>200 kHz A-scan rate). First, the transverse motion artifacts are corrected by the between-frame registration based on en face OCT angiography (OCTA). After A-scan transverse translation between B-frames, the axial motions are corrected based on the rebuilt boundary of inner limiting membrane. Finally, a within-frame registration is performed for local optimization based on cross-sectional OCTA. We evaluated this algorithm on retinal volumes of six normal subjects. The results showed significantly improved retinal smoothness in 3-D-registered structural OCT and image contrast on en face OCTA.

  4. Brookian stratigraphic plays in the National Petroleum Reserve - Alaska (NPRA)

    USGS Publications Warehouse

    Houseknecht, David W.

    2003-01-01

    The Brookian megasequence in the National Petroleum Reserve in Alaska (NPRA) includes bottomset and clinoform seismic facies of the Torok Formation (mostly Albian age) and generally coeval, topset seismic facies of the uppermost Torok Formation and the Nanushuk Group. These strata are part of a composite total petroleum system involving hydrocarbons expelled from three stratigraphic intervals of source rocks, the Lower Cretaceous gamma-ray zone (GRZ), the Lower Jurassic Kingak Shale, and the Triassic Shublik Formation. The potential for undiscovered oil and gas resources in the Brookian megasequence in NPRA was assessed by defining five plays (assessment units), one in the topset seismic facies and four in the bottomset-clinoform seismic facies. The Brookian Topset Play is estimated to contain between 60 (95-percent probability) and 465 (5-percent probability) million barrels of technically recoverable oil, with a mean (expected value) of 239 million barrels. The Brookian Topset Play is estimated to contain between 0 (95-percent probability) and 679 (5-percent probability) billion cubic feet of technically recoverable, nonassociated natural gas, with a mean (expected value) of 192 billion cubic feet. The Brookian Clinoform North Play, which extends across northern NPRA, is estimated to contain between 538 (95-percent probability) and 2,257 (5-percent probability) million barrels of technically recoverable oil, with a mean (expected value) of 1,306 million barrels. The Brookian Clinoform North Play is estimated to contain between 0 (95-percent probability) and 1,969 (5-percent probability) billion cubic feet of technically recoverable, nonassociated natural gas, with a mean (expected value) of 674 billion cubic feet. The Brookian Clinoform Central Play, which extends across central NPRA, is estimated to contain between 299 (95-percent probability) and 1,849 (5-percent probability) million barrels of technically recoverable oil, with a mean (expected value) of 973

  5. Using a semi-automated filtering process to improve large footprint lidar sub-canopy elevation models and forest structure metrics

    NASA Astrophysics Data System (ADS)

    Fricker, G. A.; Saatchi, S.; Meyer, V.; Gillespie, T.; Sheng, Y.

    2011-12-01

    Quantification of sub-canopy topography and forest structure is important for developing a better understanding of how forest ecosystems function. This study focuses on a three-step method to adapt discrete return lidar (DRL) filtering techniques to Laser Vegetation Imaging Sensor (LVIS) large-footprint lidar (LFL) waveforms to improve the accuracy of both sub-canopy digital elevation models (DEMs), as well as forest structure measurements. The results of the experiment demonstrate that LFL ground surfaces can be effectively filtered using methods adapted from DRL point filtering methods, and the resulting data will produce more accurate digital elevation models, as well as improved estimates of forest structure. The first step quantifies the slope present at the center of each LFL pulse, and the average error expected at each particular degree of slope is modeled. Areas of high terrain slope show consistently more error in LFL ground detection, and empirical relationships between terrain angle and expected LVIS ground detection error are established. These relationships are then used to create an algorithm for LFL ground elevation correction. The second step uses an iterative, expanding window filter to identify outlier points which are not part of the ground surface, as well as manual editing to identify laser pulses which are not at ground level. The semi-automated methods improved the LVIS DEM accuracy significantly by identifying significant outliers in the LVIS point cloud. The final step develops an approach which utilizes both the filtered LFL DEMs, and the modeled error introduced by terrain slope to improve both sub-canopy elevation models, and above ground LFL waveform metrics. DRL and LVIS data from Barro Colorado Island, Panama, and La Selva, Costa Rica were used to develop and test the algorithm. Acknowledgements: Special thanks to Dr. Jim Dilling for providing the DRL lidar data for Barro Colorado Island.

  6. Intensity targeted radial structure tensor analysis and its application for automated mediastinal lymph node detection from CT volumes

    NASA Astrophysics Data System (ADS)

    Oda, Hirohisa; Nimura, Yukitaka; Oda, Masahiro; Kitasaka, Takayuki; Iwano, Shingo; Honma, Hirotoshi; Takabatake, Hirotsugu; Mori, Masaki; Natori, Hiroshi; Mori, Kensaku

    2016-03-01

    This paper presents a new blob-like enhancement filter based on Intensity Targeted Radial Structure Tensor (ITRST) analysis to improve mediastinal lymph node detection from chest CT volumes. Blob-like structure enhancement filter based on Radial Structure Tensor (RST) analysis can be utilized for initial detection of lymph node candidate regions. However, some of lymph nodes cannot be detected because RST analysis is influenced by neighboring regions whose intensity is very high or low, such as contrast-enhanced blood vessels and air. To overcome the problem, we propose ITRST analysis that integrate the prior knowledge on detection target intensity into RST analysis. Our lymph node detection method consists of two steps. First, candidate regions are obtained by ITRST analysis. Second, false positives (FPs) are removed by the Support Vector Machine (SVM) classifier. We applied the proposed method to 47 cases. Among 19 lymph nodes whose short axis is no less than 10 mm, 100.0 % of them were detected with 247.7 FPs/case by ITRST analysis, while only 80.0 % were detected with 123.0 FPs/case by RST analysis. After the false positive (FP) reduction by SVM, ITRST analysis outperformed RST analysis in lymph node detection performance.

  7. Stratigraphic responses to a major tectonic event in a foreland basin: the Ecuadorian Oriente Basin from Eocene to Oligocene times

    NASA Astrophysics Data System (ADS)

    Christophoul, Frédéric; Baby, Patrice; Dávila, Celso

    2002-02-01

    The Eocene to Oligocene sediments of the Ecuadorian Oriente Basin record two kinds of second-order stratigraphic response to the tectonic evolution. Lower Eocene shows evidences of local scale syntectonic deposits. This tectonic activity can be related to right lateral convergent movements inverting pre-cretaceous extensional structures. Upper Eocene and Oligocene sediments are integrated as the expression of an isostatic rebound characterizing a basin scale syntectonic deposition. This response is evidenced by a reciprocal architecture of the depositional sequences identified in the sedimentary formations. These data have allowed us to propose a new geodynamic model for the Paleogene evolution of the Oriente Basin.

  8. Stratigraphical distribution of the Ordovician conodont Erraticodon Dzik in Argentina

    NASA Astrophysics Data System (ADS)

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

    2013-08-01

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

  9. Upper Paleozoic stratigraphic sequences in the Western Interior, USA

    SciTech Connect

    Maughan, E.K.; Macke, D.L.

    1993-04-01

    Major depositional sequences in the upper Paleozoic (Mississippian through Permian) of the Western Interior reflect either tectonism, eustatic sea-level change, or both. The stratigraphic sequences approximate (1) the Lower Mississippian Lodgepole Limestone of the Madison Group, (2) the Lower and Upper Mississippian Mission Canyon Limestone in the Madison Group, (3) the Upper Mississippian Big Snowy Group, (4) the Lower and Middle Pennsylvanian Amsden Group, (5) the Middle Pennsylvanian and Lower Permian Minnelusa Group, and (6) the Middle and Upper Permian Park City Group. These upper Paleozoic sequences in the Western Interior seem to be intricately related to similar, third-order transgressive-regressive cycles in the Cordilleran region, but precise relationships of some sequence boundaries remain to be determined. Parasequence sets evidence minor eustatic oscillations within these six major Western Interior sequences. The widespread paraconformable contact between Permian and overlying Triassic strata on the Wyoming shelf indicates that this sequence boundary resulted primarily from eustatic marine regression. Overall, the upper Paleozoic sequences of the Western Interior were deposited in a stable epeirogenic framework that succeeded Devonian tectonism but were diastrophically affected again during the Pennsylvanian. The timing of these diastrophic events in the Western Interior seem to coincide with plate collision events along the eastern and southern margins of North America, but eustatic changes may be related to other causes.

  10. Stratigraphic framework and distribution of lignite on Crowleys Ridge, Arkansas

    USGS Publications Warehouse

    Meissner, Charles R.

    1983-01-01

    The purpose of this report is to establish a stratigraphic framework of lignite beds and associated strata of Crowleys Ridge, Arkansas. Drill hole data provided by the Arkansas Geological Commission is used in the synthesis and interpretation. Areas containing lignite of potential resource value are also delineated. To illustrate the regional stratigraphic framework of Crowleys Ridge, a cross section was constructed from logs of selected oil and gas test wells, along or adjacent to the north-south trending ridge over a distance of about 115 miles. This section reveals that lignite-bearing Tertiary formations dip gently southward along the ridge. The Paleocene-Eocene Wilcox Group forms the bedrock in the northern part of the ridge and successively younger bedrock of the Eocene Claiborne and Jackson Groups is identified in the central and southern part of the ridge. Crowleys Ridge is mantled with alluvium and loess of Quaternary age, and sand and gravel beds of the Lafayette Formation of Pliocene (?) age that unconformably overlie the Paleocene and Eocene rocks. The thickness of lignite-bearing sedimentary deposits ranges from 830 feet in the north to 2,480 feet in the south. The Wilcox, Claiborne, and Jackson Groups of Paleocene and Eocene age are believed to be fluvial-deltaic in origin. The detailed vertical and horizontal stratigraphic characteristics and distribution of lignite beds in the sediments were determined by constructing seven cross sections from lithologic and geophysical logs of the lignite investigations on Crowleys Ridge by the Arkansas Geological Commission and private companies. Correlation and interpretation of the lignite-bearing strata reveal ten lignite beds of resource potential. These lignite beds range from a few inches to 9.5 ft in thickness and are assigned to stratigraphic intervals that are designated as zone 1 through 7. Zone 1 is near the middle of the Wilcox Group and zone 7 is near the middle of the overlying Claiborne Group. Some

  11. Stratigraphic placement and age of modern humans from Kibish, Ethiopia.

    PubMed

    McDougall, Ian; Brown, Francis H; Fleagle, John G

    2005-02-17

    In 1967 the Kibish Formation in southern Ethiopia yielded hominid cranial remains identified as early anatomically modern humans, assigned to Homo sapiens. However, the provenance and age of the fossils have been much debated. Here we confirm that the Omo I and Omo II hominid fossils are from similar stratigraphic levels in Member I of the Kibish Formation, despite the view that Omo I is more modern in appearance than Omo II. 40Ar/39Ar ages on feldspar crystals from pumice clasts within a tuff in Member I below the hominid levels place an older limit of 198 +/- 14 kyr (weighted mean age 196 +/- 2 kyr) on the hominids. A younger age limit of 104 +/- 7 kyr is provided by feldspars from pumice clasts in a Member III tuff. Geological evidence indicates rapid deposition of each member of the Kibish Formation. Isotopic ages on the Kibish Formation correspond to ages of Mediterranean sapropels, which reflect increased flow of the Nile River, and necessarily increased flow of the Omo River. Thus the 40Ar/39Ar age measurements, together with the sapropel correlations, indicate that the hominid fossils have an age close to the older limit. Our preferred estimate of the age of the Kibish hominids is 195 +/- 5 kyr, making them the earliest well-dated anatomically modern humans yet described.

  12. Horizontal drilling in the Austin Chalk: Stratigraphic factors

    SciTech Connect

    Durham, C.O. Jr. ); Bobigian, R.A. )

    1990-05-01

    Horizontal drilling has renewed interest in the Austin chalk in south-central Texas. Large fields on opposite sides of the San Marcos arch Giddings to the northeast and Pearsall to the southwest were active with vertical drilling 10 years ago. Giddings' 4,500 Austin wells produced 209 million BO and 934 bcfg of gas through 1988; Pearsall's 1,440 wells produced 57 million BO and 35 bcfg of gas. Most vertical wells were completed, 20% were economic successes, 40% were marginal, 40% were uneconomic due to uneven areal distribution of near-vertical fractures and small faults, which provide reservoirs in otherwise tight chalk. Horizontal drilling, led by Amoco in Giddings and Oryx in Pearsall, enhances the chances of encountering the fractures by drilling perpendicular to the fracture trend. Horizontal drilling requires preselection of the stratigraphic horizon to be penetrated. One must understand the variable Austin stratigraphy to choose the zone with the most brittle character and best matrix porosity, both reduced by increased clay content. Chalk 130 ft thick on the San Marcos arch thickens to 600 to 800 ft in central Giddings field where middle marl separates lower and upper chalk Northeastward only lower chalk is preserved beneath a post-Austin submarine channel. The Austin thickens to 300-500 ft in Pearsall field where middle member ash beds separate lower and upper chalk inhibiting vertical reservoir communication. Locally, on the Pearsall arch, ash is missing, lower chalk thickens, and upper chalk thins.

  13. Basal Murphy belt and Chilhowee Group -- Sequence stratigraphic comparison

    SciTech Connect

    Aylor, J.G. Jr. . Dept. of Geology)

    1994-03-01

    The lower Murphy belt in the central western Blue Ridge is interpreted to be correlative to the Early Cambrian Chilhowee Group of the westernmost Blue Ridge and Appalachian fold and thrust belt. Basal Murphy belt depositional sequence stratigraphy represents a second-order, type-2 transgressive systems tract initiated with deposition of lowstand turbidites of the Dean Formation. These transgressive deposits of the Nantahala and Brasstown Formations are interpreted as middle to outer continental shelf deposits. Cyclic and stacked third-order regressive, coarsening upwards sequences of the Nantahala Formation display an overall increase in feldspar content stratigraphically upsection. These transgressive siliciclastic deposits are interpreted to be conformably overlain by a carbonate highstand systems tract of the Murphy Marble. Palinspastic reconstruction indicates that the Nantahala and Brasstown Formations possibly represent a basinward extension of up to 3 km thick siliciclastic wedge. The wedge tapers to the southwest along the strike of the Murphy belt at 10[degree] and thins northwestward to 2 km in the Tennessee depocenter where it is represented by the Chilhowee Group. The Murphy belt basin is believed to represent a transitional rift-to-drift facies deposited on the lower plate of the southern Blue Ridge rift zone.

  14. Automated method for determination of dissolved organic carbon-water distribution constants of structurally diverse pollutants using pre-equilibrium solid-phase microextraction.

    PubMed

    Ripszam, Matyas; Haglund, Peter

    2015-02-01

    Dissolved organic carbon (DOC) plays a key role in determining the environmental fate of semivolatile organic environmental contaminants. The goal of the present study was to develop a method using commercially available hardware to rapidly characterize the sorption properties of DOC in water samples. The resulting method uses negligible-depletion direct immersion solid-phase microextraction (SPME) and gas chromatography-mass spectrometry. Its performance was evaluated using Nordic reference fulvic acid and 40 priority environmental contaminants that cover a wide range of physicochemical properties. Two SPME fibers had to be used to cope with the span of properties, 1 coated with polydimethylsiloxane and 1 coated with polystyrene divinylbenzene polydimethylsiloxane, for nonpolar and semipolar contaminants, respectively. The measured DOC-water distribution constants showed reasonably good reproducibility (standard deviation ≤ 0.32) and good correlation (R(2)  = 0.80) with log octanol-water partition coefficients for nonpolar persistent organic pollutants. The sample pretreatment is limited to filtration, and the method is easy to adjust to different DOC concentrations. These experiments also utilized the latest SPME automation that largely decreases total cycle time (to 20 min or shorter) and increases sample throughput, which is advantageous in cases when many samples of DOC must be characterized or when the determinations must be performed quickly, for example, to avoid precipitation, aggregation, and other changes of DOC structure and properties. The data generated by this method are valuable as a basis for transport and fate modeling studies.

  15. Automated Approaches to RFI Flagging

    NASA Astrophysics Data System (ADS)

    Garimella, Karthik; Momjian, Emmanuel

    2017-01-01

    It is known that Radio Frequency Interference (RFI) is a major issue in centimeter wavelength radio astronomy. Radio astronomy software packages include tools to excise RFI; both manual and automated utilizing the visibilities (the uv data). Here we present results on an automated RFI flagging approach that utilizes a uv-grid, which is the intermediate product when converting uv data points to an image. It is a well known fact that any signal that appears widespread in a given domain (e.g., image domain) is compact in the Fourier domain (uv-grid domain), i.e., RFI sources that appear as large scale structures (e.g., stripes) in images can be located and flagged using the uv-grid data set. We developed several automated uv-grid based flagging algorithms to detect and excise RFI. These algorithms will be discussed, and results of applying them to measurement sets will be presented.

  16. Determination of molecular structures of HIV envelope glycoproteins using cryo-electron tomography and automated sub-tomogram averaging.

    PubMed

    Meyerson, Joel R; White, Tommi A; Bliss, Donald; Moran, Amy; Bartesaghi, Alberto; Borgnia, Mario J; de la Cruz, M Jason V; Schauder, David; Hartnell, Lisa M; Nandwani, Rachna; Dawood, Moez; Kim, Brianna; Kim, Jun Hong; Sununu, John; Yang, Lisa; Bhatia, Siddhant; Subramaniam, Carolyn; Hurt, Darrell E; Gaudreault, Laurent; Subramaniam, Sriram

    2011-12-01

    Since its discovery nearly 30 years ago, more than 60 million people have been infected with the human immunodeficiency virus (HIV) (www.usaid.gov). The virus infects and destroys CD4+ T-cells thereby crippling the immune system, and causing an acquired immunodeficiency syndrome (AIDS) (2). Infection begins when the HIV Envelope glycoprotein "spike" makes contact with the CD4 receptor on the surface of the CD4+ T-cell. This interaction induces a conformational change in the spike, which promotes interaction with a second cell surface co-receptor (5,9). The significance of these protein interactions in the HIV infection pathway makes them of profound importance in fundamental HIV research, and in the pursuit of an HIV vaccine. The need to better understand the molecular-scale interactions of HIV cell contact and neutralization motivated the development of a technique to determine the structures of the HIV spike interacting with cell surface receptor proteins and molecules that block infection. Using cryo-electron tomography and 3D image processing, we recently demonstrated the ability to determine such structures on the surface of native virus, at ˜20 Å resolution (9,14). This approach is not limited to resolving HIV Envelope structures, and can be extended to other viral membrane proteins and proteins reconstituted on a liposome. In this protocol, we describe how to obtain structures of HIV envelope glycoproteins starting from purified HIV virions and proceeding stepwise through preparing vitrified samples, collecting, cryo-electron microscopy data, reconstituting and processing 3D data volumes, averaging and classifying 3D protein subvolumes, and interpreting results to produce a protein model. The computational aspects of our approach were adapted into modules that can be accessed and executed remotely using the Biowulf GNU/Linux parallel processing cluster at the NIH (http://biowulf.nih.gov). This remote access, combined with low-cost computer hardware and

  17. Determination of Molecular Structures of HIV Envelope Glycoproteins using Cryo-Electron Tomography and Automated Sub-tomogram Averaging

    PubMed Central

    Meyerson, Joel R.; White, Tommi A.; Bliss, Donald; Moran, Amy; Bartesaghi, Alberto; Borgnia, Mario J.; de la Cruz, M. Jason V.; Schauder, David; Hartnell, Lisa M.; Nandwani, Rachna; Dawood, Moez; Kim, Brianna; Kim, Jun Hong; Sununu, John; Yang, Lisa; Bhatia, Siddhant; Subramaniam, Carolyn; Hurt, Darrell E.; Gaudreault, Laurent; Subramaniam, Sriram

    2011-01-01

    Since its discovery nearly 30 years ago, more than 60 million people have been infected with the human immunodeficiency virus (HIV) (www.usaid.gov). The virus infects and destroys CD4+ T-cells thereby crippling the immune system, and causing an acquired immunodeficiency syndrome (AIDS) 2. Infection begins when the HIV Envelope glycoprotein "spike" makes contact with the CD4 receptor on the surface of the CD4+ T-cell. This interaction induces a conformational change in the spike, which promotes interaction with a second cell surface co-receptor 5,9. The significance of these protein interactions in the HIV infection pathway makes them of profound importance in fundamental HIV research, and in the pursuit of an HIV vaccine. The need to better understand the molecular-scale interactions of HIV cell contact and neutralization motivated the development of a technique to determine the structures of the HIV spike interacting with cell surface receptor proteins and molecules that block infection. Using cryo-electron tomography and 3D image processing, we recently demonstrated the ability to determine such structures on the surface of native virus, at ˜20 Å resolution 9,14. This approach is not limited to resolving HIV Envelope structures, and can be extended to other viral membrane proteins and proteins reconstituted on a liposome. In this protocol, we describe how to obtain structures of HIV envelope glycoproteins starting from purified HIV virions and proceeding stepwise through preparing vitrified samples, collecting, cryo-electron microscopy data, reconstituting and processing 3D data volumes, averaging and classifying 3D protein subvolumes, and interpreting results to produce a protein model. The computational aspects of our approach were adapted into modules that can be accessed and executed remotely using the Biowulf GNU/Linux parallel processing cluster at the NIH (http://biowulf.nih.gov). This remote access, combined with low-cost computer hardware and high

  18. Space power subsystem automation technology

    NASA Technical Reports Server (NTRS)

    Graves, J. R. (Compiler)

    1982-01-01

    The technology issues involved in power subsystem automation and the reasonable objectives to be sought in such a program were discussed. The complexities, uncertainties, and alternatives of power subsystem automation, along with the advantages from both an economic and a technological perspective were considered. Whereas most spacecraft power subsystems now use certain automated functions, the idea of complete autonomy for long periods of time is almost inconceivable. Thus, it seems prudent that the technology program for power subsystem automation be based upon a growth scenario which should provide a structured framework of deliberate steps to enable the evolution of space power subsystems from the current practice of limited autonomy to a greater use of automation with each step being justified on a cost/benefit basis. Each accomplishment should move toward the objectives of decreased requirement for ground control, increased system reliability through onboard management, and ultimately lower energy cost through longer life systems that require fewer resources to operate and maintain. This approach seems well-suited to the evolution of more sophisticated algorithms and eventually perhaps even the use of some sort of artificial intelligence. Multi-hundred kilowatt systems of the future will probably require an advanced level of autonomy if they are to be affordable and manageable.

