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Sample records for automated stratigraphic structural

  1. Stratigraphic and Structural Development of the Ontong Java Plateau

    NASA Astrophysics Data System (ADS)

    Inoue, H.; Coffin, M. F.; Nakamura, Y.; Mochizuki, K.; Kroenke, L. W.

    2005-12-01

    The Ontong Java Plateau (OJP) in the western equatorial Pacific is Earth's most voluminous large igneous province (LIP). It encompasses an area of approximately 2.0×106 km2, and its maximum crustal thickness exceeds 30 km. Emplacement of the OJP at approximately 122 Ma represents a significant transfer of mass and energy from the mantle to the crust. We completed the first east-west and north-south multichannel seismic reflection (MCS) transects of the OJP during R/V Hakuho Maru cruise KH98-01 Leg 2 (February 1998) and R/V Kairei cruise KR05-01 (January 2005). On the basis of new and existing MCS data, single channel seismic (SCS) reflection data, DSDP/ODP results, and other geophysical data, we address the stratigraphic and structural development of the OJP. Specifically, our geophysical work focuses on:1) the origin of semi-continuous reflections within acoustic basement of the OJP based on synthetic seismogram modeling and DSDP/ODP results; 2) the relationship between the OJP and its neighboring Nauru and Lyra basins based on stratigraphic and structural analysis of MCS and SCS data; 3) the development of Tauu atoll on the southern flank of the OJP based on stratigraphic and structural analysis of MCS and SCS data integrated with DSDP/ODP results. Our initial results suggest that: 1)the semi-continuous reflections are probably thick, flat igneous flows/sill or flows/sills interbedded with sediment; 2) the transition between the Nauru Basin and the OJP is relatively smooth, implying that massive OJP and Nauru Basin magmatism were contemporaneous and geographically continuous, whereas the transition between the Lyra Basin and the northern flank of the OJP is faulted, characterized by horst and graben structures; 3) strong reflections (lava flows or a volcaniclastic wedge) emanating lie beneath sediment but above OJP basement, indicating a Tertiary, probably Paleogene, age for formation of the atoll.

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

    NASA Astrophysics Data System (ADS)

    Lagmay, Alfredo Mahar Francisco A.

    2006-06-01

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

  3. Structural and stratigraphic evolution of the Anza rift, Kenya

    NASA Astrophysics Data System (ADS)

    Bosworth, William; Morley, Chris K.

    1994-09-01

    The Anza rift is a large, multi-phase continental rift basin that links the Lamu embayment of southern Kenya with the South Sudan rifts. Extension and deposition of syn-rift sediments are known to have commenced by the Neocomian. Aptian-Albian strata have, thus far, not been encountered during limited drilling campaigns and, in at least one well, are replaced by a significant unconformity. Widespread rifting occurred during the Cenomanian to Maastrichtian, and continued into the Early Tertiary. Marine waters appear to have reached the central Anza rift in the Cenomanian, and a second marine incursion may have occurred during the Campanian. As no wells have yet reached basement in the basinal deeps, the possibility exists that the Anza rift may have initiated in the Late Jurassic, in conjunction with extension to the south in the Lamu embayment and to the north in the Blue Nile rift of Sudan. Structural and stratigraphic evolution in the Anza rift followed a pattern that has now been inferred in several rift settings. Early phases of extension were accommodated by moderately dipping faults that produced large stratal rotations. Sedimentary environments were dominantly fluvial, with associated small lakes and dune fields. Volcanic activity is documented for the early Neocomian, but its extent is unknown. This initial style of deformation and sedimentation may have continued through several of the earliest pulses of rifting. By the Late Cretaceous, a new system of steeply dipping faults was established, that produced a deep basin without significant rotation of strata in the north, and only minor rotation in the south. This basin geometry favored the establishment of large, deep lakes, which occasionally were connected to the sea. The older basins were partly cannibalized during the sedimentary in-filling of these successor basins. Early Senonian volcanism was encountered in one well, and reflection seismic evidence suggests that one or more thick, regionally

  4. 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.

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

    SciTech Connect

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

    1981-01-01

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

  6. 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.

  7. 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.

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

    SciTech Connect

    Rubin, P A; Lemiszki, P J

    1992-01-01

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

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

    SciTech Connect

    Rubin, P.A.; Lemiszki, P.J.

    1992-12-31

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

  10. New structural and stratigraphic interpretation of Lake Superior basin from hydrocarbon exploration geophysics and geology

    SciTech Connect

    Dickas, A.B.

    1996-09-01

    Between October 1987 and April 1992, two deep boreholes were drilled along the south shore of Lake Superior in a test of the hydrocarbon potential of the conglomerate, sandstone and shale composing the Middle Proterozoic Oronto Group ({approximately}1 billion years). These drilling ventures, preceded by geophysical programs, and combined with wireline and core information, support new interpretations of the structural and stratigraphic geology associated with the Midcontinent Rift System in the Lake Superior district. No.7-22 Terra-Patrick: A stratigraphic, but not structural fit. This borehole in Bayfield County, Wisconsin, drilled an expected sequence of Oronto Group clastic redbeds. No viable hydrocarbon shows were encountered. Six second reflection seismology profiles collected in northwestern Wisconsin indicate the Douglas Fault decreases in throw in an easterly direction, changing to a fold northeast of the borehole. This termination is associated with the south flank of White`s Ridge, a pre-rift residual high identified through modeling studies and seismic interpretations by local absence of Midcontinent Rift volcanics and overlying strata. To the southwest of Isle Royale, the pre-rift Grand Marias Ridge exhibits similar characteristics. No.1-29 St. Amour: A structural, but not stratigraphic, fit. Drilled in Alger County, Michigan, the St. Amour well appears to bottom in pre-rift metamorphic basement rocks. This hole was 100% cored. No hydrocarbon shows were reported. Reflection seismology profile analyses verify a change in strike, from northeast to southeast, of the Keweenaw Fault in the eastern Lake Superior Basin. The drilled section included 6,000 feet of pre-Paleozoic red-beds containing cross-bedding, ripple marks, and multiple fining-upward strata.

  11. 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.

  12. Centrifuge modelling of fold—thrust structures in a tripartite stratigraphic succession

    NASA Astrophysics Data System (ADS)

    Dixon, John M.; Tirrul, Rein

    Analog models measuring 127 × 76 mm in plan were deformed at 2500-4000 g in a centrifuge. Scaled stratigraphic sequences were constructed of anisotropic multilayers with individual layers of Plasticine and silicone putty as thin as 40 μm. The plasticine—silicone putty multilayers are analogs for interbedded competent carbonates and clastics, and incompetent pelites, given the model ratios of acceleration, 2500 g; length, 5 × 10 -6; specific gravity, 0.6; time 10 -10. Modelling of fold—thrust tectonics emphasizes the influence of stratigraphic succession on structural evolution. The models are constructed with a tripartite stratigraphic succession comprising basal and upper, well-laminated and incompetent units, and a middle, somewhat more isotropic and competent unit. The models deform by three mechanisms: layer-parallel shortening, folding and thrust faulting. They reproduce a number of fold—thrust relationships that have been observed in nature. Folds are typically periclinal, in en échelon arrays. Folds and thrusts are arcuate in plan, reflecting differential shortening. Fold attitudes grade from upright at high levels to overturned at deeper levels within a structural panel, reflecting drag against the basal décollement; fold axial surfaces and thrust faults are listric. While competent units may be offset by localized displacement on thrust faults, the discrete faults may die out both upwards and downwards into regions of ductile strain in less-competent units. Thrust faults appear to follow staircase trajectories through the strata, transecting incompetent units at shallow angles to bedding and competent units at steeper angles. However, the apparent staircase pattern results from propagation of a fault along a relatively straight trajectory through previously-folded strata. Foreland-verging thrusts are more common than back thrusts; the latter have steeper dips. The models suggest a mechanism of thrust-ramp nucleation following detachment folding

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  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. 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

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

    NASA Astrophysics Data System (ADS)

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

    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.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. Tectonic-stratigraphic division and blind fold structures in Nansha Waters, South China Sea

    NASA Astrophysics Data System (ADS)

    Yan, Pin; Liu, Hailing

    2004-12-01

    Extensive multiple-channel reflection seismic data have been collected in the Nansha (Spratley Islands) Waters, the southern margin of the South China Sea. Stratigraphic correlation is shown with focus on a comprehensive geophysiXcal survey line run from offshore NW Sabah to offshore SE Vietnam. According to the varying tectono-stratigraphy from southeast to northwest, five tectonic belts can be determined, i.e. the Palawan-Borneo Nappe, Nansha Trough, Nanwei-Liyue Compressive Belt, Zheng'he Extensional Belt and the Circum-Southwest Subbasin Belt. In the Palawan-Borneo Nappe, Neogene-Quaternary deposits were highly upthrust northwestwards, resulting in a series of moderately to tightly folded anticlines separated by open synclines. The Nansha Trough was a narrow, deep-water belt filled with thick, undisturbed Neogene-Quaternary deposits. The Nanwei-Liyue Compressive Belt was dominated by strongly folded paleo-anticlines overlain by an undeformed sedimentary cap with a pronounced hiatus of Paleogene sediments. The Zheng'he Extensional Belt consisted of a rugged topography and Paleogene half-grabens bounded by listic faults. The major extensional faults were reactivated to cut through the overlying Neogene-Quaternary deposits. Over the Circum-Southwest Subbasin Belt, Neogene-Quaternary deposits draped on the largely subsided fault blocks related to the Late Oligocene-Mid-Miocene seafloor spreading. Based on the regional stratigraphic correlation, the prominent paleo-anticlines found within the Nanwei-Liyue Compressive Belt are deduced to consist of mainly Mesozoic marine sediments that were compressed in the Late Mesozoic Era. Therefore, the Nansha Microcontinent Block is shown to be a collision complex assembled during Late Mesozoic Era.