  19. Tectono-stratigraphic evolution of an inverted extensional basin: the Cameros Basin (north of Spain)

    NASA Astrophysics Data System (ADS)

    Omodeo Salè, Silvia; Guimerà, Joan; Mas, Ramón; Arribas, José

    2014-09-01

    The Cameros Basin is a part of the Mesozoic Iberian Rift. It is an extensional basin formed during the late Jurassic and early Cretaceous, in the Mesozoic Iberian Rift context, and it was inverted in the Cenozoic as a result of the Alpine contraction. This work aims to reconstruct the tectono-stratigraphic evolution of the basin during the Mesozoic, using new and revised field, geophysical and subsurface data. The construction of a basin-wide balanced section with partial restorations herein offers new insights into the geometry of the syn-rift deposits. Field data, seismic lines and oil well data were used to identify the main structures of the basin and the basin-forming mechanisms. Mapping and cross-sectional data indicate the marked thickness variation of the depositional sequences across the basin, suggesting that the extension of the depositional area varied during the syn-rift stage and that the depocentres migrated towards the north. From field observation and seismic line interpretation, an onlap of the depositional sequences to the north, over the marine Jurassic substratum, can be deduced. In the last few decades, the structure and geometry of the basin have been strongly debated. The structure and geometry of the basin infill reconstructed herein strongly support the interpretation of the Cameros Basin as an extensional-ramp synclinal basin formed on a blind south-dipping extensional ramp. The gradual hanging-wall displacement to the south shifted the depocentres to the north over time, thus increasing the basin in size northwards, with onlap geometry on the pre-rift substratum. The basin was inverted by means of a main thrust located in a detachment located in the Upper Triassic beds (Keuper), which branched in depth with the Mesozoic extensional fault flat. The reconstruction of the tectono-stratigraphic evolution of the Cameros Basin proposed herein represents a synthesis and an integration of previous studies of the structure and geometry of the

  20. Use of conditional rule structure to automate clinical decision support: a comparison of artificial intelligence and deterministic programming techniques

    SciTech Connect

    Friedman, R.H.; Frank, A.D.

    1983-08-01

    A rule-based computer system was developed to perform clinical decision-making support within a medical information system, oncology practice, and clinical research. This rule-based system, which has been programmed using deterministic rules, possesses features of generalizability, modularity of structure, convenience in rule acquisition, explanability, and utility for patient care and teaching, features which have been identified as advantages of artificial intelligence (AI) rule-based systems. Formal rules are primarily represented as conditional statements; common conditions and actions are stored in system dictionaries so that they can be recalled at any time to form new decision rules. Important similarities and differences exist in the structure of this system and clinical computer systems utilizing artificial intelligence (AI) production rule techniques. The non-AI rule-based system posesses advantages in cost and ease of implementation. The degree to which significant medical decision problems can be solved by this technique remains uncertain as does whether the more complex AI methodologies will be required. 15 references.

  1. A linear programming approach to reconstructing subcellular structures from confocal images for automated generation of representative 3D cellular models.

    PubMed

    Wood, Scott T; Dean, Brian C; Dean, Delphine

    2013-04-01

    This paper presents a novel computer vision algorithm to analyze 3D stacks of confocal images of fluorescently stained single cells. The goal of the algorithm is to create representative in silico model structures that can be imported into finite element analysis software for mechanical characterization. Segmentation of cell and nucleus boundaries is accomplished via standard thresholding methods. Using novel linear programming methods, a representative actin stress fiber network is generated by computing a linear superposition of fibers having minimum discrepancy compared with an experimental 3D confocal image. Qualitative validation is performed through analysis of seven 3D confocal image stacks of adherent vascular smooth muscle cells (VSMCs) grown in 2D culture. The presented method is able to automatically generate 3D geometries of the cell's boundary, nucleus, and representative F-actin network based on standard cell microscopy data. These geometries can be used for direct importation and implementation in structural finite element models for analysis of the mechanics of a single cell to potentially speed discoveries in the fields of regenerative medicine, mechanobiology, and drug discovery.

  2. Fossils out of sequence: Computer simulations and strategies for dealing with stratigraphic disorder

    SciTech Connect

    Cutler, A.H.; Flessa, K.W. )

    1990-06-01

    Microstratigraphic resolution is limited by vertical mixing and reworking of fossils. Stratigraphic disorder is the degree to which fossils within a stratigraphic sequence are not in proper chronological order. Stratigraphic disorder arises through in situ vertical mixing of fossils and reworking of older fossils into younger deposits. The authors simulated the effects of mixing and reworking by simple computer models, and measured stratigraphic disorder using rank correlation between age and stratigraphic position (Spearman and Kendall coefficients). Mixing was simulated by randomly transposing pairs of adjacent fossils in a sequence. Reworking was simulated by randomly inserting older fossils into a younger sequence. Mixing is an inefficient means of producing disorder; after 500 mixing steps stratigraphic order is still significant at the 99% to 95% level, depending on the coefficient used. Reworking disorders sequences very efficiently: significant order begins to be lost when reworked shells make up 35% of the sequence. Thus a sequence can be dominated by undisturbed, autochthonous shells and still be disordered. The effects of mixing-produced disorder can be minimized by increasing sample size at each horizon. Increased spacing between samples is of limited utility in dealing with disordered sequences: while widely separated samples are more likely to be stratigraphically ordered, the smaller number of samples makes the detection of trends problematic.

  3. Autonomy and Automation

    NASA Technical Reports Server (NTRS)

    Shively, Jay

    2017-01-01

    A significant level of debate and confusion has surrounded the meaning of the terms autonomy and automation. Automation is a multi-dimensional concept, and we propose that Remotely Piloted Aircraft Systems (RPAS) automation should be described with reference to the specific system and task that has been automated, the context in which the automation functions, and other relevant dimensions. In this paper, we present definitions of automation, pilot in the loop, pilot on the loop and pilot out of the loop. We further propose that in future, the International Civil Aviation Organization (ICAO) RPAS Panel avoids the use of the terms autonomy and autonomous when referring to automated systems on board RPA. Work Group 7 proposes to develop, in consultation with other workgroups, a taxonomy of Levels of Automation for RPAS.

  4. Extensional tectonics, halokinesis, eustacy in the Norwegian Central Graben, North Sea: A testing ground for sequence and seismic stratigraphic principles

    SciTech Connect

    Spencer, P.A. ); Prosser, S.D. )

    1996-01-01

    The Norwegian Central Graben is a mature hydrocarbon province with proven reserves within the Upper Jurassic succession. Several phases of extensional tectonics ranging from the Permo-Triassic to the Upper Jurassic, and a thick mobile salt section, serve to complicate a clear regional understanding of the area. A full integration of structural interpretation, seismic and sequence stratigraphic principles, biostratigraphy and core studies is required to achieve a realistic interpretation and predict Upper Jurassic facies distributions within this complex area. Utilizing some 30 wells, regional seismic data and biostratigraphy, candidate sequence boundaries and regionally correlatable flooding surfaces (e.g. Eudoxus), have been identified. Horizon flattening on these surfaces has allowed the recognition of thickening-away reflection geometries adjacent to salt features and divergent geometries into graben boundary faults. This facilitates the identification of the dominant local or regional controls on accommodation space creation. Detailed seismic facies analysis was then used to reveal the relative expansion or suppression of depositional systems tracts as a response to either regional or local structural controls. It was subsequently possible to place these systems within a biostratigraphically constrained regional framework. Mapping the base Zechstein, base Jurassic and base Cretaceous horizons has provided a map view of the active faults and slopes controlling sediment transport at any given time. This provided the third dimension essential in depicting the spatial distribution of depositional systems, and is a crucial component of any sequence stratigraphic interpretation. A regional picture of the progressive evolution of this complex area has been thus been derived, and the effect of both regional and local controls on sequence stratigraphic expressions has been determined.

  5. Extensional tectonics, halokinesis, eustacy in the Norwegian Central Graben, North Sea: A testing ground for sequence and seismic stratigraphic principles

    SciTech Connect

    Spencer, P.A.; Prosser, S.D.

    1996-12-31

    The Norwegian Central Graben is a mature hydrocarbon province with proven reserves within the Upper Jurassic succession. Several phases of extensional tectonics ranging from the Permo-Triassic to the Upper Jurassic, and a thick mobile salt section, serve to complicate a clear regional understanding of the area. A full integration of structural interpretation, seismic and sequence stratigraphic principles, biostratigraphy and core studies is required to achieve a realistic interpretation and predict Upper Jurassic facies distributions within this complex area. Utilizing some 30 wells, regional seismic data and biostratigraphy, candidate sequence boundaries and regionally correlatable flooding surfaces (e.g. Eudoxus), have been identified. Horizon flattening on these surfaces has allowed the recognition of thickening-away reflection geometries adjacent to salt features and divergent geometries into graben boundary faults. This facilitates the identification of the dominant local or regional controls on accommodation space creation. Detailed seismic facies analysis was then used to reveal the relative expansion or suppression of depositional systems tracts as a response to either regional or local structural controls. It was subsequently possible to place these systems within a biostratigraphically constrained regional framework. Mapping the base Zechstein, base Jurassic and base Cretaceous horizons has provided a map view of the active faults and slopes controlling sediment transport at any given time. This provided the third dimension essential in depicting the spatial distribution of depositional systems, and is a crucial component of any sequence stratigraphic interpretation. A regional picture of the progressive evolution of this complex area has been thus been derived, and the effect of both regional and local controls on sequence stratigraphic expressions has been determined.

  6. Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY

    PubMed Central

    2012-01-01

    Background Chemical shift mapping is an important technique in NMR-based drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule's introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically, which is not efficient for high-throughput drug screening. Results We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C-labeling, to resolve the ambiguities for a one-to-one mapping. On the three proteins, it achieves an average accuracy of 94% or better. Conclusions Our mathematical programming approach for modeling chemical shift mapping as a graph problem, while modeling the errors directly, is potentially a time- and cost-effective first step for high-throughput drug screening based on limited NMR data and homologous 3D structures. PMID:22536902

  7. The oligocene stratigraphic framework of the coastal plain of the southeastern United States

    SciTech Connect

    Huddlestun, P.F. )

    1993-03-01

    Four lithostratigraphic associations are recognized in the Oligocene of the southeastern Coastal Plain: (1) an eastern Gulf of Mexico stratigraphic association, (2) a Gulf Trough stratigraphic association, (3) a Florida Bank stratigraphic association and (4), an Atlantic continental shelf stratigraphic association. Oligocene formations and faunal provinces appear to be directly related to the stratigraphic associations. The Vicksburg Group is restricted to the eastern Gulf of Mexico continental shelf stratigraphic association and to the Coastal Plain north and west of the Gulf Trough. The Gulf Trough stratigraphic association includes the Ochlockonee Formation, Wolf Pit Dolostone, Okapilco Limestone, and Bridgeboro Limestone (the Bridgeboro Limestones occurs only on and adjacent to the northern and southern flanks of the trough). The Florida Bank stratigraphic association is largely restricted to the area south of the Gulf Trough and includes the Ellaville Limestone, Suwannacoochee Dolostone, and Suwannee Limestone (the Suwannee Limestone also occurs immediately north of the Gulf Trough in the central Georgia Coastal Plain). The Cooper and Lazaretto Creek Formations are restricted to the Atlantic continental shelf stratigraphic association and occur only in the coastal area of Georgia, South Carolina, and beneath the continental shelf. Three faunal provinces (or subprovinces) are recognized in the southeastern Coastal Plain during the Oligocene: (1) a Gulf of Mexico continental shelf faunal province that characterizes the Gulf Trough and the region north and west of the trough, (2) a Florida province characteristic and largely restricted to the Florida Bank and (3), an Atlantic continental shelf faunal province. Through the Early Oligocene, the trough marked the limits of the Gulf of Mexico and Florida provinces.

  8. Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum.

    PubMed

    Brunger, Axel T; Das, Debanu; Deacon, Ashley M; Grant, Joanna; Terwilliger, Thomas C; Read, Randy J; Adams, Paul D; Levitt, Michael; Schröder, Gunnar F

    2012-04-01

    Phasing by molecular replacement remains difficult for targets that are far from the search model or in situations where the crystal diffracts only weakly or to low resolution. Here, the process of determining and refining the structure of Cgl1109, a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum, at ∼3 Å resolution is described using a combination of homology modeling with MODELLER, molecular-replacement phasing with Phaser, deformable elastic network (DEN) refinement and automated model building using AutoBuild in a semi-automated fashion, followed by final refinement cycles with phenix.refine and Coot. This difficult molecular-replacement case illustrates the power of including DEN restraints derived from a starting model to guide the movements of the model during refinement. The resulting improved model phases provide better starting points for automated model building and produce more significant difference peaks in anomalous difference Fourier maps to locate anomalous scatterers than does standard refinement. This example also illustrates a current limitation of automated procedures that require manual adjustment of local sequence misalignments between the homology model and the target sequence.

  9. Workflow automation architecture standard

    SciTech Connect

    Moshofsky, R.P.; Rohen, W.T.

    1994-11-14

    This document presents an architectural standard for application of workflow automation technology. The standard includes a functional architecture, process for developing an automated workflow system for a work group, functional and collateral specifications for workflow automation, and results of a proof of concept prototype.

  10. Applying high-resolution sequence stratigraphic tools to the Texas continental margin to fine-tune conventional sequence stratigraphic models and improve reservoir prediction

    SciTech Connect

    Anderson, J.A.; Banfield, L.A.; Eckles, B.J.

    1996-12-31

    A regional sequence stratigraphic study of the Texas continental margin resulted in an improved understanding of Pleistocene-Holocene eustatic sea level fluctuations and their influence on depositional environments associated with several distinct systems: the Colorado/Brazos system, the Texas interfluve region, and the Rio Grande system. The dataset consists of approximately 7500 kilometers of high-resolution seismic profiloes, 200 borehole descriptions, and 12 sediment cores. The study involved analysis of three independent variables to better constrain Pleistocene-Holocene sea level history: coastal onlap derived from high-resolution seismic profiles; oxygen isotope data determined from selected sediment cores; and paleoenvironmental data developed from high-resolution micropaleontologic analyses. Combined lithologic data and seismic facies analysis is used to map the distribution of major depositional systems on the shelf during one complete glacial eustatic cycle. Our study provided anopportunity to fine tune conventional stratigraphic models with regard to the distribution of potential reservoirs relative to regionally mappable stratigraphic surfaces.

  11. Applying high-resolution sequence stratigraphic tools to the Texas continental margin to fine-tune conventional sequence stratigraphic models and improve reservoir prediction

    SciTech Connect

    Anderson, J.A.; Banfield, L.A.; Eckles, B.J. )

    1996-01-01

    A regional sequence stratigraphic study of the Texas continental margin resulted in an improved understanding of Pleistocene-Holocene eustatic sea level fluctuations and their influence on depositional environments associated with several distinct systems: the Colorado/Brazos system, the Texas interfluve region, and the Rio Grande system. The dataset consists of approximately 7500 kilometers of high-resolution seismic profiloes, 200 borehole descriptions, and 12 sediment cores. The study involved analysis of three independent variables to better constrain Pleistocene-Holocene sea level history: coastal onlap derived from high-resolution seismic profiles; oxygen isotope data determined from selected sediment cores; and paleoenvironmental data developed from high-resolution micropaleontologic analyses. Combined lithologic data and seismic facies analysis is used to map the distribution of major depositional systems on the shelf during one complete glacial eustatic cycle. Our study provided anopportunity to fine tune conventional stratigraphic models with regard to the distribution of potential reservoirs relative to regionally mappable stratigraphic surfaces.

  12. Sequence stratigraphic framework of Neogene strata in offshore Nigeria

    SciTech Connect

    Pacht, J.A.; Bowen, B.E.; Hall, D.J.

    1996-08-01

    The western portion of the Nigerian continental margin (Dahomey Basin) exhibits stable to moderately unstable progradation. Systems tracts are similar to those described by Vail for stable progradational margins. In contrast, strata off the central and eastern portions of the Nigerian coast (Niger Delta Complex) exhibit highly unstable progradation, and systems tracts are similar to those in Neogene strata of the offshore Gulf of Mexico. Lowstand basin floor fans in both areas are defined by a well-developed upper reflection. This reflection downlaps along the sequence boundary or abuts against the downthrown side of a growth fault surface. Most lower lowstand (slope fan) strata exhibit discontinuous to semi-continuous subparallel reflections. However, this systems tract also contains channel complexes characterized by chaotic bedding with small bright spots and less common large channels, which exhibit concave-upward reflections. In the western portion of the study area, lower lowstand deposits commonly pinch out on the slope. Deposition occurred largely from point sources. In contrast, contemporaneous shallow-water facies are developed in lower lowstand systems tracts in the Niger Delta Complex. Deposition occurred along a line source. Large amplitude anomalies in the upper lowstand (prograding wedge) suggest well-developed sheet sands occur in shallow-water and deep-water in the Niger Delta complex. However, in the Dahomey Basin there is little evidence of deep-water sands in this interval. The transgressive and highstand systems tracts are usually very thin in outer shelf to basin floor strata in both areas. Both the Dahomey Basin and Niger Delta Complex exhibit different stratigraphic geometries, and therefore, require different exploration strategies.

  13. Investigation of a Major Stratigraphic Unconformity with the Curiosity Rover

    NASA Astrophysics Data System (ADS)

    Lewis, K. W.; Grotzinger, J. P.; Gupta, S.; Rubin, D. M.

    2015-12-01

    Since its departure from the plains of Aeolis Palus, the Curiosity rover has traversed through a number of new geologic units at the base of Mount Sharp in Gale crater. These have included both units inferred to comprise the lower strata of Mount Sharp itself, along with units that appear to superpose Mount Sharp. Over the last 100 sols, Curiosity has documented several occurrences of a stratigraphic contact between fine-grained mudstones of the Murray Formation, and coarser sandstones of the overlying Stimson Unit. Detailed mapping from both orbital and rover image and topographic data suggests an unconformable relationship between the two units. From orbit, inferred exposures of the unconformity span at least several tens of meters, climbing up the lowermost slopes of Mount Sharp. Although the absolute timing of the two units is poorly constrained, this unconformity between likely represents a geologically significant gap in time. Deposition of the overlying Stimson Unit is inferred to post-date the large-scale erosion of Mount Sharp, likely requiring late stage aqueous interaction in the lithification of the Stimson Unit. From the rover, stereo imaging reveals the small-scale topography preserved at the Murray-Stimson contact, and allows the determination of bedding geometries within the units. Where laminations are expressed, the basal Mount Sharp rocks exhibit planar stratification at low angles to horizontal. In contrast, the coarser-grained Stimson Unit exhibits large-scale cross stratification. Three dimensional bedding geometry within this unit indicates a predominant southward transport direction uphill towards Mount Sharp. The observation of rounded calcium sulfate clasts in the lowermost Stimson Unit, interpreted to be reworked veins from the underlying Murray formation, supports the interpretation of an erosional unconformity. Investigations at the boundary between these two distinct units present a unique opportunity to probe the long

  14. A method and knowledge base for automated inference of patient problems from structured data in an electronic medical record

    PubMed Central

    Pang, Justine; Feblowitz, Joshua C; Maloney, Francine L; Wilcox, Allison R; Ramelson, Harley Z; Schneider, Louise I; Bates, David W

    2011-01-01

    Background Accurate knowledge of a patient's medical problems is critical for clinical decision making, quality measurement, research, billing and clinical decision support. Common structured sources of problem information include the patient problem list and billing data; however, these sources are often inaccurate or incomplete. Objective To develop and validate methods of automatically inferring patient problems from clinical and billing data, and to provide a knowledge base for inferring problems. Study design and methods We identified 17 target conditions and designed and validated a set of rules for identifying patient problems based on medications, laboratory results, billing codes, and vital signs. A panel of physicians provided input on a preliminary set of rules. Based on this input, we tested candidate rules on a sample of 100 000 patient records to assess their performance compared to gold standard manual chart review. The physician panel selected a final rule for each condition, which was validated on an independent sample of 100 000 records to assess its accuracy. Results Seventeen rules were developed for inferring patient problems. Analysis using a validation set of 100 000 randomly selected patients showed high sensitivity (range: 62.8–100.0%) and positive predictive value (range: 79.8–99.6%) for most rules. Overall, the inference rules performed better than using either the problem list or billing data alone. Conclusion We developed and validated a set of rules for inferring patient problems. These rules have a variety of applications, including clinical decision support, care improvement, augmentation of the problem list, and identification of patients for research cohorts. PMID:21613643

  15. Stratigraphic evidence of past fluvial activity in southern Melas Chasma, Valles Marineris, Mars

    NASA Astrophysics Data System (ADS)

    Davis, Joel; Grindrod, Peter

    2014-05-01

    During the late Noachian and early Hesperian periods, listric faulting led to the development of a series of hanging depressions throughout the Valles Marineris canyon system [1]. One such depression, situated on the southern wall of Melas Chasma, forms an enclosed basin which has since undergone modification from the late Hesperian to Amazonian. There is a multitude of evidence suggesting that the basin (hereon in referred to as the Southern Melas Chasma Basin; SMCB) was once host to active fluvial processes, that at minimum lasted for several hundred years [2,3]. Central to this is what appears to be the remains of a palaeolake, which is approximately 80 by 40 kilometres in area. The palaeolake contains a complex sequence of sedimentary stratigraphy, which includes several structures that resemble deltas and/or submarine fans on both the east and west side of the basin [4], and appear to originate from a network of channels and valleys that terminate in the basin. Previous studies have shown that the western valley network has drainage densities similar to terrestrial values and a dendritic nature that is indicative of precipitation and surface runoff [3]. Higher resolution mapping of the SMCB is important to further understand the stratigraphic succession and geomorphology, and to quantify how long liquid water may have been present within the basin. For this study, new digital elevation models (DEMs) have been produced in SOCET SET using stereo images from the Context Camera (CTX) and the High Resolution Imaging Science Experiment (HiRISE), both aboard the Mars Reconnaissance Orbiter. The DEMs have been produced at ~6 and ~1 m/pixel vertical resolution for CTX and HiRISE respectively. There is approximately 150-200 m of sediment within the stratigraphic succession; some individual strata are less than 10 m thick. The delta/fan structures appear to occur at different stratigraphic positions low down within the sequence. Clinoform-like and cross-bedded structures

  16. A brief lithostratigraphic review of the Abrahamskraal and Koonap formations of the Beaufort Group, South Africa: Towards a basin-wide stratigraphic scheme for the Middle Permian Karoo

    NASA Astrophysics Data System (ADS)

    Day, Michael Oliver; Rubidge, Bruce Sidney

    2014-12-01

    The basal strata of the Beaufort Group of the South African Karoo Basin, comprising the western Abrahamskraal and eastern Koonap formations, contain the most time extensive record of Middle Permian fossil tetrapods and hold the key to understanding Middle Permian biodiversity change in the continental realm. To determine faunal stratigraphic ranges a reliable lithostratigraphic framework for Middle Permian Beaufort deposits is essential. Until now this has proved difficult to achieve, largely due to the homogeneity of the fluvial succession coupled with structural complexity as a result of Cape Fold Belt orogenesis. Accordingly, the Abrahamskraal Formation has been only locally subdivided on the basis of sandstone packages but regional stratigraphic subdivision has not yet achieved satisfactorily. Collation of stratigraphic sections from around the Karoo Basin for this study demonstrates the presence of four sandstone packages are present within the Abrahamskraal Formation in the south-western corner of the basin. These sandstone packages are given member status, based upon the nomenclature of Le Roux (1985) with the addition of the newly recognised Grootfontein Member. The Combrinkskraal and Grootfontein Members occur in the lower half of the Abrahamskraal Formation and are laterally persistent along the southern margin of the basin. The Koornplaats Member is more restricted to the south west corner of the basin, where it quite thick, suggesting the narrowing of the highly channelized area. The overlying Moordenaars Member, more extensive towards the north than underlying packages, indicates subsequent northwesterly expansion of the locus of active channelization with time. Although thin sandstone packages in the more easterly positioned and stratigraphically equivalent Koonap Formation, this does not facilitate lithostratigraphic subdivision of this part of the stratigraphic succession and may indicate a different form of fluvial architecture. Our study provides

  17. ELECTRIC WELDING EQUIPMENT AND AUTOMATION OF WELDING IN CONSTRUCTION,

    DTIC Science & Technology

    WELDING , *ARC WELDING , AUTOMATION, CONSTRUCTION, INDUSTRIES, POWER EQUIPMENT, GENERATORS, POWER TRANSFORMERS, RESISTANCE WELDING , SPOT WELDING , MACHINES, AUTOMATIC, STRUCTURES, WIRING DIAGRAMS, USSR.

  18. Automation in Clinical Microbiology

    PubMed Central

    Ledeboer, Nathan A.

    2013-01-01

    Historically, the trend toward automation in clinical pathology laboratories has largely bypassed the clinical microbiology laboratory. In this article, we review the historical impediments to automation in the microbiology laboratory and offer insight into the reasons why we believe that we are on the cusp of a dramatic change that will sweep a wave of automation into clinical microbiology laboratories. We review the currently available specimen-processing instruments as well as the total laboratory automation solutions. Lastly, we outline the types of studies that will need to be performed to fully assess the benefits of automation in microbiology laboratories. PMID:23515547

  19. Shoe-String Automation

    SciTech Connect

    Duncan, M.L.

    2001-07-30

    Faced with a downsizing organization, serious budget reductions and retirement of key metrology personnel, maintaining capabilities to provide necessary services to our customers was becoming increasingly difficult. It appeared that the only solution was to automate some of our more personnel-intensive processes; however, it was crucial that the most personnel-intensive candidate process be automated, at the lowest price possible and with the lowest risk of failure. This discussion relates factors in the selection of the Standard Leak Calibration System for automation, the methods of automation used to provide the lowest-cost solution and the benefits realized as a result of the automation.

  20. Lithofacies and sequence stratigraphic analysis of the Upper Jurassic siliciclastics in the eastern Kopet-Dagh Basin, NE Iran

    NASA Astrophysics Data System (ADS)

    Zand-Moghadam, Hamed; Moussavi-Harami, Reza; Mahboubi, Asadollah; Aghaei, Ali

    2016-05-01

    The Upper Jurassic (Oxfordian-Kimmeridgian) Mozduran Formation is the most important gas reservoirs of the northeast Iran. Siliciclastic facies of this formation in eastern most parts of the basin have not been studied yet. Therefore, four stratigraphic sections of Mozduran Formation have been selected in the Kole-Malekabad, Kale-Karab, Deraz-Ab and Karizak to interpret depositional history and analyze depositional sequences. Based on texture and sedimentary structures, 14 slilciclastic lithofacies were identified and classified into four categories, including conglomerate (Gms, Gp, Gt), sandstone (Sh, Sp, St, Sr, Sl, Sm, Se), mud rock (Fl) and intermediate sandstone-mud rock (Sr (Fl), Sr/Fl, Fl (Sr)). Identified lithofacies formed four architectural elements CH, SB, LA and FF. Lithofacies characteristics and architectural elements with mostly bimodal pattern of paleocurrents show that the majority of Mozduran lithofacies deposited in the coastal environment (tidal influence). Sequence stratigraphic analysis shows that the Kole-Malekabad section consists of two depositional sequences while other sections are characterized by three depositional sequences. The lower and upper sequence boundaries of the Mozduran Formation in all stratigraphic sections are SB1 that are distinguished by paleosol and sometime conglomerate horizons. Most of depositional sequences in studied sections are composed only of TST and HST. The TST deposits consist mostly of quartzarenite and litharenite petrofacies that have been deposited in the tidal zone. HST packages are mostly including mud rocks with interdeds of sandstone lithofacies that are deposited in supratidal setting. The LST facies is recognized only in the DS3 (equivalent to the second depositional sequences of the Kole-Malekabad), which consist of conglomerate facies. Instead, the Kole-Malekabad section is often composed of supratidal gypsiferrous shales, indicating sea level fall in the study area.

  1. NACSN, note 67--Application for revision of Articles 36 and 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

    2015-01-01

    Currently the North American Stratigraphic Code, (NACSN 2005, Article 37) sets restrictions on the use of the term “complex” for lithodemic units. With exceptions for “volcanic complex” and “structural complex,” a complex must consist of more than one genetic class of rock (i.e., sedimentary, igneous or metamorphic). Thus, the use of the term “complex” to describe masses of intrusive rocks is not allowed. Asimilar restriction is also included in a recent British Geological Survey proposal for using lithodemic units to classify igneous rocks (Gillespie et al. 2008).Currently the North American Stratigraphic Code, (NACSN 2005, Article 37) sets restrictions on the use of the term “complex” for lithodemic units. With exceptions for “volcanic complex” and “structural complex,” a complex must consist of more than one genetic class of rock (i.e., sedimentary, igneous or metamorphic). Thus, the use of the term “complex” to describe masses of intrusive rocks is not allowed. Asimilar restriction is also included in a recent British Geological Survey proposal for using lithodemic units to classify igneous rocks (Gillespie et al. 2008).

  2. Automating the multiprocessing environment

    NASA Technical Reports Server (NTRS)

    Arpasi, Dale J.

    1989-01-01

    An approach to automate the programming and operation of tree-structured networks of multiprocessor systems is discussed. A conceptual, knowledge-based operating environment is presented, and requirements for two major technology elements are identified as follows: (1) An intelligent information translator is proposed for implementating information transfer between dissimilar hardware and software, thereby enabling independent and modular development of future systems and promoting a language-independence of codes and information; (2) A resident system activity manager, which recognizes the systems capabilities and monitors the status of all systems within the environment, is proposed for integrating dissimilar systems into effective parallel processing resources to optimally meet user needs. Finally, key computational capabilities which must be provided before the environment can be realized are identified.

  3. Protein fabrication automation

    PubMed Central

    Cox, J. Colin; Lape, Janel; Sayed, Mahmood A.; Hellinga, Homme W.

    2007-01-01

    Facile “writing” of DNA fragments that encode entire gene sequences potentially has widespread applications in biological analysis and engineering. Rapid writing of open reading frames (ORFs) for expressed proteins could transform protein engineering and production for protein design, synthetic biology, and structural analysis. Here we present a process, protein fabrication automation (PFA), which facilitates the rapid de novo construction of any desired ORF from oligonucleotides with low effort, high speed, and little human interaction. PFA comprises software for sequence design, data management, and the generation of instruction sets for liquid-handling robotics, a liquid-handling robot, a robust PCR scheme for gene assembly from synthetic oligonucleotides, and a genetic selection system to enrich correctly assembled full-length synthetic ORFs. The process is robust and scalable. PMID:17242375

  4. Automated Standard Hazard Tool

    NASA Technical Reports Server (NTRS)

    Stebler, Shane

    2014-01-01

    The current system used to generate standard hazard reports is considered cumbersome and iterative. This study defines a structure for this system's process in a clear, algorithmic way so that standard hazard reports and basic hazard analysis may be completed using a centralized, web-based computer application. To accomplish this task, a test server is used to host a prototype of the tool during development. The prototype is configured to easily integrate into NASA's current server systems with minimal alteration. Additionally, the tool is easily updated and provides NASA with a system that may grow to accommodate future requirements and possibly, different applications. Results of this project's success are outlined in positive, subjective reviews complete by payload providers and NASA Safety and Mission Assurance personnel. Ideally, this prototype will increase interest in the concept of standard hazard automation and lead to the full-scale production of a user-ready application.

  5. Seismic paleoceanography and the stratigraphic signature of rapid climate changes

    NASA Astrophysics Data System (ADS)

    Berne, Serge; Sierro, Francisco Javier

    2015-04-01

    ka, have a distinct seismic stratigraphic signature, in the form of a mappable transgressive parasequence. Once identified at a specific location, such distinct seismic signatures might become important guides in the selection of coring sites along margins that have not yet been cored extensively. Sierro, F. J. et al. (2009). Phase relationship between sea level and abrupt climate change." Quaternary Science Reviews 28(25-26): 2867-2881.

  6. Automated DNA Sequencing System

    SciTech Connect

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

    1999-04-25

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

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

    USGS Publications Warehouse

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

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Montoya, Patricia

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

  9. Stratigraphic analysis of the carboniferous rocks of the Central Appalachian Basin

    SciTech Connect

    Chesnut, D.R. Jr.

    1988-01-01

    A series of seven cross sections was constructed across part of the Central Appalachian Basin in Kentucky, Tennessee, Virginia, West Virginia, and Ohio. Information used to make these sections included well logs, coal-company core descriptions, measured sections, and mapped surface geology. Newly discovered surface and subsurface structural features such as faults, folds, and flexures, are described. A new, unofficial lithostratigraphic nomenclature was introduced to illustrate the stratigraphic framework, and a regional unconformity was interpreted to occur between the Pennsylvanian Pocahontas Formation and the Pennsylvanian New River Formation. The cross sections reveal that sequential truncation of formations below the unconformity occurs t the northwest in the basin. A regional unconformity and biostratigraphic evidence indicate that the Carboniferous rocks were deposited in a series of several small-scale environmental continua. Pennsylvanian rocks overlying the regional unconformity sequentially overlap the underlying rocks to the northwest in the basin. Belts of quartzose sandstones (Lee Formation) within the overlying rocks, are oriented northeast-southwest. Succeeding sandstone belts onlap the unconformity to the northwest within the basin. A fluvial origin is suggested for the quartzose, conglomeratic sands of the Lee Formation. The source for these sands may have been reworked sediments derived from the Old Red Sandstone continent to the northwest in Canada. The remaining Pennsylvanian coal-bearing clastic rocks (Breathitt Group) were deposited as clastic wedges derived from the east and southeast on coastal lowlands.

  10. Stratigraphic record of the Yellowstone hotspot track, Neogene Sixmile Creek Formation grabens, southwest Montana

    NASA Astrophysics Data System (ADS)

    Sears, James W.; Hendrix, Marc S.; Thomas, Robert C.; Fritz, William J.

    2009-11-01

    The Sixmile Creek Formation fills deep grabens in southwest Montana and preserves a stratigraphic record of the evolution of the Yellowstone hotspot track from ~ 17 Ma to ~ 2 Ma. The Ruby, Beaverhead, Big Hole, Deer Lodge, Medicine Lodge-Grasshopper, Three Forks, Canyon Ferry, Jefferson, Melrose, Wise River, and Paradise grabens were active during outbreak of the hotspot. They appear to be parts of a radial system of extensional structures that may have formed on a broad dome that was centered on the hotspot outbreak area in southwest Idaho and southeast Oregon. Early in the evolution of the grabens, massive debris flows surged down Paleogene paleovalleys from uplifted and tilted horst blocks and accumulated in the grabens. The grabens captured runoff from the hotspot dome with thick deposits of river gravel that appear to have been derived, in part, from east-central Idaho. As the hotspot track propagated along the eastern Snake River Plain, silicic ash fell into the graben drainage basins and was reworked into thick fluvial beds along graben axes. The grabens were cross-cut by northwest-trending late Neogene grabens that propagated on the flanks of silicic volcanic centers along the hotspot track. The late Neogene grabens diverted the Middle Miocene drainage patterns in southwest Montana.

  11. Sequence stratigraphic framework of the Upper Jurassic Smackover and related units, western Gulf of Mexico

    SciTech Connect

    Moore, C.H.; Druckman, Y. )

    1991-03-01

    Post-Norphlet Upper Jurassic subsurface rocks of the western Gulf may be divided into four sequences encompassing some 12 million years (Lower Zuni A-4). The transgressive systems tract of the lower sequence (Smackover) consists of laminated muddy carbonate rocks and is the source for upper Jurassic hydrocarbons. The highstand systems tract of the Smackover consists of blanket ooid grainstones deposited on a platform. The Buckner 'B' begins with a siliciclastic lowstand fan ('C' sand). Highstand deposits of the 'B' consist of subaqueous lagoonal evaporites and an ooid grainstone prograding barrier system. Reflux of Buckner brines into Smackover grainstones resulted in regional dolomitization. The Buckner 'A' is similar to the 'B' except that the lagoon is dominated by siliciclastics. The Gray Sands of northern Louisiana may represent a lowstand fan initiating the 'A' sequence. The last sequence (Gilmer) is dominated by siliciclastics in Arkansas and Louisiana and limestones in east Texas. Its highstand systems tract in Texas is ooid dominated and is similar to the Buckner 'B' and 'A.' The regionally extensive Bossier Shale represents the transgressive systems tract of the next major sequence (Cotton Valley). Jurassic hydrocarbon production is controlled by sequence architecture: porosity of Smackover highstand deposits are dominantly secondary, developed by exposure during sea level fall and by dolomitization during the subsequent Buckner 'B' highstand, while Buckner and Gilmer highstand porosity is primary; Smackover traps are structural because of the blanket nature of the highstand system, while Buckner traps are stratigraphic developed in progradational highstand wedges.

  12. Magneto-stratigraphic studies in Neogene deposits of Taylor Valley and McMurdo Sound, Antarctica.

    USGS Publications Warehouse

    Elston, D.P.; Bressler, S.L.

    1981-01-01

    Magnetic polarity and susceptibility zonations obtained from drill cores have served to refine temporal correlations in glaciogenic sections cored in eastern Taylor Valley. The zonations have led to a better understanding of the glacial and structural history for an interval of time that extends from the late Miocene (about 7Ma) to perhaps near the end of the Pliocene (approx 2.4-1.8Ma). However polarity data from a core drilled in McMurdo Sound (hole MSSTS-1) were found to be less useful. In this core, normal and reverse polarity deposits of Holocene, Pleistocene, and Pliocene age are nearly 40m thick and appear to uncomformably overlie strata assigned to the middle Miocene on the basis of a reworked fauna and flora. Gaps in the stratigraphic coverage of the Miocene strata, and two intervals in which the magnetisation post-dates deposition, however, have made development of a reliable polarity zonation impossible, and no firm correlation could be made with the magnetic polarity time scale. -Authors

  13. Stratigraphic architecture and depositional history of lower Miocene, Planulina Zone, Southern Louisiana

    SciTech Connect

    Gates, B.C.; Galloway, W.E.

    1988-01-01

    The Planulina zone is a wedge of clastic sediment positioned between the Anahuac shale below and the Oakville sandstone interval above. Planulna sediments were deposited on an erosional surface, during a general rise in the sea level, and formed a retrogradational wedge. Within the study area, the Planulina zone consists of two large depositional complexes: the Mud Lake complex in west Cameron Parish, Louisiana, and the East Cameron complex in east Cameron Parish. The lowermost depositional sequence in the East Cameron complex is preserved in a network of submarine canyons that were eroded into the upper slope. Framework sands were deposited in channel systems confined to the axis of the canyons, and the sands are encased in marine shale containing benthonic foraminifera indicative of an upper to middle slope paleoenvironment. Two younger depositional sequences overlie the submarine canyon facies and were deposited by deltaic systems that prograded basinward. A zone of expansion extends east to west through the Planulina interval and is named the ''Planulina flexure.'' The flexure is a large fault located at the relict shelf edge and soles out downdip inn the Anahuac shale. Several thousand feet of sediment downthrown on the flexure is equivalent to several hundred feet upthrown, and the flexure represented the boundary dividing updip deltaic processes from downdip slope processes during the beginning of Planulina deposition. The Planulina depositional history and stratigraphic architecture are directly related to the displacement along the flexure and the structural deformation of the underlying Anahuac shale.

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

    USGS Publications Warehouse

    Reese, Ronald S.; Cunningham, Kevin J.

    2013-01-01

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

  15. The International Subcommission on Stratigraphic Classification of the International Commission on Stratigraphy: The Knowledge

    NASA Astrophysics Data System (ADS)

    Pratt, Brian

    2014-05-01

    The International Subcommission on Stratigraphic Classification (ISSC) was born in 1955 as an effort to promote awareness of stratigraphic principles and encourage worldwide standardization of stratigraphic approaches and terminology. The first major achievement of ISSC was the 1976 publication of the International Stratigraphic Guide. It was revised in 1994, with an abridged version appearing in 1999. These documents achieved their goals magnificently: cited innumerable times and forming the core of many national stratigraphic codes. As the discipline has evolved, particularly from technological advances and ocean drilling, new tools and methodologies have been developed and these have led to ever finer resolution of geological time and ever more exact correlation of stratigraphic units and events, thereby enhancing the understanding of the genesis of the geological record. Under the leadership of M. B. Cita, ISSC embarked in 2002 on a renewed initiative to disseminate to the global geological community these newer developments, and ultimately incorporate them into a third edition of the Guide. To this aim, traditional and new branches of stratigraphy are being treated: chemostratigraphy, cyclostratigraphy, magnetostratigraphy, lithostratigraphy, sequence stratigraphy, biostratigraphy, and chronostratigraphy. An open-access review paper is dedicated to each and published in Newsletters on Stratigraphy. The next edition of the Guide will be inclusive of all branches of stratigraphy and also embrace igneous and metamorphic rocks. It is envisaged that a textbook on stratigraphy based on these papers and the revised Guide could prove a timely contribution, especially to younger generations of practitioners, and aid global communication and understanding of stratigraphic principles and methods.

  16. Beaufortian stratigraphic plays in the National Petroleum Reserve - Alaska (NPRA)

    USGS Publications Warehouse

    Houseknecht, David W.

    2003-01-01

    The Beaufortian megasequence in the National Petroleum Reserve in Alaska (NPRA) includes Jurassic through lower Cretaceous (Neocomian) strata of the Kingak Shale and the overlying pebble shale unit. These strata are part of a composite total petroleum system involving hydrocarbons expelled from source rocks in three stratigraphic intervals, the Lower Jurassic part of the Kingak Shale, the Triassic Shublik Formation, and the Lower Cretaceous gamma-ray zone (GRZ) and associated strata. The potential for undiscovered oil and gas resources in the Beaufortian megasequence in NPRA was assessed by defining eight plays (assessment units), two in lower Cretaceous (Neocomian) topset seismic facies, four in Upper Jurassic topset seismic facies, one in Lower Jurassic topset seismic facies, and one in Jurassic through lower Cretaceous (Neocomian) clinoform seismic facies. The Beaufortian Cretaceous Topset North Play is estimated to contain between 0 (95-percent probability) and 239 (5-percent probability) million barrels of technically recoverable oil, with a mean (expected value) of 103 million barrels. The Beaufortian Cretaceous Topset North Play is estimated to contain between 0 (95-percent probability) and 1,162 (5-percent probability) billion cubic feet of technically recoverable, nonassociated natural gas, with a mean (expected value) of 405 billion cubic feet. The Beaufortian Cretaceous Topset South Play is estimated to contain between 635 (95-percent probability) and 4,004 (5-percent probability) billion cubic feet of technically recoverable, nonassociated natural gas, with a mean (expected value) of 2,130 billion cubic feet. No technically recoverable oil is assessed in the Beaufortian Cretaceous Topset South Play, as it lies at depths that are entirely in the gas window. The Beaufortian Upper Jurassic Topset Northeast Play is estimated to contain between 2,744 (95-percent probability) and 8,086 (5-percent probability) million barrels of technically recoverable oil

  17. Management Planning for Workplace Automation.

    ERIC Educational Resources Information Center

    McDole, Thomas L.

    Several factors must be considered when implementing office automation. Included among these are whether or not to automate at all, the effects of automation on employees, requirements imposed by automation on the physical environment, effects of automation on the total organization, and effects on clientele. The reasons behind the success or…

  18. Laboratory Automation and Middleware.

    PubMed

    Riben, Michael

    2015-06-01

    The practice of surgical pathology is under constant pressure to deliver the highest quality of service, reduce errors, increase throughput, and decrease turnaround time while at the same time dealing with an aging workforce, increasing financial constraints, and economic uncertainty. Although not able to implement total laboratory automation, great progress continues to be made in workstation automation in all areas of the pathology laboratory. This report highlights the benefits and challenges of pathology automation, reviews middleware and its use to facilitate automation, and reviews the progress so far in the anatomic pathology laboratory.

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

  20. Tectono-Stratigraphic framework and Palaeozoic evolution of the Chinese South Tianshan

    NASA Astrophysics Data System (ADS)

    Alexeiev, D. V.; Biske, Yu. S.; Wang, Bo; Djenchuraeva, A. V.; Getman, O. F.; Aristov, V. A.; Kröner, A.; Liu, Hongsheng; Zhong, Linglin

    2015-03-01

    A stratigraphic and structural study was carried out in the central part of the Chinese South Tianshan (STS) within a 50-100 km-wide transect centered on the Dushanzi-Kuqa road (83°-85° E). Our data elucidate the tectonic structure and evolution of the Palaeozoic sedimentary basin, document overthrust structures in the late Carboniferous-early Permian orogenic belt and suggest correlations between the western and eastern segments of the STS in Kyrgyzstan and China. We recognise a series of lithotectonic units in the study area that have different stratigraphic characteristics and were formed within (a) continental margin and slope of the Kazakhstan continent, (b) Turkestan (South Tianshan) ocean, (c) intra-oceanic carbonate sea-mounts, which at least partly evolved on top of an extinct island arc, (d) a back-arc oceanic-crust basin, (e) external deeper marine and internal shallow-marine areas of the Tarim shelf and (f) Tarim craton. The overall structure of the basin was similar within Kyrgyzstan and China. The main distinction of the western areas is a lack of ophiolites on the southern flank of the belt, a poorly expressed arc in the axial part, and a more complicated facial setting of the central area, where carbonate banks were separated by deeper marine depressions with cherty deposits. The eastern sector is defined by a continental arc that evolved on the northern margin of the Tarim craton in the Silurian and became separated from the continent in the latest Silurian-early Devonian. There is also a middle Palaeozoic metamorphic belt on the southern flank of the STS. A pre-Carboniferous unconformity, previously assumed throughout the study area, is only confirmed within the continental massifs of Kazakhstan and Tarim. As in the western areas, the unconformity does not exist within the STS. Continuous sedimentation in the STS occurred from the Early Devonian to the early Bashkirian in marginal parts of the belt and up to Gzhelian age in the axial part

  1. An automation simulation testbed

    NASA Technical Reports Server (NTRS)

    Cook, George E.; Sztipanovits, Janos; Biegl, Csaba; Karsai, Gabor; Springfield, James F.; Mutammara, Atheel

    1988-01-01

    The work being done in porting ROBOSIM (a graphical simulation system developed jointly by NASA-MSFC and Vanderbilt University) to the HP350SRX graphics workstation is described. New additional ROBOSIM features, like collision detection and new kinematics simulation methods are also discussed. Based on the experiences of the work on ROBOSIM, a new graphics structural modeling environment is suggested which is intended to be a part of a new knowledge-based multiple aspect modeling testbed. The knowledge-based modeling methodologies and tools already available are described. Three case studies in the area of Space Station automation are also reported. First a geometrical structural model of the station is presented. This model was developed using the ROBOSIM package. Next the possible application areas of an integrated modeling environment in the testing of different Space Station operations are discussed. One of these possible application areas is the modeling of the Environmental Control and Life Support System (ECLSS), which is one of the most complex subsystems of the station. Using the multiple aspect modeling methodology, a fault propagation model of this system is being built and is described.

  2. Automating checks of plan check automation.

    PubMed

    Halabi, Tarek; Lu, Hsiao-Ming

    2014-07-08

    While a few physicists have designed new plan check automation solutions for their clinics, fewer, if any, managed to adapt existing solutions. As complex and varied as the systems they check, these programs must gain the full confidence of those who would run them on countless patient plans. The present automation effort, planCheck, therefore focuses on versatility and ease of implementation and verification. To demonstrate this, we apply planCheck to proton gantry, stereotactic proton gantry, stereotactic proton fixed beam (STAR), and IMRT treatments.

  3. WANTED: Fully Automated Indexing.

    ERIC Educational Resources Information Center

    Purcell, Royal

    1991-01-01

    Discussion of indexing focuses on the possibilities of fully automated indexing. Topics discussed include controlled indexing languages such as subject heading lists and thesauri, free indexing languages, natural indexing languages, computer-aided indexing, expert systems, and the need for greater creativity to further advance automated indexing.…

  4. The Automated Office.

    ERIC Educational Resources Information Center

    Naclerio, Nick

    1979-01-01

    Clerical personnel may be able to climb career ladders as a result of office automation and expanded job opportunities in the word processing area. Suggests opportunities in an automated office system and lists books and periodicals on word processing for counselors and teachers. (MF)

  5. Planning for Office Automation.

    ERIC Educational Resources Information Center

    Sherron, Gene T.

    1982-01-01

    The steps taken toward office automation by the University of Maryland are described. Office automation is defined and some types of word processing systems are described. Policies developed in the writing of a campus plan are listed, followed by a section on procedures adopted to implement the plan. (Author/MLW)

  6. Work and Programmable Automation.

    ERIC Educational Resources Information Center

    DeVore, Paul W.

    A new industrial era based on electronics and the microprocessor has arrived, an era that is being called intelligent automation. Intelligent automation, in the form of robots, replaces workers, and the new products, using microelectronic devices, require significantly less labor to produce than the goods they replace. The microprocessor thus…

  7. Order Division Automated System.

    ERIC Educational Resources Information Center

    Kniemeyer, Justin M.; And Others

    This publication was prepared by the Order Division Automation Project staff to fulfill the Library of Congress' requirement to document all automation efforts. The report was originally intended for internal use only and not for distribution outside the Library. It is now felt that the library community at-large may have an interest in the…

  8. Automation and Cataloging.

    ERIC Educational Resources Information Center

    Furuta, Kenneth; And Others

    1990-01-01

    These three articles address issues in library cataloging that are affected by automation: (1) the impact of automation and bibliographic utilities on professional catalogers; (2) the effect of the LASS microcomputer software on the cost of authority work in cataloging at the University of Arizona; and (3) online subject heading and classification…

  9. Tectono-stratigraphic evolution and crustal architecture of the Orphan Basin during North Atlantic rifting

    NASA Astrophysics Data System (ADS)

    Gouiza, Mohamed; Hall, Jeremy; Welford, J. Kim

    2016-06-01

    The Orphan Basin is located in the deep offshore of the Newfoundland margin, and it is bounded by the continental shelf to the west, the Grand Banks to the south, and the continental blocks of Orphan Knoll and Flemish Cap to the east. The Orphan Basin formed in Mesozoic time during the opening of the North Atlantic Ocean between eastern Canada and western Iberia-Europe. This work, based on well data and regional seismic reflection profiles across the basin, indicates that the continental crust was affected by several extensional episodes between the Jurassic and the Early Cretaceous, separated by events of uplift and erosion. The preserved tectono-stratigraphic sequences in the basin reveal that deformation initiated in the eastern part of the Orphan Basin in the Jurassic and spread towards the west in the Early Cretaceous, resulting in numerous rift structures filled with a Jurassic-Lower Cretaceous syn-rift succession and overlain by thick Upper Cretaceous to Cenozoic post-rift sediments. The seismic data show an extremely thinned crust (4-16 km thick) underneath the eastern and western parts of the Orphan Basin, forming two sub-basins separated by a wide structural high with a relatively thick crust (17 km thick). Quantifying the crustal architecture in the basin highlights the large discrepancy between brittle extension localized in the upper crust and the overall crustal thinning. This suggests that continental deformation in the Orphan Basin involved, in addition to the documented Jurassic and Early Cretaceous rifting, an earlier brittle rift phase which is unidentifiable in seismic data and a depth-dependent thinning of the crust driven by localized lower crust ductile flow.

  10. Automation in Immunohematology

    PubMed Central

    Bajpai, Meenu; Kaur, Ravneet; Gupta, Ekta

    2012-01-01

    There have been rapid technological advances in blood banking in South Asian region over the past decade with an increasing emphasis on quality and safety of blood products. The conventional test tube technique has given way to newer techniques such as column agglutination technique, solid phase red cell adherence assay, and erythrocyte-magnetized technique. These new technologies are adaptable to automation and major manufacturers in this field have come up with semi and fully automated equipments for immunohematology tests in the blood bank. Automation improves the objectivity and reproducibility of tests. It reduces human errors in patient identification and transcription errors. Documentation and traceability of tests, reagents and processes and archiving of results is another major advantage of automation. Shifting from manual methods to automation is a major undertaking for any transfusion service to provide quality patient care with lesser turnaround time for their ever increasing workload. This article discusses the various issues involved in the process. PMID:22988378

  11. Stratigraphic and palaeoenvironmental summary of the south-east Georgia Embayment: a correlation of exploratory wells

    USGS Publications Warehouse

    Poppe, L.J.; Popenoe, P.; Poag, C.W.; Swift, B.A.

    1995-01-01

    A Continental Offshore Stratigraphic Test (COST) well and six exploratory wells have been drilled in the south-east Georgia embayment. The oldest rocks penetrated are weakly metamorphosed Lower Ordovician quartz arenites and Silurian shales and argillites in the Transco 1005-1 well and Upper Devonian argillites in the COST GE-1 well. The Palaeozoic strata are unconformably overlain by interbedded non-marine Jurassic sandstones and shales and marginal marine Lower Cretaceous rocks. Together, these rocks are stratigraphically equivalent to the onshore Fort Pierce and Cotton Valley(?) Formations and rocks of the Lower Cretaceous Comanchean Provincial Series. The Upper Cretaceous part of the section is composed mainly of neritic calcareous shales and shaley limestones stratigraphically equivalent to the primarily marginal marine facies of the onshore Atkinson, Cape Fear and Middendorf Formations and Black Creek Group, and to limestones and shales of the Lawson Limestone and Peedee Formations. Cenozoic strata are also described. -from Authors

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

    SciTech Connect

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

    1996-08-01

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

  13. The Implications of Stratigraphic Compatibility for Character Integration among Fossil Taxa.

    PubMed

    Wagner, Peter J; Estabrook, George F

    2015-09-01

    Two characters are stratigraphically compatible if some phylogenies indicate that their combinations (state-pairs) evolved without homoplasy and in an order consistent with the fossil record. Simulations assuming independent character change indicate that we expect approximately 95% of compatible character pairs to also be stratigraphically compatible over a wide range of sampling regimes and general evolutionary models. However, two general models of rate heterogeneity elevate expected stratigraphic incompatibility: "early burst" models, where rates of change are higher among early members of a clade than among later members of that clade, and "integration" models, where the evolution of characters is correlated in some manner. Both models have important theoretical and methodological implications. Therefore, we examine 259 metazoan clades for deviations from expected stratigraphic compatibility. We do so first assuming independent change with equal rates of character change through time. We then repeat the analysis assuming independent change with separate "early" and "late" rates (with "early" = the first third of taxa in a clade), with the early and late rates chosen to maximize the probability of the observed compatibility among the early taxa and then the whole clade. We single out Cambrian trilobites as a possible "control" group because morphometric studies suggest that integration patterns are not conserved among closely related species. Even allowing for early bursts, we see excess stratigraphic incompatibility (i.e., negative deviations) in significantly more clades than expected at 0.50, 0.25, and 0.05 [Formula: see text] values. This pattern is particularly strong in chordates, echinoderms, and arthropods. However, stratigraphic compatibility among Cambrian trilobites matches the expectations of integration studies, as they (unlike post-Cambrian trilobites) do not deviate from the expectations of independent change with no early bursts. Thus, these

  14. Identification and Mapping of the Edwards Stratigraphic Sequence in the State of Chihuahua Assisted by ten ArcMap Based Layers

    NASA Astrophysics Data System (ADS)

    Martinez-Pina, C.; Granados, A.; Goodell, P.

    2007-05-01

    Edwards Formation is a reef limestone that hosts one of the largest aquifers of the State of Texas. In 2004 the United States and Mexico signed an agreement intended to characterize and identify the shared binational underground resources. Texas Water Development Board Report 360 established for the Edwards Aquifer an area of more than 31,000 km2, half of which is in the State of Coahuila, Mexico (the agreement did not include the State of Chihuahua). This led to the idea that Chihuahua may also have hydrologic potential in the Edwards equivalent, where numerous large cavern systems are already recognized (Naica's Sword Cavern, and the Coyame, Nombre de Dios and Bocagrande Caverns). The objective of this study is to establish the existence, in the State of Chihuahua, of the stratigraphic sequence and geohydrologic properties such as faulting, sinkholes, and springs, within the Edwards equivalent. The Consejo de Recursos Minerales geologic map, INEGI's hydrologic study, petroleum, mining and hydrogeology studies of Chihuahua, and many others, constitute the database used. ArcMap is used to define the geologic framework and construct different thematic layers (structural, lithological, hydrological) that would aid in the identification of the stratigraphic sequence. The results show that all the Edwards Stratigraphic Sequence (ESS) exists in Chihuahua; that there are isolated areas of groundwater production in eastern Chihuahua possibly from ESS but this is not well established. Overall the ESS presents an unusual opportunity as a potentially productive aquifer in the State of Chihuahua.

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

    SciTech Connect

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

    1992-01-01

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

  16. Stratigraphic Profiles for Selected Hanford Site Seismometer Stations and Other Locations

    SciTech Connect

    Last, George V.

    2014-02-01

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

  17. Inquiring into indicators and origin of catastrophic events at stratigraphic boundaries.

    PubMed

    Zhang, Q; Xu, D

    1996-01-01

    Since 1982, numerous indicators of catastrophic events have been observed at the main stratigraphic boundaries in China during the Phanerozoic, i.e. Precambrian-Cambrian, Permian-Triassic, Cretaceous-Tertiary as well as Ordovician-Silurian and Devonian-Carboniferous boundaries. These markers are boundary clay layer, microspherules, high Ir anomaly, mass extinction of organisms and impact of meteorite. We support the hypothesis of the extraterrestrial origin of catastrophic events and suggest that the events at different stratigraphic boundaries might be different in features and processes.

  18. A simple high-precision Jacob's staff design for the high-resolution stratigrapher

    USGS Publications Warehouse

    Elder, W.P.

    1989-01-01

    The new generation of high-resolution stratigraphic research depends upon detailed bed-by-bed analysis to enhance regional correlation potential. The standard Jacob's staff is not an efficient and precise tool for measuring thin-bedded strata. The high-precision Jacob's staff design presented and illustrated in this paper meets the qualifications required of such an instrument. The prototype of this simple design consists of a sliding bracket that holds a Brunton-type compass at right angles to a ruled-off staff. This instrument provides rapid and accurate measurement of both thick- or thin-bedded sequences, thus decreasing field time and increasing stratigraphic precision. -Author

  19. Definitive Metabolite Identification Coupled with Automated Ligand Identification System (ALIS) Technology: A Novel Approach to Uncover Structure-Activity Relationships and Guide Drug Design in a Factor IXa Inhibitor Program.

    PubMed

    Zhang, Ting; Liu, Yong; Yang, Xianshu; Martin, Gary E; Yao, Huifang; Shang, Jackie; Bugianesi, Randal M; Ellsworth, Kenneth P; Sonatore, Lisa M; Nizner, Peter; Sherer, Edward C; Hill, Susan E; Knemeyer, Ian W; Geissler, Wayne M; Dandliker, Peter J; Helmy, Roy; Wood, Harold B

    2016-03-10

    A potent and selective Factor IXa (FIXa) inhibitor was subjected to a series of liver microsomal incubations, which generated a number of metabolites. Using automated ligand identification system-affinity selection (ALIS-AS) methodology, metabolites in the incubation mixture were prioritized by their binding affinities to the FIXa protein. Microgram quantities of the metabolites of interest were then isolated through microisolation analytical capabilities, and structurally characterized using MicroCryoProbe heteronuclear 2D NMR techniques. The isolated metabolites recovered from the NMR experiments were then submitted directly to an in vitro FIXa enzymatic assay. The order of the metabolites' binding affinity to the Factor IXa protein from the ALIS assay was completely consistent with the enzymatic assay results. This work showcases an innovative and efficient approach to uncover structure-activity relationships (SARs) and guide drug design via microisolation-structural characterization and ALIS capabilities.

  20. Systematic review automation technologies.

    PubMed

    Tsafnat, Guy; Glasziou, Paul; Choong, Miew Keen; Dunn, Adam; Galgani, Filippo; Coiera, Enrico

    2014-07-09

    Systematic reviews, a cornerstone of evidence-based medicine, are not produced quickly enough to support clinical practice. The cost of production, availability of the requisite expertise and timeliness are often quoted as major contributors for the delay. This detailed survey of the state of the art of information systems designed to support or automate individual tasks in the systematic review, and in particular systematic reviews of randomized controlled clinical trials, reveals trends that see the convergence of several parallel research projects.We surveyed literature describing informatics systems that support or automate the processes of systematic review or each of the tasks of the systematic review. Several projects focus on automating, simplifying and/or streamlining specific tasks of the systematic review. Some tasks are already fully automated while others are still largely manual. In this review, we describe each task and the effect that its automation would have on the entire systematic review process, summarize the existing information system support for each task, and highlight where further research is needed for realizing automation for the task. Integration of the systems that automate systematic review tasks may lead to a revised systematic review workflow. We envisage the optimized workflow will lead to system in which each systematic review is described as a computer program that automatically retrieves relevant trials, appraises them, extracts and synthesizes data, evaluates the risk of bias, performs meta-analysis calculations, and produces a report in real time.

  1. Systematic review automation technologies

    PubMed Central

    2014-01-01

    Systematic reviews, a cornerstone of evidence-based medicine, are not produced quickly enough to support clinical practice. The cost of production, availability of the requisite expertise and timeliness are often quoted as major contributors for the delay. This detailed survey of the state of the art of information systems designed to support or automate individual tasks in the systematic review, and in particular systematic reviews of randomized controlled clinical trials, reveals trends that see the convergence of several parallel research projects. We surveyed literature describing informatics systems that support or automate the processes of systematic review or each of the tasks of the systematic review. Several projects focus on automating, simplifying and/or streamlining specific tasks of the systematic review. Some tasks are already fully automated while others are still largely manual. In this review, we describe each task and the effect that its automation would have on the entire systematic review process, summarize the existing information system support for each task, and highlight where further research is needed for realizing automation for the task. Integration of the systems that automate systematic review tasks may lead to a revised systematic review workflow. We envisage the optimized workflow will lead to system in which each systematic review is described as a computer program that automatically retrieves relevant trials, appraises them, extracts and synthesizes data, evaluates the risk of bias, performs meta-analysis calculations, and produces a report in real time. PMID:25005128

  2. Sequence stratigraphic setting of the Priob Field within the Neocomian prograding complex of the West Siberian Basin, Russia

    SciTech Connect

    Mkrtchyan, O.M.; Armentrout, J.M.

    1995-08-01

    The Neocomian strata of the West Siberian Basin are a prograding complex unique in its aerial extent, structure and hydrocarbon reserves, such as Priob Field in the Ob River area. Interpretation of the basin history is based on well data and seismic reflection profile. As many as 45 transgressive-regressive depositional sequences, called cyclites, prograde into the deep-water basin formed during Late Jurassic and Early Cretaceous. Each transgressive-regressive sequence is defined by a coarsening-upward cycle of shale, siltstone and sandstone, and is considered a chronostratigraphic subdivision of the prograding complex. Each sequence boundary is regionally correlatable on seismic reflection profiles, and is identified on well logs by sharp contacts between regressive sandstones below and thin transgressive shales above. Subordinate progradational wedges are locally developed within these sequences and contain major hydrocarbon reserves. These depositional wedges map as lens-shaped packages downlapping the outermost shelf (Priob zone) or as narrow progradational wedges downlapping the foreset reflections of the slope clinoforms immediately beyond the shelf break (Sugmut zone). Regressive facies of the shelf consist of thin but wide spread sandstones that also contain major hydrocarbon reserves. Pervasive sediment starvation during the Late Neocomian resulted in deposition of thin regionally extensive shales that provide top-seal to the Neocomian hydrocarbon system. At the Priob field, a deep erosional incision has been mapped at the AS11 shelf-edge. Sands transported through this incised valley were deposited as a prograding wedge along the shoreline, forming the reservoir facies for the Priob hydrocarbon accumulation. Stratigraphic aspects of the Priob trap include top and lateral shale seals and subtle regional structural tilt. Types of stratigraphic traps are discussed and the possibility of predicting additional such traps are analyzed.

  3. Automated Fabrication Technologies for High Performance Polymer Composites

    NASA Technical Reports Server (NTRS)

    Shuart , M. J.; Johnston, N. J.; Dexter, H. B.; Marchello, J. M.; Grenoble, R. W.

    1998-01-01

    New fabrication technologies are being exploited for building high graphite-fiber-reinforced composite structure. Stitched fiber preforms and resin film infusion have been successfully demonstrated for large, composite wing structures. Other automatic processes being developed include automated placement of tacky, drapable epoxy towpreg, automated heated head placement of consolidated ribbon/tape, and vacuum-assisted resin transfer molding. These methods have the potential to yield low cost high performance structures by fabricating composite structures to net shape out-of-autoclave.

  4. Reconstructing the geomorphic history of Liang Bua, Flores, Indonesia: a stratigraphic interpretation of the occupational environment.

    PubMed

    Westaway, K E; Sutikna, T; Saptomo, W E; Jatmiko; Morwood, M J; Roberts, R G; Hobbs, D R

    2009-11-01

    Liang Bua, in Flores, Indonesia, was formed as a subterranean chamber over 600ka. From this time to the present, a series of geomorphic events influenced the structure of the cave and cave deposits, creating a complex stratigraphy. Within these deposits, nine main sedimentary units have been identified. The stratigraphic relationships between these units provide the evidence needed to reconstruct the geomorphic history of the cave. This history was dominated by water action, including slope wash processes, channel formation, pooling of water, and flowstone precipitation, which created waterfalls, cut-and-fill stratigraphy, large pools of water, and extensive flowstone cappings. The reconstructed sequence of events over the last 190k.yr. has been summarized by a series of time slices that demonstrate the nature of the occupational environment in Liang Bua. The earliest artifacts at the site, dated to approximately 190ka, testify to hominin presence in the area, but the reconstructions suggest that occupation of the cave itself may not have been possible until after approximately 100ka. At approximately 95ka, channel erosion of a basal unit, which displays evidence of deposition in a pond environment, created a greater relief on the cave floor, and formed remanent areas of higher ground that later became a focus for hominin occupation from 74-61ka by the west wall and in the center of the cave, and from approximately 18-17ka by the east wall. These zones have been identified according to the sloping nature of the stratigraphy and the distribution of artifacts, and their locations have implications for the archaeological interpretation of the site.

  5. Stratigraphic, lithologic, and major element geochemical constraints on magmatic evolution at Lassen volcanic center, California

    SciTech Connect

    Clynne, M.A. )

    1990-11-10

    The evolution of the Lassen volcanic center is described in three stages. Stages 1 and 2 comprise the Brokeoff volcano, and 80 km{sup 3} andesitic stratocone, active from 600 to 400 ka. Brokeoff volcano is compositionally equivalent to the regional basaltic andesite to andesite volcanism in the Lassen region and is the result of structurally controlled focusing of the diffuse regional magic magmatism. Stage 3 comprises a silicic dome field and adjacent area of hybrid andesites and has a total volume of about 100 km{sup 3}. Volcanism during stage III was episodic and is subdivided into four sequences of lithologically and temporarily distinct lavas. Stage 3 began at 400 ka with a rhyolitic, caldera-forming pyroclastic eruption and chemically related lavas. Additional sequences of dacite erupted between 250-200 ka and 100-0 ka. Hybrid andesites erupted adjacent to the silicic dome field between 300 and 0 ka. Porphyritic andesite and dacite with high Al{sub 2}O{sub 3}, low TiO{sub 2}, medium K{sub 2}O and FeO/MgO ratios of 1.5-2.0 are the most abundant rock types in the Lassen volcanic center. However, the single most voluminous unit is sparsely phyric rhyolite pumice. Although major element variation can be modeled by fractional crystallization, petrographic and stratigraphic evidence indicates that magma mixing is an important but subtle process in Brokeoff lavas and suggests that lavas evolved in small independent batches. Disequilibrium mineral assemblages in the stage 3 lavas indicate that they are not directly derived from Brokeoff andesite by fractional crystallization. Mixing of silicic magma with regional mafic magma and disaggregation of andesite quenched magmatic inclusions play dominant roles in the compositional diversity of stage 3 lavas.

  6. The stratigraphic record of prebreakup geodynamics: Evidence from the Barrow Delta, offshore Northwest Australia

    NASA Astrophysics Data System (ADS)

    Reeve, Matthew T.; Jackson, Christopher A.-L.; Bell, Rebecca E.; Magee, Craig; Bastow, Ian D.

    2016-08-01

    The structural and stratigraphic evolution of rift basins and passive margins has been widely studied, with many analyses demonstrating that delta systems can provide important records of postrift geodynamic processes. However, the apparent lack of ancient synbreakup delta systems and the paucity of seismic imaging across continent-ocean boundaries mean that the transition from continental rifting to oceanic spreading remains poorly understood. The Early Cretaceous Barrow Group of the North Carnarvon Basin, offshore NW Australia, was a major deltaic system that formed during the latter stages of continental rifting and represents a rich sedimentary archive, documenting uplift, subsidence, and erosion of the margin. We use a regional database of 2-D and 3-D seismic and well data to constrain the internal architecture of the Barrow Group. Our results highlight three major depocenters: the Exmouth and Barrow subbasins and southern Exmouth Plateau. Overcompaction of pre-Cretaceous sedimentary rocks in the South Carnarvon Basin, and pervasive reworking of Permian and Triassic palynomorphs in the offshore Barrow Group, suggests that the onshore South Carnarvon Basin originally contained a thicker sedimentary succession, which was uplifted and eroded prior to breakup. Backstripping of sedimentary successions encountered in wells in the Exmouth Plateau depocenter indicates that anomalously rapid tectonic subsidence (≤0.24 mm yr-1) accommodated Barrow Group deposition, despite evidence for minimal, contemporaneous upper crustal extension. Our results suggest that classic models of uniform extension cannot account for the observations of uplift and subsidence in the North Carnarvon Basin and may indicate a period of depth-dependent extension or dynamic topography preceding breakup.

  7. Managing laboratory automation

    PubMed Central

    Saboe, Thomas J.

    1995-01-01

    This paper discusses the process of managing automated systems through their life cycles within the quality-control (QC) laboratory environment. The focus is on the process of directing and managing the evolving automation of a laboratory; system examples are given. The author shows how both task and data systems have evolved, and how they interrelate. A BIG picture, or continuum view, is presented and some of the reasons for success or failure of the various examples cited are explored. Finally, some comments on future automation need are discussed. PMID:18925018

  8. Automating network meta-analysis.

    PubMed

    van Valkenhoef, Gert; Lu, Guobing; de Brock, Bert; Hillege, Hans; Ades, A E; Welton, Nicky J

    2012-12-01

    Mixed treatment comparison (MTC) (also called network meta-analysis) is an extension of traditional meta-analysis to allow the simultaneous pooling of data from clinical trials comparing more than two treatment options. Typically, MTCs are performed using general-purpose Markov chain Monte Carlo software such as WinBUGS, requiring a model and data to be specified using a specific syntax. It would be preferable if, for the most common cases, both could be derived from a well-structured data file that can be easily checked for errors. Automation is particularly valuable for simulation studies in which the large number of MTCs that have to be estimated may preclude manual model specification and analysis. Moreover, automated model generation raises issues that provide additional insight into the nature of MTC. We present a method for the automated generation of Bayesian homogeneous variance random effects consistency models, including the choice of basic parameters and trial baselines, priors, and starting values for the Markov chain(s). We validate our method against the results of five published MTCs. The method is implemented in freely available open source software. This means that performing an MTC no longer requires manually writing a statistical model. This reduces time and effort, and facilitates error checking of the dataset. Copyright © 2012 John Wiley & Sons, Ltd.

  9. Neogene Stratigraphic Development of the Arabian (Persian) Gulf

    DTIC Science & Technology

    2000-09-30

    terrace extends for 50-60 km southwestward across the floor of the basin (Figure 1a) and appears to represent a still-stand in relative sealevel . The...Marine Geology, 160, 1-23. 4 Figure 1. (a) Structure map on Horizon 1 shows the depth below sealevel to the LGM unconformity. Black dotes indicate

  10. Automated fiber placement: Evolution and current demonstrations

    NASA Technical Reports Server (NTRS)

    Grant, Carroll G.; Benson, Vernon M.

    1993-01-01

    The automated fiber placement process has been in development at Hercules since 1980. Fiber placement is being developed specifically for aircraft and other high performance structural applications. Several major milestones have been achieved during process development. These milestones are discussed in this paper. The automated fiber placement process is currently being demonstrated on the NASA ACT program. All demonstration projects to date have focused on fiber placement of transport aircraft fuselage structures. Hercules has worked closely with Boeing and Douglas on these demonstration projects. This paper gives a description of demonstration projects and results achieved.

  11. Monitoring of the physical status of Mars-500 subjects as a model of structuring an automated system in support of the training process in an exploration mission

    NASA Astrophysics Data System (ADS)

    Fomina, Elena; Savinkina, Alexandra; Kozlovskaya, Inesa; Lysova, Nataliya; Angeli, Tomas; Chernova, Maria; Uskov, Konstantin; Kukoba, Tatyana; Sonkin, Valentin; Ba, Norbert

    Physical training sessions aboard the ISS are performed under the permanent continuous control from Earth. Every week the instructors give their recommendations on how to proceed with the training considering the results of analysis of the daily records of training cosmonauts and data of the monthly fitness testing. It is obvious that in very long exploration missions this system of monitoring will be inapplicable. For this reason we venture to develop an automated system to control the physical training process using the current ISS locomotion test parameters as the leading criteria. Simulation of an extended exploration mission in experiment MARS-500 enabled the trial application of the automated system for assessing shifts in cosmonauts’ physical status in response to exercises of varying category and dismissal periods. Methods. Six subjects spent 520 days in the analog of an interplanetary vehicle at IBMP (Moscow). A variety of training regimens and facilities were used to maintain a high level of physical performance of the subjects. The resistance exercises involved expanders, strength training device (MDS) and vibrotraining device (Galileo). The cycling exercises were performed on the bicycle ergometer (VB-3) and a treadmill with the motor in or out of motion. To study the effect of prolonged periods of dismissal from training on physical performance, the training flow was interrupted for a month once in the middle and then at the end of isolation. In addition to the in-flight locomotion test integrated into the automated training control system, the physical status of subjects was attested by analysis of the records of the monthly incremental testing on the bicycle ergometer and MDS. Results. It was demonstrated that the recommended training regimens maintained high physical performance levels despite the limited motor activities in isolation. According to the locomotion testing, the subjects increased velocity significantly and reduced the physiological

  12. Automated decision stations

    NASA Technical Reports Server (NTRS)

    Tischendorf, Mark

    1990-01-01

    This paper discusses the combination of software robots and expert systems to automate everyday business tasks. Tasks which require people to repetitively interact with multiple systems screens as well as multiple systems.

  13. Automating the Media Center.

    ERIC Educational Resources Information Center

    Holloway, Mary A.

    1988-01-01

    Discusses the need to develop more efficient information retrieval skills by the use of new technology. Lists four stages used in automating the media center. Describes North Carolina's pilot programs. Proposes benefits and looks at the media center's future. (MVL)

  14. Planning for Office Automation.

    ERIC Educational Resources Information Center

    Mick, Colin K.

    1983-01-01

    Outlines a practical approach to planning for office automation termed the "Focused Process Approach" (the "what" phase, "how" phase, "doing" phase) which is a synthesis of the problem-solving and participatory planning approaches. Thirteen references are provided. (EJS)

  15. Xenon International Automated Control

    SciTech Connect

    2016-08-05

    The Xenon International Automated Control software monitors, displays status, and allows for manual operator control as well as fully automatic control of multiple commercial and PNNL designed hardware components to generate and transmit atmospheric radioxenon concentration measurements every six hours.

  16. Stratigraphic data for wells at and near the Idaho National Engineering Laboratory, Idaho

    SciTech Connect

    Anderson, S.R.; Ackerman, D.J.; Liszewski, M.J.; Frieburger, R.M.

    1996-05-01

    A stratigraphic data base containing 230 stratigraphic units in 333 wells was constructed for deposits that make up the unsaturated zone and the Snake River Plain aquifer at and near INEL in eastern Idaho. Stratigraphic units, which were identified and correlated using data from numerous outcrops, 26 continuous cores, and 328 natural-gamma logs available in Dec. 1993, include 121 basalt-flow groups, 102 sedimentary interbeds, 6 andesite-flow groups, and 1 rhyolite dome. By volume, basalt flows make up about 90% of the deposits underlying most of this 890 mi{sup 2} area. Basalt, sediment, andesite, and rhyolite were identified from outcrops and cores that were selectively evaluated. Stratigraphic units were correlated using these data and natural-gamma logs. Best correlations were for basalt and sediment at Test Area North, the Naval Reactors Area, the Test Reactor Area, ICPP, and the Radioactive Waste Management Complex (RWMC), where most cores and 2/3 of the logs were obtained. Correlations range from good at the RWMC to uncertain the eastern half of the study area. A computer diskette containing the data is included.

  17. Neoproterozoic variations in the C-isotopic composition of seawater: stratigraphic and biogeochemical implications

    NASA Technical Reports Server (NTRS)

    Kaufman, A. J.; Knoll, A. H.

    1995-01-01

    The recent proliferation of stratigraphic studies of delta 13C variation in carbonates and organic C in later Neoproterozoic and basal Cambrian successions (approximately 850-530 Ma) indicates a strong oscillating trend in the C-isotopic composition of surface seawater. Alone, this trend does not adequately characterize discrete intervals in Neoproterozoic time. However, integrated with the vectorial signals provided by fossils and Sr-isotopic variations, C isotope chemostratigraphy facilitates the interbasinal correlation of later Neoproterozoic successions. Results of these studies are evaluated in terms of four stratigraphic intervals: (1) the Precambrian/Cambrian boundary, (2) the post-Varanger terminal Proterozoic, (3) the late Cryogenian, and (4) the early Cryogenian. Where biostratigraphic or radiometric data constrain the age of Neoproterozoic sedimentary sequences, secular variations in C and Sr isotopes can provide a level of stratigraphic resolution exceeding that provided by fossils alone. Isotopic data place strong constraints on the chemical evolution of seawater, linking it to major tectonic and paleoclimatic events. They also provide a biogeochemical framework for the understanding of the initial radiation of macroscopic metazoans, which is associated stratigraphically, and perhaps causally, with a global increase in the burial of organic C and a concomitant rise of atmospheric O2.

  18. Selected stratigraphic contacts for drill holes in LANL use areas of Yucca Flat, NTS

    SciTech Connect

    Drellack, S.L. Jr.

    1988-07-01

    This report is a compilation of selected stratigraphic contacts in drill holes of Yucca Flat, Nevada Test Site (NTS), used by the Los Alamos National Laboratory (LANL). This is the product of an ongoing effort to establish and maintain the most up-to-date database of formation tops in LANL use areas of Yucca Flat. Figure 1 is an index map showing areas of the NTS covered in this report. A drill hole planning map showing hole locations is in the rear pocket. Data presented for each drill hole include drill hole name; year drill hole completed; ground level elevations, above mean sea level (MSL), at drill hole site; total depth (TD) of drill hole at completion of drilling; and depth below surface to selected stratigraphic contacts. The geologic data presented here was generated by numerous individuals. Published references, from which most of these data originated, are listed on page 54 of this report. Information regarding other drill hole statistics can be found in the NTS Drilling and Mining Summary (``The Redbook``) compiled by the Technical Support Division of Fenix and Scisson, Inc. We continue the ``revised`` stratigraphic nomenclature for the bedded tuffs between the Rainier Mesa Member of the Timber Mountain Tuff and the Grouse Canyon Member of the Belted Range Tuff (formerly the ``Paintbrush Tuff``). Confidence in these stratigraphic assignments for these bedded tuffs is consolidating. 13 refs., 4 figs., 2 tabs.

  19. Storage Thresholds for Relative Sea Level Signals in the Stratigraphic Record

    NASA Astrophysics Data System (ADS)

    Li, Q.; Yu, L.; Straub, K. M.

    2015-12-01

    Many argue that the tug of Relative Sea Level (RSL) change represents the most important allogenic forcing affecting deltas and is the primary control on stratigraphic architecture of deltas. However, the range of amplitudes and periodicities of RSL cycles stored in stratigraphy remains unknown. Here we use a suite of physical experiments to show that RSL cycles with magnitudes and periodicities less than the spatial and temporal scales of deltaic internal (autogenic) dynamics cannot confidently be extracted from the physical stratigraphic record. Additional analysis of deltaic morphodynamics also suggest no significant differences between an experiment with constant boundary conditions (control experiment) and an experiment with small magnitude and short periodicity RSL cycles, relative to the autogenic dynamics. Significant differences in the aspect ratio of channel bodies and deposit sand fractions do exists between our control experiment and those experiments with either large magnitudes or long periodicities RSL cycles. Using a compilation of data from major river delta systems, we show that our predicted thresholds for RSL signal storage often overlap with the magnitudes and periodicities of commonly discussed drivers of global sea level. This theory defines quantitative limits on the range of paleo-RSL information that can be extracted from the stratigraphic record, which could aid stratigraphic prediction and the inversion of stratigraphy for paleo- deltaic response to climate change.

  20. Chert horizons as time-stratigraphic markers in Ordovician and Silurian of eastern Great Basin

    SciTech Connect

    Cameron, G.J.

    1986-08-01

    Data from numerous measured sections show that distinct chert horizons occur at or near the same stratigraphic intervals in a number of Ordovician and Silurian dolomite sequences in the eastern Great basin of Nevada and Utah. In many cases a shallow-water origin for the chert is inferred because of silicified shelfal fauna and lack of deeper water indicators. The cherty intervals appear to transgress across environmentally controlled lithologic boundaries. This fact, coupled with the regional extent of the chert, suggests that these intervals can be used as time-stratigraphic marker horizons. This concept is useful in assessing the degree of stratigraphic thinning of Upper Silurian strata along a regional unconformity. Although chert is almost ubiquitously present in certain stratigraphic intervals, the abundance of chert-bearing horizons within an individual section varies. By contouring the abundance of chert-bearing intervals within the Silurian system, a well-defined pattern is documented that increases in abundance to the northeast toward the northwestern corner of Utah. The ratio of chert to dolomite within the intervals increases correspondingly. It is suggested that the chert is the result of silica supersaturation from the settling of wind-blow volcanic ash on the Silurian epicontinental sea. The distribution of the chert was largely a function of paleowind currents from an easterly or northerly active volcanic source area.

  1. Seismic stratigraphy and stratigraphic modelling of the South-eastern German Molasse Basin

    SciTech Connect

    Aigner, T.; Jin, J.; Luterbacher, P.

    1995-08-01

    Although the German Molasse Basin can be regarded as a mature hydrocarbon province, no regional sequence stratigraphic analysis has been carried out so far. We have studied seismic lines and well data from the region between the Isar and Inn rivers (SE Germany) that have been generously supplied by German oil companies (DEE, BEB, Mobil, RWE-DEA and Wintershall). Initial work indicates that five major seismic sequences within three main depositional cycles are developed. The Alpine thrust belt to the south serves as the primary sediment source in the foreland basin. However, sedimentary infill mainly took place parallel to the basin axis. Our analysis suggests that the stratigraphic development of the Molasse Basin was mainly controlled by eustatic sea-level changes which caused the shoreline to shift in the W-E direction. The shifting of the depocenter axis in a N-S direction was controlled by the tectonic evolution of the thrust belt. The sea-level curve determined by seismic stratigraphy and well-derived subsidence curves have been used as input parameters for stratigraphic modelling, using the programs GeoMOD and PHIL. Basin-fill simulations with PHIL are in good agreement with the main features of the sequence stratigraphy and the distribution of the systems tracts observed in the study area. The qualitative sea-level curve for the German Molasse Basin derived from the seismostratigraphic analysis could be quantified by the stratigraphic exercises.

  2. Stratigraphic signature of lithospheric deformation style in post-rift passive margin basins

    NASA Astrophysics Data System (ADS)

    Rouby, Delphine; Huismans, Ritske; Robin, Cecile; Braun, Jean; Granjeon, Didier

    2016-04-01

    We revise commonly accepted models explaining long-term stratigraphic trends along Atlantic-type passive margins by including the impact of complex lithosphere deformation at depth and it's coupling with surface processes. To achieve this, we simulated the evolution of a passive margin basin using a cascade of three modeling tools: a thermo-mechanical model of the syn-rift stretching of the lithosphere, a flexural and thermal model of the post-rift stage that includes coupling with surface processes and, finally, a stratigraphic model of the associated sedimentary basin architecture. We compare two necking styles that lead to different margin geometries: wide and narrow margins that form by heterogeneous stretching. Wide margins, forming thinner and wider sedimentary wedges, show significantly larger aggradation component and longer preservation duration, in more continental/proximal depositional facies. Narrow margins are characterized by enhanced erosion and by-pass during transgression. Through a parametric analysis we constrain the relative contribution of lithosphere deformation and surface processes on the stratigraphic trends and show that both may contribute equally to the stratigraphic architecture. For example, enhanced erosion in narrow margins impacts the volume of sediments delivered to the basin, which, in turn, significantly increases the subsidence. Our simulations also underline the importance of the assumed sediment transport length, which controls whether the main depocentres remain in the necking zone or reach the more distal parts of the margin.

  3. Facies, Stratigraphic and Depositional Model of the Sediments in the Abrolhos Archipelago (Bahia, BRAZIL)

    NASA Astrophysics Data System (ADS)

    Matte, R. R.; Zambonato, E. E.

    2012-04-01

    Located in the Mucuri Basin on the continental shelf of southern Bahia state, northeast Brazil, about 70 km from the city of Caravelas,the Abrolhos archipelago is made up of five islands; Santa Barbara, Redonda, Siriba, Guarita and Sueste. The exhumed sediments in the Abrolhos archipelago are a rare record of the turbidite systems which fill the Brazilian Atlantic Basin, and are probably an unprecedented example of a plataform turbidite system (Dr. Mutti, personal communication). Despite the limited area, the outcrops display a wide facies variation produced by different depositional processes, and also allow for the observation of the layer geometries. Associated with such sedimentary rocks, the Abrolhos Volcanic Complex belongs stratigraphically to the Abrolhos Formation. These igneous rocks were dated by the Ar / Ar method, with ages ranging from 60 to 40 My, placing such Volcanic Complex between the Paleocene and Eocene. The sedimentary section is best exposed in the Santa Barbara and Redonda islands and altogether it is 70 m thick. The measured vertical sections show a good stratigraphic correlation between the rocks of the western portion of the first island and those of Redonda Island. However, there is no correlation between the eastern and western portions of Santa Barbara Island, since they are very likely interrupted by the igneous intrusion and possibly by faulting. The sedimentary stack consists of deposits with alternated regressive and transgressive episodes interpreted as high frequency sequences. The coarse facies, sandstones and conglomerates, with abrupt or erosive bases record regressive phases. On the other hand, finer sandstones and siltstones facies, which are partly bioturbated, correspond to phases of a little sediment supply. In the central and eastern portions of Santa Barbara Island, there is a trend of progradational stacking, while both in the western portion of Santa Barbara and in Redonda islands an agradational trend is observed

  4. ROSSMAP; Regional Seismic Stratigraphic Correlations in the Victoria Land Basin and the Timing of Rifting Episodes

    NASA Astrophysics Data System (ADS)

    Davy, B. W.; Henrys, S. A.; Wilson, T. J.; Fielding, C. R.; Levy, R. H.; Andrill Mis-Science Team

    2010-12-01

    ROSSMAP aims to produce a new series of digital seismic stratigraphic and structural maps for the Ross Sea region, and develop reconstructions of past sedimentary volumes and paleo-bathymetry that will be used in numerical models to help identify tectonic and climate feedbacks. In particular, ROSSMAP will define targets for future drilling initiatives in the Ross Sea region, and provide a legacy of web-based electronic databases that will be available to other researcher. Interpretation in the Victoria Land Basin (VLB) has focused on establishing links to new and existing drill holes. Several regional seismic reflectors were mapped throughout the southern portion of the Victoria Land Basin (VLB) and are tied to the ANDRILL McMurdo Sound drill cores. The age of one prominent reflector (Ri - red, correlative with RSU-2) is 4.7-4.3 Ma based on a tie to AND-1B and extensively mapped in the VLB. Mapping, together with quantitative biostratigraphic correlation techniques, indicates that the red reflector is associated with relative sea-level fall resulting from ice-sheet growth and/or local tectonic uplift. Correlative sediments preserved in AND-1B indicate regional climatic warmth, which suggests that the red reflector is more likely related to a tectonic event. Furthermore, the onset of sediment accumulation at CIROS-2 post-dates 4.5 Ma, suggesting that local subsidence and creation of accommodation space began at this time. Two other stratigraphic horizons (Rh and Rg) have been extensively mapped where seismic data image above the seafloor multiple. Reflector Rh (dark green and correlative with RSU-4a marks a basin-wide unconformity. Near the western margin of the Victoria Land Basin, this horizon is a marked angular discordance with angularity increasing westward. In AND-1B Rh is correlated with the base of a ~180-m-thick interval of late Miocene-early Pliocene, pyrite-cemented, high-velocity volcanic sandstone and mudstone. Volcanic rocks in a tongue extending from

  5. Paleomagnetic Evidence for the Tectono-Stratigraphic Evolution of the Mt.Galili Area / MER / Ethiopia

    NASA Astrophysics Data System (ADS)

    Popp, F.; Scholger, R.

    2007-12-01

    zone in respect to the migration of the Afar triple junction since~4my *[6]. Another impact of this tectonic environment concerns the generation of weakened zones within the thinned crust induced by crosscutting structural items, subsequently allowing the supply of supercritical crustal melts and finally resulting in explosive eruptions. An extensive dispersed ignimbrite layer (Dhidinley Mb.) yielded an absolute age of ~4,1 my( sanidine, Ar/Ar)*[5]. B: Our stratigraphic age determination of the MGF is focused on magnetic reversal events documented in magmatic layers upon and below the mentioned Dhidinley ignimbrite selfsame demonstrating reverse polarity of its PMV. The uppermost Caashacado Mb. of the MGF exhibits normal polarity contained in gray ignimbrite layers at the top of the pile. We consider this reversal event providing a max. age of 3,58 my (Gauss/Gilbert crossover)*[2]. On the other hand the lowermost lava flow containing normal polarity was excavated by rotational rift block tilting. We consider this reversal event providing a min. age of 4,18 my (Gilbert/Cochiti crossover)*[2]. The mentioned age classifications are consistent with biochronological valuations *[3, 5]. References cited: *[1]: Besse, J. & Courtillot, V. (2002): J.Geophys.Res.107/B11/2300 *[2]: Cande, S.C., & Kent D.V.,(1995): J. Geophys. Res., 100, 6,093-6,095. *[3]: Kullmer O.et al (in rev.): Palaios. *[4]: Macchiarelli R.et al (2004): Coll. Antropol. 28 Suppl 2:65-76. *[5]: Urbanek C. et al (2005): Joannea Geologie und Paläontologie 6: 29-43. *[6]: Wolfenden E.,et al(2004): EPSL 224: 213-228.

  6. Tectono-stratigraphic evolution of the northeastern Pyrenean Foreland Basin

    NASA Astrophysics Data System (ADS)

    Christophoul, Frédéric; Ford, Mary; Grool, Arjan; Géraldine, Rougier; Louis, Hemmer

    2016-04-01

    The Aquitaine basin, on the northern flank of the Pyrenees was subject to intense hydrocarbon exploration until the 1990's, generating a huge dataset that has been under-exploited until now. In the framework of the French Pyramid ANR project this dataset was used, together with new field data, to reconstruct the evolution of this retroforeland basin. This study focuses on the eastern retroforeland, from the Corbières to east to the Toulouse Fault to the west. In terms of age, the main depocentres are however contemporary along the whole eastern basin: 1) From Upper Cretaceous to Paleocene (Campanian to Selandian) the early foreland basin, known as the "Flysch Trough", was filled by a succession of turbidites passing upward into fluvial sediments that prograded axially from the east. 2) From Thanetian to Oligocene, a second cycle started with a deepening upward trend until the Ypresian (inner carbonate platform to mixed open marine) and changed to a shallowing upward succession, passing from open marine sediments, coastal clastic deposits and then to coarse fluvial deposits from Upper Ypresian to Oligocene. Progradation was again initially axial from the east. However, a new south to north fluvial drainage developed from the emerging relief of the Pyrenees to the south. In terms of location and structural style of these depocentres, the salt-free eastern basin (from the Corbières in the east to the Toulouse Fault to the west) reveals a distinctive style to the salt-rich western basin. In eastern foreland (Corbières to Aude Valley), syntectonic depocentres migrated north as a series of wedge-top basins between Late Cretaceous and Late Eocene. The thick-skinned syn-sedimentary foreland structures progressively die out westward. In the western part of the study area (Plantaurel to Petites Pyrenees) stacked depocentres of the same age are preserved in the footwall of the North Pyrenean Frontal thrust recording a slower northward migration associated with a northward

  7. Automated Cyber Red Teaming

    DTIC Science & Technology

    2015-04-01

    possible attack paths for CRT. This report surveys the current state-of-the- art planning techniques, tools and frameworks, their performance at...6 3.3 State of the art Automated Planning ..................................................................... 7 3.3.1...automated planning to CRT problems. Finally, we recommend several state-of-the- art planning tools for trial and, more generally, when it is suitable to use

  8. Automating Index Preparation

    DTIC Science & Technology

    1987-03-23

    Automating Index Preparation* Pehong Chent Michael A. Harrison Computer Science Division University of CaliforniaI Berkeley, CA 94720 March 23, 1987...Abstract Index preparation is a tedious and time-consuming task. In this paper we indicate * how the indexing process can be automated in a way which...identified and analyzed. Specifically, we describe a framework for placing index commands in the document and a general purpose index processor which

  9. Automated Pilot Advisory System

    NASA Technical Reports Server (NTRS)

    Parks, J. L., Jr.; Haidt, J. G.

    1981-01-01

    An Automated Pilot Advisory System (APAS) was developed and operationally tested to demonstrate the concept that low cost automated systems can provide air traffic and aviation weather advisory information at high density uncontrolled airports. The system was designed to enhance the see and be seen rule of flight, and pilots who used the system preferred it over the self announcement system presently used at uncontrolled airports.

  10. Automated Lattice Perturbation Theory

    SciTech Connect

    Monahan, Christopher

    2014-11-01

    I review recent developments in automated lattice perturbation theory. Starting with an overview of lattice perturbation theory, I focus on the three automation packages currently "on the market": HiPPy/HPsrc, Pastor and PhySyCAl. I highlight some recent applications of these methods, particularly in B physics. In the final section I briefly discuss the related, but distinct, approach of numerical stochastic perturbation theory.

  11. Automated Status Notification System

    NASA Technical Reports Server (NTRS)

    2005-01-01

    NASA Lewis Research Center's Automated Status Notification System (ASNS) was born out of need. To prevent "hacker attacks," Lewis' telephone system needed to monitor communications activities 24 hr a day, 7 days a week. With decreasing staff resources, this continuous monitoring had to be automated. By utilizing existing communications hardware, a UNIX workstation, and NAWK (a pattern scanning and processing language), we implemented a continuous monitoring system.

  12. Automated Groundwater Screening

    SciTech Connect

    Taylor, Glenn A.; Collard, Leonard, B.

    2005-10-31

    The Automated Intruder Analysis has been extended to include an Automated Ground Water Screening option. This option screens 825 radionuclides while rigorously applying the National Council on Radiation Protection (NCRP) methodology. An extension to that methodology is presented to give a more realistic screening factor for those radionuclides which have significant daughters. The extension has the promise of reducing the number of radionuclides which must be tracked by the customer. By combining the Automated Intruder Analysis with the Automated Groundwater Screening a consistent set of assumptions and databases is used. A method is proposed to eliminate trigger values by performing rigorous calculation of the screening factor thereby reducing the number of radionuclides sent to further analysis. Using the same problem definitions as in previous groundwater screenings, the automated groundwater screening found one additional nuclide, Ge-68, which failed the screening. It also found that 18 of the 57 radionuclides contained in NCRP Table 3.1 failed the screening. This report describes the automated groundwater screening computer application.

  13. Metrology automation reliability

    NASA Astrophysics Data System (ADS)

    Chain, Elizabeth E.

    1996-09-01

    At Motorola's MOS-12 facility automated measurements on 200- mm diameter wafers proceed in a hands-off 'load-and-go' mode requiring only wafer loading, measurement recipe loading, and a 'run' command for processing. Upon completion of all sample measurements, the data is uploaded to the factory's data collection software system via a SECS II interface, eliminating the requirement of manual data entry. The scope of in-line measurement automation has been extended to the entire metrology scheme from job file generation to measurement and data collection. Data analysis and comparison to part specification limits is also carried out automatically. Successful integration of automated metrology into the factory measurement system requires that automated functions, such as autofocus and pattern recognition algorithms, display a high degree of reliability. In the 24- hour factory reliability data can be collected automatically on every part measured. This reliability data is then uploaded to the factory data collection software system at the same time as the measurement data. Analysis of the metrology reliability data permits improvements to be made as needed, and provides an accurate accounting of automation reliability. This reliability data has so far been collected for the CD-SEM (critical dimension scanning electron microscope) metrology tool, and examples are presented. This analysis method can be applied to such automated in-line measurements as CD, overlay, particle and film thickness measurements.

  14. Elements of EAF automation processes

    NASA Astrophysics Data System (ADS)

    Ioana, A.; Constantin, N.; Dragna, E. C.

    2017-01-01

    Our article presents elements of Electric Arc Furnace (EAF) automation. So, we present and analyze detailed two automation schemes: the scheme of electrical EAF automation system; the scheme of thermic EAF automation system. The application results of these scheme of automation consists in: the sensitive reduction of specific consummation of electrical energy of Electric Arc Furnace, increasing the productivity of Electric Arc Furnace, increase the quality of the developed steel, increasing the durability of the building elements of Electric Arc Furnace.

  15. Automated Telerobotic Inspection Of Surfaces

    NASA Technical Reports Server (NTRS)

    Balaram, J.; Prasad, K. Venkatesh

    1996-01-01

    Method of automated telerobotic inspection of surfaces undergoing development. Apparatus implementing method includes video camera that scans over surfaces to be inspected, in manner of mine detector. Images of surfaces compared with reference images to detect flaws. Developed for inspecting external structures of Space Station Freedom for damage from micrometeorites and debris from prior artificial satellites. On Earth, applied to inspection for damage, missing parts, contamination, and/or corrosion on interior surfaces of pipes or exterior surfaces of bridges, towers, aircraft, and ships.

  16. Stratigraphic And Lithofacies Study Of Distal Rain-Triggered Lahars: The Case Of West Coast Of Ecuador

    NASA Astrophysics Data System (ADS)

    Mulas, M.; Chunga, K.; Peña Carpio, E.; Falquez Torres, D. A.; Alcivar, R., Sr.; Lopez Coronel, M. C.

    2015-12-01

    The central zone of the coast of Ecuador at the north of Manabí Province, on the area comprised between Salango and Jama communities, is characterized by the presence of whitish to grey, centimeters to meters thick, consolidated to loose distal ash deposits. Recent archeological studies on Valdivia (3500 BC) and Manteña (800-1500 AC - Harris et al. 2004) civilizations remains link this deposits with the intense eruptive phases that afflicted Ecuador 700-900 years ago (Usselman, 2006). Stratigraphic evidences and bibliographic datations of paleosols (Estrada, 1962; Mothes and Hall, 2008), allowed to estimate that these deposits are linked with the 800 BP eruption of Quilotoa and the following eruptions of Cotopaxi. According to the Smith and Lowe classification (1991), the deposits outcropping on the coast (located at a distance greater than 160 km from the volcanic vents), varied from whitish to grey, loose to weakly consolidated, massive to weakly stratified, centimeters to meters thick, coarse to fine ash matrix layers (diluite streamflow facies) to massive, large angular to sub-rounded siltitic blocks-rich and coarse to medium ash matrix deposits (debris flow facies). These types of lithofacies are associated to a rain-triggered lahar (De Belizal et al., 2013). The presence in some stratigraphic sections of sharp contacts, laminated layers of very fine ash, and also cm-thick sand and silt layers between the ash beds of the same deposits permit to understand that the different pulses were generated in short periods and after a long period. Structures like water pipes imply that the lahar went into the sea (Schneider, 2004), and allow the reconstruction of the paleotopographic condition during the emplacement of these deposits. This study focuses on the characterization of these types of deposits, permit to understand the kind of risk that may affect the towns located on the coast of Ecuador after VEI 4 to 6 eruptions on short time and within years.

  17. Geodynamic Evolution of Northeastern Tunisia During the Maastrichtian-Paleocene Time: Insights from Integrated Seismic Stratigraphic Analysis

    NASA Astrophysics Data System (ADS)

    Abidi, Oussama; Inoubli, Mohamed Hédi; Sebei, Kawthar; Amiri, Adnen; Boussiga, Haifa; Nasr, Imen Hamdi; Salem, Abdelhamid Ben; Elabed, Mahmoud

    2016-12-01

    The Maastrichtian-Paleocene El Haria formation was studied and defined in Tunisia on the basis of outcrops and borehole data; few studies were interested in its three-dimensional extent. In this paper, the El Haria formation is reviewed in the context of a tectono-stratigraphic interval using an integrated seismic stratigraphic analysis based on borehole lithology logs, electrical well logging, well shots, vertical seismic profiles and post-stack surface data. Seismic analysis benefits from appropriate calibration with borehole data, conventional interpretation, velocity mapping, seismic attributes and post-stack model-based inversion. The applied methodology proved to be powerful for charactering the marly Maastrichtian-Paleocene interval of the El Haria formation. Migrated seismic sections together with borehole measurements are used to detail the three-dimensional changes in thickness, facies and depositional environment in the Cap Bon and Gulf of Hammamet regions during the Maastrichtian-Paleocene time. Furthermore, dating based on their microfossil content divulges local and multiple internal hiatuses within the El Haria formation which are related to the geodynamic evolution of the depositional floor since the Campanian stage. Interpreted seismic sections display concordance, unconformities, pinchouts, sedimentary gaps, incised valleys and syn-sedimentary normal faulting. Based on the seismic reflection geometry and terminations, seven sequences are delineated. These sequences are related to base-level changes as the combination of depositional floor paleo-topography, tectonic forces, subsidence and the developed accommodation space. These factors controlled the occurrence of the various parts of the Maastrichtian-Paleocene interval. Detailed examinations of these deposits together with the analysis of the structural deformation at different time periods allowed us to obtain a better understanding of the sediment architecture in depth and the delineation of

  18. Application of ground penetrating radar for identification of washover deposits and other stratigraphic features: Assateague Island, MD

    USGS Publications Warehouse

    Zaremba, Nicholas; Smith, Christopher G.; Bernier, Julie C.; Forde, Arnell S.

    2016-01-01

    A combination of ground penetrating radar (GPR) data, core data, and aerial photographs were analyzed to better understand the evolution of two portions of Assateague Island, Maryland. The focus of the study was to investigate the applicability of using GPR data to image washover deposits in the stratigraphic record. High amplitude reflections observed in two shore-perpendicular GPR profiles were correlated to shallow ( < 1 m) lithologic contacts observed in sediment cores. At these contacts, deposits consisting primarily of quartz sand overlie sediments with organic matter that include degraded plant root or stem material. The underlying organic matter likely represents the vegetated portion of the barrier island that was buried by washover fans deposited during hurricanes Irene (2011) and Sandy (2012), as indicated in high-resolution aerial photographs. The GPR data were able to delineate the washover deposits from the underlying stratigraphic unit; however, the radar data did not resolve finer structures necessary to definitively differentiate washover facies from other sand-rich deposits (e.g., flood-tide deltas and dunes). Other GPR profiles contain reflections that likely correlate to geomorphic features like tidal channels and vegetated zones observed in historical aerial imagery. Burial of these features by overwash fluxes were observed in the aerial imagery and thus the resulting radar sequence is largely interpreted as washover deposits. Deeper, channel-like features that have been infilled were also observed in shore-parallel profiles and these features coincide with scour channels observed in the 1966 aerial photography. Additional sedimentological data are required to determine what role overwash played in the in-filling of these features.

  19. Approaches to automated protein crystal harvesting

    PubMed Central

    Deller, Marc C.; Rupp, Bernhard

    2014-01-01

    The harvesting of protein crystals is almost always a necessary step in the determination of a protein structure using X-ray crystallographic techniques. However, protein crystals are usually fragile and susceptible to damage during the harvesting process. For this reason, protein crystal harvesting is the single step that remains entirely dependent on skilled human intervention. Automation has been implemented in the majority of other stages of the structure-determination pipeline, including cloning, expression, purification, crystallization and data collection. The gap in automation between crystallization and data collection results in a bottleneck in throughput and presents unfortunate opportunities for crystal damage. Several automated protein crystal harvesting systems have been developed, including systems utilizing microcapillaries, microtools, microgrippers, acoustic droplet ejection and optical traps. However, these systems have yet to be commonly deployed in the majority of crystallography laboratories owing to a variety of technical and cost-related issues. Automation of protein crystal harvesting remains essential for harnessing the full benefits of fourth-generation synchrotrons, free-electron lasers and microfocus beamlines. Furthermore, automation of protein crystal harvesting offers several benefits when compared with traditional manual approaches, including the ability to harvest microcrystals, improved flash-cooling procedures and increased throughput. PMID:24637746

  20. Automated fully-stressed design with NASTRAN

    NASA Technical Reports Server (NTRS)

    Wallerstein, D. V.; Haggenmacher, G. W.

    1976-01-01

    An automated strength sizing capability is described. The technique determines the distribution of material among the elements of a structural model. The sizing is based on either a fully stressed design or a scaled feasible fully stressed design. Results obtained from the application of the strength sizing to the structural sizing of a composite material wing box using material strength allowables are presented. These results demonstrate the rapid convergence of the structural sizes to a usable design.

  1. Stratigraphic and interregional changes in Pennsylvanian coal-swamp vegetation: Environmental inferences

    USGS Publications Warehouse

    Phillips, T.L.; Peppers, R.A.; DiMichele, W.A.

    1985-01-01

    Quantitative analysis of Pennsylvanian coal-swamp vegetation provides a means of inferring organization and structure of communities. Distribution of these communities further provides inferences about environmental factors, including paleoclimate. Our observations are based on in situ, structurally preserved peat deposits in coal-ball concretions from 32 coal seams in the eastern one-half of the United States and from several seams in western Europe and on spore assemblages from more than 150 seams. There were three times of particularly significant and nearly synchronous vegetational changes in the Midcontinent and Appalachian coal regions during the Pennsylvanian Period. Each was different in kind and magnitude. The first marked changes occurred during the early part of the Middle Pennsylvanian with the fluctuating decline in the high level of lycopod dominance. The abundance of cordaites increased. There was a rise in the occurrences of the lycopod herbs to form intercalated marshlands and an overall increase in floral diversity. Changes ensuing from this time also include shifts in dominant species of lycopod trees and a sustained rise in abundance and diversity of tree-fern spores. The next significant time of change was during the middle part of the Middle Pennsylvanian, representing both a culmination of earlier trends and expansions of cordaites in the Midcontinent where there was a maximum change in species without net loss of diversity. Tree ferns and medullosan pteridosperms attained subdominant levels of abundance and diverse lycopod species dominated except in the Atokan-Desmoinesian transition of the Midcontinent. The third and sharpest break occurred near the Middle-Late Pennsylvanian boundary when extinctionsof the dominant, coal-swamp lycopods allowed development of tree-fern dominance. The Late Pennsylvanian coal swamps apparently were colonized or recolonized mainly by species from outside coal swamps rather than by the survivor populations of

  2. Design Methodology for Automated Construction Machines

    DTIC Science & Technology

    1987-12-11

    positioning of structural members, and tunneling [3,5]. U.S. construction firms typically allocate little or no funding for R & D; progress to date...addition, four general purpose robots for building construction tasks [1] and the automation of sandblasting and concrete formwork cleaning have been

  3. A Process Model of Trust in Automation: A Signal Detection Theory Based Approach

    DTIC Science & Technology

    2014-01-01

    lead to trust in automation. We also discuss a simple process model , which helps us understand the results. Our experimental paradigm suggests that...participants are agnostic to the automation s behavior; instead, they merely focus on alarm rate. A process model suggests this is the result of a simple reward structure and a non-explicit cost of trusting the automation.

  4. Gas production from a cold, stratigraphically-bounded gas hydrate deposit at the Mount Elbert Gas Hydrate Stratigraphic Test Well, Alaska North Slope: Implications of uncertainties

    USGS Publications Warehouse

    Moridis, G.J.; Silpngarmlert, S.; Reagan, M.T.; Collett, T.; Zhang, K.

    2011-01-01

    As part of an effort to identify suitable targets for a planned long-term field test, we investigate by means of numerical simulation the gas production potential from unit D, a stratigraphically bounded (Class 3) permafrost-associated hydrate occurrence penetrated in the BPXA-DOE-USGS Mount Elbert Gas Hydrate Stratigraphic Test Well on North Slope, Alaska. This shallow, low-pressure deposit has high porosities (?? = 0.4), high intrinsic permeabilities (k = 10-12 m2) and high hydrate saturations (SH = 0.65). It has a low temperature (T = 2.3-2.6 ??C) because of its proximity to the overlying permafrost. The simulation results indicate that vertical wells operating at a constant bottomhole pressure would produce at very low rates for a very long period. Horizontal wells increase gas production by almost two orders of magnitude, but production remains low. Sensitivity analysis indicates that the initial deposit temperature is by the far the most important factor determining production performance (and the most effective criterion for target selection) because it controls the sensible heat available to fuel dissociation. Thus, a 1 ??C increase in temperature is sufficient to increase the production rate by a factor of almost 8. Production also increases with a decreasing hydrate saturation (because of a larger effective permeability for a given k), and is favored (to a lesser extent) by anisotropy. ?? 2010.

  5. Automated mesoscale winds determined from satellite imagery

    NASA Technical Reports Server (NTRS)

    1987-01-01

    A new automated technique for extracting mesoscale fields from GOES visible/infrared satellite imagery was developed. Quality control parameters were defined to allow objective editing of the wind fields. The system can produce equivalent or superior cloud wind estimates compared to the time consuming manual methods used on various interactive meteorological processing systems. Analysis of automated mesoscale cloud wind for a test case yields an estimated random error value one meter per second and produces both regional and mesoscale vector wind field structure and divergence patterns that are consistent in time and highly correlated with subsequent severe thunderstorm development.

  6. Power subsystem automation study

    NASA Technical Reports Server (NTRS)

    Imamura, M. S.; Moser, R. L.; Veatch, M.

    1983-01-01

    Generic power-system elements and their potential faults are identified. Automation functions and their resulting benefits are defined and automation functions between power subsystem, central spacecraft computer, and ground flight-support personnel are partitioned. All automation activities were categorized as data handling, monitoring, routine control, fault handling, planning and operations, or anomaly handling. Incorporation of all these classes of tasks, except for anomaly handling, in power subsystem hardware and software was concluded to be mandatory to meet the design and operational requirements of the space station. The key drivers are long mission lifetime, modular growth, high-performance flexibility, a need to accommodate different electrical user-load equipment, onorbit assembly/maintenance/servicing, and potentially large number of power subsystem components. A significant effort in algorithm development and validation is essential in meeting the 1987 technology readiness date for the space station.

  7. Automated telescope scheduling

    NASA Technical Reports Server (NTRS)

    Johnston, Mark D.

    1988-01-01

    With the ever increasing level of automation of astronomical telescopes the benefits and feasibility of automated planning and scheduling are becoming more apparent. Improved efficiency and increased overall telescope utilization are the most obvious goals. Automated scheduling at some level has been done for several satellite observatories, but the requirements on these systems were much less stringent than on modern ground or satellite observatories. The scheduling problem is particularly acute for Hubble Space Telescope: virtually all observations must be planned in excruciating detail weeks to months in advance. Space Telescope Science Institute has recently made significant progress on the scheduling problem by exploiting state-of-the-art artificial intelligence software technology. What is especially interesting is that this effort has already yielded software that is well suited to scheduling groundbased telescopes, including the problem of optimizing the coordinated scheduling of more than one telescope.

  8. Success with an automated computer control system

    NASA Astrophysics Data System (ADS)

    Roberts, M. L.; Moore, T. L.

    1991-05-01

    LLNL has successfully implemented a distributed computer control system for automated operation of an FN tandem accelerator. The control system software utilized is the Thaumaturgic Automated Control Logic (TACL) written by the Continuous Electron Beam Accelerator Facility and co-developed with LLNL. Using TACL, accelerator components are controlled through CAMAC using a two-tiered structure. Analog control and measurement are at 12 or 16 bit precision as appropriate. Automated operation has been implemented for several nuclear analytical techniques including hydrogen depth profiling and accelerator mass Spectrometry. An additional advantage of TACL lies in its expansion capabilities. Without disturbing existing control definitions and algorithms, additional control algorithms and display functions can be implemented quickly.

  9. Testing the Origins of Nonmarine Stratigraphic Sequences, Iglesia Basin, Northwest Argentina

    NASA Astrophysics Data System (ADS)

    Ruskin, B. G.; Jordan, T.

    2003-12-01

    The Iglesia Basin is an entirely nonmarine Andean foreland basin consisting of approximately 3.5 km of Tertiary strata unconformably overlying Paleozoic basement. Best described as a wedge-top basin, Iglesia Basin is located in San Juan Province, Argentina at S 30-31\\deg between the Frontal Cordillera and Precordillera fold-thrust belt. Interpretations of seismic reflection profiles and field reconnaissance have suggested basin-wide stratigraphic sequences. Additionally, radiometric and magnetostratigraphic data constrain sequence deposition between approximately 17 and 4 Ma. However, a fundamental question remains unanswered: temporal variability of which control caused development of unconformity-bound nonmarine sequences? Prior to this work, hypotheses about the factors at play, notably tectonism and climate change, remained untested, and fieldwork provided only localized information about the nature of the sequences. The present study examines basin lithofacies more broadly and will independently constrain discharge history (a proxy for climate) and intrabasinal tectonics. Thus far, fuller knowledge of the sedimentation patterns, structural expression, and volcanic history of Iglesia Basin is supplied by information from new outcrop localities near the northern paleomargin and basin center, and from reinterpretation of previously studied localities. A substantial volcanic component to the history of the oldest sequences is inferred from age relationships and continuity of deposits in proximity to the Cerro Negro intrabasinal andesitic center. Reassessment of field-assigned sequence boundaries in terms of continuity and expression, both along-strike and across intrabasinal faults, suggests that lithofacies shifts are more prevalent than erosive surfaces. Radiometric dating of additional tuffaceous units in the Tertiary sequences will allow more conclusive correlation among discontinuous outcrops. Floodplain assemblages of Aridosols and Inceptisols indicate

  10. Stratigraphic significance and global distribution of the δ13C Suess effect during the Anthropocene

    NASA Astrophysics Data System (ADS)

    Paul, André; Mulitza, Stefan

    2015-04-01

    The Anthropocene is the proposed term for the present geological epoch (from the time of the Industrial Revolution onwards), during which human influence significantly impacts the environment. We argue that the burning of isotopically light fossil fuel that causes the so-called 'δ13C Suess effect' leaves such a strong imprint on marine sediments that it may serve to define the onset of this geological epoch, at least since the so-called 'Great Acceleration', i.e., the second half of the 20th century. Sediment data with high temporal resolution from the recent past indeed reveal a trend that corresponds to a negative carbon isotope excursion of the order of one permil, comparable to carbon isotope excursions in the deep past that define stratigraphic boundaries such as the Paleocene-Eocene Thermal Maximum (PETM). A global carbon cycle model based on the MIT general circulation model (MITgcm), fitted with carbon isotopes 13C and 14C and forced with observed changes in the atmospheric carbon dioxide partial pressure and carbon isotopic ratio 13C/12C, allows to investigate the temporal evolution and three-dimensional structure of the anomaly. We show the carbon isotopic ratios of fossil shells of benthic foraminifera (δ13Cc) from two ocean sediment cores GeoB6008 (31° N) und GeoB9501 (17° N) over the Anthropocene (mainly the 20th century). The decrease in δ13Cc at 31° N is about 0.8 permil; off Mauretania (at 17° N in the shadow zone of the subtropical gyre) it still amounts to about 0.4 permil. While the magnitude of the change in the global carbon cycle model is similar, the difference is smaller: The decrease in the model is around 0.9 permil near the location of the northern core and around 0.8 permil near the location of the southern core. The smaller difference of only about 0.1 permil points to a bias in the simulated as opposed to the observed ventilation of the thermocline. We further use a carbon cycle multi-box model to extrapolate this change in δ13

  11. Source potential and sequence stratigraphic characterization of microbial evaporitic mudrocks: Upper Permian Zechstein Group, Northern Germany

    NASA Astrophysics Data System (ADS)

    Hammes, Ursula; Mutti, Maria

    2013-04-01

    Microbial evaporitic carbonate mudrocks are important source rocks throughout much of the earth history. Some of the largest hydrocarbon provinces are potentially sourced by evaporite source rocks such as the Cretaceous and Jurassic in the Middle East, the Tertiary in Spain, the Permian in northern Germany, the Devonian in Canada, and the Pennsylvanian in the USA. Carbonate mudrocks deposited under mesosaline conditions are often over-looked and dismissed as potential source rocks. However, preservation and accumulation of organic matter in salinity-layered intraplatform epeiric depressions and restricted basin centers are significant. These mudrocks may not only constitute the source but also exhibit reservoir qualities. Slope and basin laminated mudrocks were investigated for their source and reservoir potential using sequence stratigraphic and geochemical techniques to investigate the exploration potential of the northern German Upper Permian Zechstein Formation. The lower Zechstein cycles Z1 and Z2 are characterized by calcareous to argillaceous, laminated, organic-rich mudstones with TOC (total organic carbon) contents ranging mostly <1% in the Z2 and >6% in the Z1 cycle. Maturities range from 0.9 to >3% Ro depending on depth of burial for these two cycles. While the Z1 mudrocks deposited above the Rotliegend clastic section are more argillaceous and clay-rich grading upward from calcareous mudstones to intraclast, coated grain, thrombolitic wacke- and packstones into coated-grain grainstones, the Z2 mudrocks are dominated by calcareous to dolomitic laminated mudstones. Both cycles are characterized by microbially bound carbonates ranging from thrombolytic to crenulated laminated structures that are overlain by anhydrite and salt. Stacking patterns of the Z1 3rd-order cycle reveal three 5th-order parasequences stacking into two 4th-order sequences; Z2 3rd-order cycle is composed of three 4th-order parasequences that first deepen and then shallow upwards

  12. The Manannan Impact Crater on Europa: Determination of Surface Compositions of Key Stratigraphic Units

    NASA Astrophysics Data System (ADS)

    Dalton, J. B.; Prockter, L. M.; Shirley, J. H.; Phillips, C. B.; Kamp, L.

    2011-12-01

    Mannanan is a 22-km-diameter impact crater located at 3 N, 240 W on Europa's orbital trailing side. Detailed high resolution geologic mapping by Moore et al. (2001) revealed the likely presence of extensive deposits of impact melt materials largely filling the crater floor, together with surrounding continuous ejecta deposits that may have been excavated from Europa's interior. Terrains surrounding Mannanàn include some of Europa's visibly darkest surfaces, with extensive areas of chaos, traversed by the prominent structure of Belus Linea. The Mannannàn impact crater and its surrounding areas were imaged during the C3 orbital encounter of the Galileo Mission by the orbiter's Near-Infrared Mapping Spectrometer (NIMS). This NIMS observation (C3ENLINEA01A) has not been subjected to a detailed investigation until now, possibly due to the presence of moderate levels of radiation noise. A "despiked" version of this observation has been produced using methods described in Shirley et al. (2010). In addition, new geologic mapping precisely registered to the NIMS coverage of Manannàn and its surroundings allows the extraction of high-quality near-infrared spectra that are specific to individual geologic units and morphological features. We will present linear mixture modeling solutions for the compositions of several of Manannàn's key stratigraphic units, including the crater floor deposits and the adjacent chaos and linea materials. We will interpret these results in the context of ongoing investigations of the interplay of exogenic and endogenic influences on the surface composition of Europa. This work was performed at the Jet Propulsion Laboratory-California Institute of Technology, Johns Hopkins University-Applied Physics Laboratory, and the SETI Institute under a contract with NASA. Support by NASA's Outer Planets Research program is gratefully acknowledged. Moore, J. M. and 25 others 2001. Impact Features on Europa: Results of the Galileo Europa Mission (GEM

  13. Automating the CMS DAQ

    SciTech Connect

    Bauer, G.; et al.

    2014-01-01

    We present the automation mechanisms that have been added to the Data Acquisition and Run Control systems of the Compact Muon Solenoid (CMS) experiment during Run 1 of the LHC, ranging from the automation of routine tasks to automatic error recovery and context-sensitive guidance to the operator. These mechanisms helped CMS to maintain a data taking efficiency above 90% and to even improve it to 95% towards the end of Run 1, despite an increase in the occurrence of single-event upsets in sub-detector electronics at high LHC luminosity.

  14. Automated Library System Specifications.

    DTIC Science & Technology

    1986-06-01

    AD-A78 95 AUTOMATED LIBRARY SYSTEM SPECIFICATIONS(U) ARMY LIBRARY /i MANAGEMENT OFFICE ALEXANDRIA VA ASSISTANT CHIEF OF STAFF FOR INFORMATION... MANAGEMENT M B BONNETT JUN 86 UNCLASSIFIED F/G 9/2 NLEElIIhllEEEEE IllEEEEEllllEI .1lm lliml * ~I fI.L25 MI, [OCM RL,;OCLUTO fl. ’N k~ AUTOMATED LIBRARY...SYSTEM SPECIFICATIONS .,I Prepared by Mary B. Bonnett ARMY LIBRARY MANAGEMENT OFFICE OFFICE OF THE ASSISTANT CHIEF OF STAFF FOR INFORMATION MANAGEMENT Lij

  15. Automated gas chromatography

    DOEpatents

    Mowry, Curtis D.; Blair, Dianna S.; Rodacy, Philip J.; Reber, Stephen D.

    1999-01-01

    An apparatus and process for the continuous, near real-time monitoring of low-level concentrations of organic compounds in a liquid, and, more particularly, a water stream. A small liquid volume of flow from a liquid process stream containing organic compounds is diverted by an automated process to a heated vaporization capillary where the liquid volume is vaporized to a gas that flows to an automated gas chromatograph separation column to chromatographically separate the organic compounds. Organic compounds are detected and the information transmitted to a control system for use in process control. Concentrations of organic compounds less than one part per million are detected in less than one minute.

  16. Automated knowledge generation

    NASA Technical Reports Server (NTRS)

    Myler, Harley R.; Gonzalez, Avelino J.

    1988-01-01

    The general objectives of the NASA/UCF Automated Knowledge Generation Project were the development of an intelligent software system that could access CAD design data bases, interpret them, and generate a diagnostic knowledge base in the form of a system model. The initial area of concentration is in the diagnosis of the process control system using the Knowledge-based Autonomous Test Engineer (KATE) diagnostic system. A secondary objective was the study of general problems of automated knowledge generation. A prototype was developed, based on object-oriented language (Flavors).

  17. The stratigraphic sequence of volcanic and sedimentary units in the north polar region of Mars

    NASA Technical Reports Server (NTRS)

    Botts, M. E.

    1980-01-01

    Based on photogeologic mapping of Viking orbiter images of Mars, four distinct informal stratigraphic units are defined for the region north of 70 degrees N latitude. They are: (a) bulbous plains, (b) mantled plains, (c) dune deposits, and (d) layered deposits/perennial ice. Background information on the Martian polar caps is provided from telescopic observation, Mariner mission results, and Viking mission results (August 1976-November 1978). A description, and an interpretation and distribution of the stratigraphic units are presented. Surface winds, which were determined from dune orientations, and discussed and implications for the source of circumpolar dune materials are delineated. A list of the Viking Orbiter imagery used in the research, the computer programs for crater size frequency distributions, and the crater size frequency data are presented.

  18. Time-stratigraphic correlation of lower Wilcox valley-fill sequences, Colorado and Lavaca Counties, Texas

    SciTech Connect

    Devine, P.E.; Wheeler, D.M. )

    1989-09-01

    Late Paleocene and early Eocene lower Wilcox strata in southeast Texas are characterized principally by sandstone-rich deposits of fluvial and deltaic systems that prograded from a stable platform area into an unstable growth-faulted shelf margin setting. In contrast, incised valley systems, initiated during episodes of sea level lowering and filled dominantly with mud during subsequent transgressions, punctuate several lower Wilcox intervals. Further, valley-fill sequences are known to provide seals and/or reservoirs for a number of stratigraphically trapped hydrocarbon accumulations. Time-stratigraphic correlation of lower Wilcox strata provides improved differentiation of stacked valley-fill sequences and thereby more refined interpretation of depositional history and more accurate mapping for exploration purposes.

  19. Stratigraphic Subdivision of the Transvaal Dolomite from ERTS imagery. [South Africa

    NASA Technical Reports Server (NTRS)

    Grootenboer, J.; Eriksson, K.; Truswell, J.

    1974-01-01

    ERTS imagery has revealed the presence of broad stratigraphic subdivisions in the previously undifferentiated Transvaal Dolomite of the western Tranvaal, Republic of South Africa. While detailed field mapping in areas of good outcrop, as well as borehole logging has recently led to the recognition of a stratigraphy in the Transvaal Dolomite of the central Transvaal, poor outcrop in the western Transvaal has to date prevented this. The ERTS-imagery, however, clearly reveals the presence of six, and in the far west seven, distinct stratigraphic zones extending along strike for a distance of at least 200 km. The investigation clearly demonstrates the potential applications of ERTS-imagery in geological studies, even in a country where the geology is supposedly well known.

  20. Tectono-stratigraphic development of the Coastal Group of south-eastern Jamaica

    NASA Astrophysics Data System (ADS)

    James-Williamson, Sherene A.; Mitchell, Simon F.; Ramsook, Ryan

    2014-03-01

    The sedimentary succession of southeastern Jamaica preserves a depositional record of accommodation changes and tectonic events for the last 14 Ma. The depositional systems which occur in the area have been classified according to distinct tectono-stratigraphic packages based on the depositional environments, rapid facies changes, and or significant erosion surfaces. This paper places the sedimentology and geochemistry within a tectonic evolutionary framework for the northern margin of the Caribbean Plate over the last 14 Ma. This involves considering issues of changing accommodation; deformation episodes including folding and faulting and the subsequent cutting of unconformities. A model for the tectono-stratigraphic development of southeastern Jamaica is also proposed. The model incorporates critical surfaces, major faults, subsidence and uplift which later influence the depositional environments.

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

    SciTech Connect

    Drellack, S.L. Jr.

    1997-02-01

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

  2. An integrated sequence stratigraphic and chronostratigraphic analysis of the Pliocene, Tiburon Basin succession, Mejillones Peninsula, Chile

    NASA Astrophysics Data System (ADS)

    Tapia, Claudio A.; Wilson, Gary S.; Ishman, Scott E.; Wilke, Hans G.; Wartho, Jo-Anne; Winter, Diane; Martínez-Pardo, Rubén

    2015-08-01

    We present new findings from Pliocene marine sediments from the Mejillones Peninsula Tiburon Basin of the northern Chile continental margin that provide constraints for the global sea level record. Sedimentologic and sequence stratigraphic studies reveal facies associations of a continental shelf setting. Textural variations indicate that coarsening and fining up of the succession are due to relative sea level rise and fall, respectively. Magnetostratigraphy was integrated with bio- and tephro- stratigraphic data to construct a record of high-resolution chronology. The age model constrains the Tiburon Basin lower section between 4.2 Ma and 2.8 Ma. The record is likely to be controlled in part by sea level change with orbital periodicities of obliquity (∼ 40 ka of frequency) and, between 3.2 Ma and 2.9 Ma a high-amplitude sea level fall is correlated to global climatic deterioration and the onset of major Northern Hemisphere glaciations.

  3. Altering user' acceptance of automation through prior automation exposure.

    PubMed

    Bekier, Marek; Molesworth, Brett R C

    2016-08-22

    Air navigation service providers worldwide see increased use of automation as one solution to overcome the capacity constraints imbedded in the present air traffic management (ATM) system. However, increased use of automation within any system is dependent on user acceptance. The present research sought to determine if the point at which an individual is no longer willing to accept or cooperate with automation can be manipulated. Forty participants underwent training on a computer-based air traffic control programme, followed by two ATM exercises (order counterbalanced), one with and one without the aid of automation. Results revealed after exposure to a task with automation assistance, user acceptance of high(er) levels of automation ('tipping point') decreased; suggesting it is indeed possible to alter automation acceptance. Practitioner Summary: This paper investigates whether the point at which a user of automation rejects automation (i.e. 'tipping point') is constant or can be manipulated. The results revealed after exposure to a task with automation assistance, user acceptance of high(er) levels of automation decreased; suggesting it is possible to alter automation acceptance.

  4. Remote Stratigraphic Analysis: Combined TM and AIS Results in the Wind River/bighorn Basin Area, Wyoming

    NASA Technical Reports Server (NTRS)

    Lang, H. R.; Paylor, E. D.; Adams, S.

    1985-01-01

    An in-progress study demonstrates the utility of airborne imaging spectrometer (AIS) data for unraveling the stratigraphic evolution of a North American, western interior foreland basin. AIS data are used to determine the stratigraphic distribution of mineralogical facies that are diagnostic of specific depositional environments. After wavelength and amplitude calibration using natural ground targets with known spectral characteristics, AIS data identify calcite, dolomite, gypsum and montmorillonite-bearing strata in the Permian-Cretaceous sequence. Combined AIS and TM results illustrate the feasibility of spectral stratigraphy, remote analysis of stratigraphic sequences.

  5. RCrane: semi-automated RNA model building.

    PubMed

    Keating, Kevin S; Pyle, Anna Marie

    2012-08-01

    RNA crystals typically diffract to much lower resolutions than protein crystals. This low-resolution diffraction results in unclear density maps, which cause considerable difficulties during the model-building process. These difficulties are exacerbated by the lack of computational tools for RNA modeling. Here, RCrane, a tool for the partially automated building of RNA into electron-density maps of low or intermediate resolution, is presented. This tool works within Coot, a common program for macromolecular model building. RCrane helps crystallographers to place phosphates and bases into electron density and then automatically predicts and builds the detailed all-atom structure of the traced nucleotides. RCrane then allows the crystallographer to review the newly built structure and select alternative backbone conformations where desired. This tool can also be used to automatically correct the backbone structure of previously built nucleotides. These automated corrections can fix incorrect sugar puckers, steric clashes and other structural problems.

  6. The 3D Euler solutions using automated Cartesian grid generation

    NASA Technical Reports Server (NTRS)

    Melton, John E.; Enomoto, Francis Y.; Berger, Marsha J.

    1993-01-01

    Viewgraphs on 3-dimensional Euler solutions using automated Cartesian grid generation are presented. Topics covered include: computational fluid dynamics (CFD) and the design cycle; Cartesian grid strategy; structured body fit; grid generation; prolate spheroid; and ONERA M6 wing.

  7. Architecture of delta plain deposits in a sequence stratigraphic framework: The upper carboniferous of eastern Kentucky

    SciTech Connect

    Buter, S.J. )

    1993-09-01

    Fluvio-deltaic sequences of the Upper Carboniferous Four Corners formation in the Appalachian basin of eastern Kentucky are reinterpreted using sequence stratigraphic techniques. A data set of correlated large-scale road-cut exposures and continuous coring records was processed and used in a three-dimensional (3-D) reservoir modeling program in order to obtain a detailed model of the 3-D architecture of the stratigraphic succession. The architecture of the sediment bodies is related to the position within the depositional system. The 140-m-thick Four Corners formation comprises three facies associations, which are cyclically organized. The boundaries between the cycles are formed by erosive surfaces, and are developed as lowstand incised valleys. A subsequent base-level rise resulted in the infilling of these valleys with amalgamated stacked channel deposits (early transgressive systems tract). Flood plain aggradation and extensive peat accumulation occurred during progressive rise (transgressive systems tracts). Marine flooding took place in the upper part of the sequence (late transgressive systems tract) and was followed by prograding mouthbar deposits during base-level stabilization (highstand). The sequence stratigraphic approach to these Upper Carboniferous cyclothems highlights the importance of relative sea level changes and may improve our understanding of sediment body geometries and architecture, resulting in more accurate predictive geological reservoir models of the subsurface.

  8. Modeling of stratigraphic columns using Markov Chains and Gibbs sampling algorithms, Campo Oritupano, Venezuela.

    NASA Astrophysics Data System (ADS)

    Durán, E.

    2012-04-01

    The interbeded sandstones, siltstones and shale layers within the stratigraphic units of the Oficina Formation were stochastically characterized. The units within the Oritupano field are modeled using the information from 12 wells and a post-stack 3-D seismic cube. The Markov Chain algorithm was successful at maintaining the proportion of lithotypes of the columns in the study area. Different transition probability matrixes are evaluated by changing the length of the sequences represented in the transition matrix and how this choice of length affects ciclicity and the genetic relations between lithotypes. The Gibbs algorithm, using small sequences as building blocks for modeling, kept the main stratigraphic succession according to the geology. Although the modeled stratigraphy depends strongly on initial conditions, the use of longer sequences in the substitution helps not to overweight the transition counts from one lithotype to the same in the main diagonal of the probability matrix of the Markov Chain in the Gibbs algorithm. A methodology based on the phase spectrum of the seismic trace for tying the modeled sequences with the seismic data is evaluated and discussed. The results point to the phase spectrum as an alternate way to cross-correlate synthetic seismograms with the seismic trace in favor of the well known amplitude correlation. Finally, a map of net sand over the study area is generated from the modeled columns and compared with previous stratigraphic and facies analysis at the levels of interest.

  9. Spheroidal carbonaceous particles are a defining stratigraphic marker for the Anthropocene

    NASA Astrophysics Data System (ADS)

    Swindles, Graeme T.; Watson, Elizabeth; Turner, T. Edward; Galloway, Jennifer M.; Hadlari, Thomas; Wheeler, Jane; Bacon, Karen L.

    2015-05-01

    There has been recent debate over stratigraphic markers used to demarcate the Anthropocene from the Holocene Epoch. However, many of the proposed markers are found only in limited areas of the world or do not reflect human impacts on the environment. Here we show that spheroidal carbonaceous particles (SCPs), a distinct form of black carbon produced from burning fossil fuels in energy production and heavy industry, provide unambiguous stratigraphic markers of the human activities that have rapidly changed planet Earth over the last century. SCPs are found in terrestrial and marine sediments or ice cores in every continent, including remote areas such as the high Arctic and Antarctica. The rapid increase in SCPs mostly occurs in the mid-twentieth century and is contemporaneous with the ‘Great Acceleration’. It therefore reflects the intensification of fossil fuel usage and can be traced across the globe. We integrate global records of SCPs and propose that the global rapid increase in SCPs in sedimentary records can be used to inform a Global Standard Stratigraphic Age for the Anthropocene. A high-resolution SCP sequence from a lake or peatland may provide the much-needed ‘Golden Spike’ (Global Boundary Stratotype Section and Point).

  10. Spheroidal carbonaceous particles are a defining stratigraphic marker for the Anthropocene.

    PubMed

    Swindles, Graeme T; Watson, Elizabeth; Turner, T Edward; Galloway, Jennifer M; Hadlari, Thomas; Wheeler, Jane; Bacon, Karen L

    2015-05-28

    There has been recent debate over stratigraphic markers used to demarcate the Anthropocene from the Holocene Epoch. However, many of the proposed markers are found only in limited areas of the world or do not reflect human impacts on the environment. Here we show that spheroidal carbonaceous particles (SCPs), a distinct form of black carbon produced from burning fossil fuels in energy production and heavy industry, provide unambiguous stratigraphic markers of the human activities that have rapidly changed planet Earth over the last century. SCPs are found in terrestrial and marine sediments or ice cores in every continent, including remote areas such as the high Arctic and Antarctica. The rapid increase in SCPs mostly occurs in the mid-twentieth century and is contemporaneous with the 'Great Acceleration'. It therefore reflects the intensification of fossil fuel usage and can be traced across the globe. We integrate global records of SCPs and propose that the global rapid increase in SCPs in sedimentary records can be used to inform a Global Standard Stratigraphic Age for the Anthropocene. A high-resolution SCP sequence from a lake or peatland may provide the much-needed 'Golden Spike' (Global Boundary Stratotype Section and Point).

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

    USGS Publications Warehouse

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

    2003-01-01

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

  12. Stratigraphic Context of Old Crow Tephra, Holitna Lowland, Interior Southwest Alaska

    USGS Publications Warehouse

    Waythomas, C.F.; Lea, P.D.; Walter, R.C.

    1993-01-01

    A thick deposit of Old Crow tephra was discovered in a bluff exposure along the middle Holitna River near the Kulukbuk Hills (61??20???N latitude, 157??10???W longitude) in interior southwest Alaska. This locality is the southwesternmost-known deposit of Old Crow tephra in Alaska. Thickness and grain-size data from this site support a source volcano in the eastern Aleutian arc. Pleistocene stratigraphic sequences in the lowland are dominated by upward-fining eolian sand-sheet deposits and loess separated by organic silt. These deposits record at least two episodes of regional glaciation and an intervening nonglacial period (marine oxygen isotope stage 3, stage 5, or both). Old Crow tephra crops out near the top of the lower upward-fining eolian unit, indicating that the ash erupted near the end of an interval of periglacial eolian sedimentation. The sequence of eolian deposits that contain Old Crow tephra probably accumulated during the latter part of marine oxygen isotope stage 6, whereas the overlying eolian sequence formed during the last glaciation (stage 2). This stratigraphic position is consistent with other stratigraphic contexts for the tephra and with fission-track and thermoluminescence ages of ca. 140,000 ?? 10,000 yr B.P.

  13. Spheroidal carbonaceous particles are a defining stratigraphic marker for the Anthropocene

    PubMed Central

    Swindles, Graeme T.; Watson, Elizabeth; Turner, T. Edward; Galloway, Jennifer M.; Hadlari, Thomas; Wheeler, Jane; Bacon, Karen L.

    2015-01-01

    There has been recent debate over stratigraphic markers used to demarcate the Anthropocene from the Holocene Epoch. However, many of the proposed markers are found only in limited areas of the world or do not reflect human impacts on the environment. Here we show that spheroidal carbonaceous particles (SCPs), a distinct form of black carbon produced from burning fossil fuels in energy production and heavy industry, provide unambiguous stratigraphic markers of the human activities that have rapidly changed planet Earth over the last century. SCPs are found in terrestrial and marine sediments or ice cores in every continent, including remote areas such as the high Arctic and Antarctica. The rapid increase in SCPs mostly occurs in the mid-twentieth century and is contemporaneous with the ‘Great Acceleration’. It therefore reflects the intensification of fossil fuel usage and can be traced across the globe. We integrate global records of SCPs and propose that the global rapid increase in SCPs in sedimentary records can be used to inform a Global Standard Stratigraphic Age for the Anthropocene. A high-resolution SCP sequence from a lake or peatland may provide the much-needed ‘Golden Spike’ (Global Boundary Stratotype Section and Point). PMID:26020614

  14. A technique for recording polycrystalline structure and orientation during in situ deformation cycles of rock analogues using an automated fabric analyser.

    PubMed

    Peternell, M; Russell-Head, D S; Wilson, C J L

    2011-05-01

    Two in situ plane-strain deformation experiments on norcamphor and natural ice using synchronous recording of crystal c-axis orientations have been performed with an automated fabric analyser and a newly developed sample press and deformation stage. Without interrupting the deformation experiment, c-axis orientations are determined for each pixel in a 5 × 5 mm sample area at a spatial resolution of 5 μm/pixel. In the case of norcamphor, changes in microstructures and associated crystallographic information, at a strain rate of ∼2 × 10(-5) s(-1), were recorded for the first time during a complete in situ deformation-cycle experiment that consisted of an annealing, deformation and post-deformation annealing path. In the case of natural ice, slower external strain rates (∼1 × 10(-6) s(-1)) enabled the investigation of small changes in the polycrystal aggregate's crystallography and microstructure for small amounts of strain. The technical setup and first results from the experiments are presented.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  16. Automating Small Libraries.

    ERIC Educational Resources Information Center

    Swan, James

    1996-01-01

    Presents a four-phase plan for small libraries strategizing for automation: inventory and weeding, data conversion, implementation, and enhancements. Other topics include selecting a system, MARC records, compatibility, ease of use, industry standards, searching capabilities, support services, system security, screen displays, circulation modules,…

  17. Automated conflict resolution issues

    NASA Technical Reports Server (NTRS)

    Wike, Jeffrey S.

    1991-01-01

    A discussion is presented of how conflicts for Space Network resources should be resolved in the ATDRSS era. The following topics are presented: a description of how resource conflicts are currently resolved; a description of issues associated with automated conflict resolution; present conflict resolution strategies; and topics for further discussion.

  18. Automated Accounting. Instructor Guide.

    ERIC Educational Resources Information Center

    Moses, Duane R.

    This curriculum guide was developed to assist business instructors using Dac Easy Accounting College Edition Version 2.0 software in their accounting programs. The module consists of four units containing assignment sheets and job sheets designed to enable students to master competencies identified in the area of automated accounting. The first…

  19. Automated Student Model Improvement

    ERIC Educational Resources Information Center

    Koedinger, Kenneth R.; McLaughlin, Elizabeth A.; Stamper, John C.

    2012-01-01

    Student modeling plays a critical role in developing and improving instruction and instructional technologies. We present a technique for automated improvement of student models that leverages the DataShop repository, crowd sourcing, and a version of the Learning Factors Analysis algorithm. We demonstrate this method on eleven educational…

  20. Personnel Department Automation.

    ERIC Educational Resources Information Center

    Wilkinson, David

    In 1989, the Austin Independent School District's Office of Research and Evaluation was directed to monitor the automation of personnel information and processes in the district's Department of Personnel. Earlier, a study committee appointed by the Superintendent during the 1988-89 school year identified issues related to Personnel Department…

  1. Validating Automated Speaking Tests

    ERIC Educational Resources Information Center

    Bernstein, Jared; Van Moere, Alistair; Cheng, Jian

    2010-01-01

    This paper presents evidence that supports the valid use of scores from fully automatic tests of spoken language ability to indicate a person's effectiveness in spoken communication. The paper reviews the constructs, scoring, and the concurrent validity evidence of "facility-in-L2" tests, a family of automated spoken language tests in Spanish,…

  2. Automated Essay Scoring

    ERIC Educational Resources Information Center

    Dikli, Semire

    2006-01-01

    The impacts of computers on writing have been widely studied for three decades. Even basic computers functions, i.e. word processing, have been of great assistance to writers in modifying their essays. The research on Automated Essay Scoring (AES) has revealed that computers have the capacity to function as a more effective cognitive tool (Attali,…

  3. Automated Microbial Genome Annotation

    SciTech Connect

    Land, Miriam

    2009-05-29

    Miriam Land of the DOE Joint Genome Institute at Oak Ridge National Laboratory gives a talk on the current state and future challenges of moving toward automated microbial genome annotation at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  4. Automated Administrative Data Bases

    NASA Technical Reports Server (NTRS)

    Marrie, M. D.; Jarrett, J. R.; Reising, S. A.; Hodge, J. E.

    1984-01-01

    Improved productivity and more effective response to information requirements for internal management, NASA Centers, and Headquarters resulted from using automated techniques. Modules developed to provide information on manpower, RTOPS, full time equivalency, and physical space reduced duplication, increased communication, and saved time. There is potential for greater savings by sharing and integrating with those who have the same requirements.

  5. Automated Management Of Documents

    NASA Technical Reports Server (NTRS)

    Boy, Guy

    1995-01-01

    Report presents main technical issues involved in computer-integrated documentation. Problems associated with automation of management and maintenance of documents analyzed from perspectives of artificial intelligence and human factors. Technologies that may prove useful in computer-integrated documentation reviewed: these include conventional approaches to indexing and retrieval of information, use of hypertext, and knowledge-based artificial-intelligence systems.

  6. Building Automation Systems.

    ERIC Educational Resources Information Center

    Honeywell, Inc., Minneapolis, Minn.

    A number of different automation systems for use in monitoring and controlling building equipment are described in this brochure. The system functions include--(1) collection of information, (2) processing and display of data at a central panel, and (3) taking corrective action by sounding alarms, making adjustments, or automatically starting and…

  7. Guide to Library Automation.

    ERIC Educational Resources Information Center

    Toohill, Barbara G.

    Directed toward librarians and library administrators who wish to procure automated systems or services for their libraries, this guide offers practical suggestions, advice, and methods for determining requirements, estimating costs and benefits, writing specifications procuring systems, negotiating contracts, and installing systems. The advice…

  8. Microcontroller for automation application

    NASA Technical Reports Server (NTRS)

    Cooper, H. W.

    1975-01-01

    The description of a microcontroller currently being developed for automation application was given. It is basically an 8-bit microcomputer with a 40K byte random access memory/read only memory, and can control a maximum of 12 devices through standard 15-line interface ports.

  9. Automated EEG acquisition

    NASA Technical Reports Server (NTRS)

    Frost, J. D., Jr.; Hillman, C. E., Jr.

    1977-01-01

    Automated self-contained portable device can be used by technicians with minimal training. Data acquired from patient at remote site are transmitted to centralized interpretation center using conventional telephone equipment. There, diagnostic information is analyzed, and results are relayed back to remote site.

  10. Automated Inadvertent Intruder Application

    SciTech Connect

    Koffman, Larry D.; Lee, Patricia L.; Cook, James R.; Wilhite, Elmer L.

    2008-01-15

    The Environmental Analysis and Performance Modeling group of Savannah River National Laboratory (SRNL) conducts performance assessments of the Savannah River Site (SRS) low-level waste facilities to meet the requirements of DOE Order 435.1. These performance assessments, which result in limits on the amounts of radiological substances that can be placed in the waste disposal facilities, consider numerous potential exposure pathways that could occur in the future. One set of exposure scenarios, known as inadvertent intruder analysis, considers the impact on hypothetical individuals who are assumed to inadvertently intrude onto the waste disposal site. Inadvertent intruder analysis considers three distinct scenarios for exposure referred to as the agriculture scenario, the resident scenario, and the post-drilling scenario. Each of these scenarios has specific exposure pathways that contribute to the overall dose for the scenario. For the inadvertent intruder analysis, the calculation of dose for the exposure pathways is a relatively straightforward algebraic calculation that utilizes dose conversion factors. Prior to 2004, these calculations were performed using an Excel spreadsheet. However, design checks of the spreadsheet calculations revealed that errors could be introduced inadvertently when copying spreadsheet formulas cell by cell and finding these errors was tedious and time consuming. This weakness led to the specification of functional requirements to create a software application that would automate the calculations for inadvertent intruder analysis using a controlled source of input parameters. This software application, named the Automated Inadvertent Intruder Application, has undergone rigorous testing of the internal calculations and meets software QA requirements. The Automated Inadvertent Intruder Application was intended to replace the previous spreadsheet analyses with an automated application that was verified to produce the same calculations and

  11. Automating spectral measurements

    NASA Astrophysics Data System (ADS)

    Goldstein, Fred T.

    2008-09-01

    This paper discusses the architecture of software utilized in spectroscopic measurements. As optical coatings become more sophisticated, there is mounting need to automate data acquisition (DAQ) from spectrophotometers. Such need is exacerbated when 100% inspection is required, ancillary devices are utilized, cost reduction is crucial, or security is vital. While instrument manufacturers normally provide point-and-click DAQ software, an application programming interface (API) may be missing. In such cases automation is impossible or expensive. An API is typically provided in libraries (*.dll, *.ocx) which may be embedded in user-developed applications. Users can thereby implement DAQ automation in several Windows languages. Another possibility, developed by FTG as an alternative to instrument manufacturers' software, is the ActiveX application (*.exe). ActiveX, a component of many Windows applications, provides means for programming and interoperability. This architecture permits a point-and-click program to act as automation client and server. Excel, for example, can control and be controlled by DAQ applications. Most importantly, ActiveX permits ancillary devices such as barcode readers and XY-stages to be easily and economically integrated into scanning procedures. Since an ActiveX application has its own user-interface, it can be independently tested. The ActiveX application then runs (visibly or invisibly) under DAQ software control. Automation capabilities are accessed via a built-in spectro-BASIC language with industry-standard (VBA-compatible) syntax. Supplementing ActiveX, spectro-BASIC also includes auxiliary serial port commands for interfacing programmable logic controllers (PLC). A typical application is automatic filter handling.

  12. An Automated Biological Dosimetry System

    NASA Astrophysics Data System (ADS)

    Lorch, T.; Bille, J.; Frieben, M.; Stephan, G.

    1986-04-01

    The scoring of structural chromosome aberrations in peripheral human blood lymphocytes can be used in biological dosimetry to estimate the radiation dose which an individual has received. Especially the dicentric chromosome is a rather specific indicator for an exposure to ionizing radiation. For statistical reasons, in the low dose range a great number of cells must be analysed, which is a very tedious task. The resulting high cost of a biological dose estimation limits the application of this method to cases of suspected irradiation for which physical dosimetry is not possible or not sufficient. Therefore an automated system has been designed to do the major part of the routi