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

    USGS Publications Warehouse

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

    1976-01-01

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

  10. REdiii: a pipeline for automated structure solution.

    PubMed

    Bohn, Markus Frederik; Schiffer, Celia A

    2015-05-01

    High-throughput crystallographic approaches require integrated software solutions to minimize the need for manual effort. REdiii is a system that allows fully automated crystallographic structure solution by integrating existing crystallographic software into an adaptive and partly autonomous workflow engine. The program can be initiated after collecting the first frame of diffraction data and is able to perform processing, molecular-replacement phasing, chain tracing, ligand fitting and refinement without further user intervention. Preset values for each software component allow efficient progress with high-quality data and known parameters. The adaptive workflow engine can determine whether some parameters require modifications and choose alternative software strategies in case the preconfigured solution is inadequate. This integrated pipeline is targeted at providing a comprehensive and efficient approach to screening for ligand-bound co-crystal structures while minimizing repetitiveness and allowing a high-throughput scientific discovery process. PMID:25945571

  11. REdiii: a pipeline for automated structure solution

    PubMed Central

    Bohn, Markus-Frederik; Schiffer, Celia A.

    2015-01-01

    High-throughput crystallographic approaches require integrated software solutions to minimize the need for manual effort. REdiii is a system that allows fully automated crystallographic structure solution by integrating existing crystallographic software into an adaptive and partly autonomous workflow engine. The program can be initiated after collecting the first frame of diffraction data and is able to perform processing, molecular-replacement phasing, chain tracing, ligand fitting and refinement without further user intervention. Preset values for each software component allow efficient progress with high-quality data and known parameters. The adaptive workflow engine can determine whether some parameters require modifications and choose alternative software strategies in case the preconfigured solution is inadequate. This integrated pipeline is targeted at providing a comprehensive and efficient approach to screening for ligand-bound co-crystal structures while minimizing repetitiveness and allowing a high-throughput scientific discovery process. PMID:25945571

  12. 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.

  13. 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.

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

    SciTech Connect

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

    1986-04-01

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

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

    SciTech Connect

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

    1988-01-01

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

  16. A stratigraphic and structural reappraisal of Central Malawi:Results of a geotraverse

    NASA Astrophysics Data System (ADS)

    Piper, D. P.; Chikusa, C. M.; Chisale, R. T. K.; Kaphwiyo, C. E.; Malunga, G. W. P.; Nkhoma, J. E. S.; Klerkx, J. M.

    The Precambrian Malawi Basement Complex, metasediments and orthogneisses of central Malawi are discussed. Three metasedimentary associations, intruded by a suite of low TiO 2, olivine tholeiite gabbros, are recognised and interpreted as a continental shelf-rise assemblage. A fourth unit, the psammitic Mchinji Group, is reinterpreted as a proximal facies equivalent of the other paragneisses. Widespread, early granitoid and alkaline plutonism is recognised and interpreted as an anorogenic magmatic province. Metamorphic transformations and deformational styles are locally controlled, probably by variable H 20. The first deformation produced migmatitic fabrics in aweu> paragneisses while water-deficient orthogneisses retained their igneous textures orrecrystall ised to granoblastic aggregates, locally with granulite-facies mineralogy. Anhydrous, kelyphitic rims formed around olivine in the metagabbros. Later deformation produced tectonte fabrics with lower- amphibolite, locally greenschist, mineralogy. Fold vergence and stretching lineations suggest N or NW tectonic transport directions and the overall structure is interpreted as a foreland fold and thrust zone with steep structures produced by imbricatlon. Previous isotope studies bracket deformation between c.1100Ma and c.450Ma, contemporary with deformation of the Muva Supergroup in the Irumide Belt of Zambia which may be the foreland-ward extention of the studv area.

  17. 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.

  18. 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.

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

    SciTech Connect

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

    1988-02-01

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

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

    SciTech Connect

    Ware, G.D. )

    1987-02-01

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

  1. 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.

  2. 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.…

  3. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  5. 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.

  6. The Phenix Software for Automated Determination of Macromolecular Structures

    PubMed Central

    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.

    2011-01-01

    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 favour 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. PMID:21821126

  7. 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

  8. 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.

  9. 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.

  10. Automated assembly of a tetrahedral truss structure using machine vision

    NASA Technical Reports Server (NTRS)

    Doggett, William R.

    1992-01-01

    The Automated Structures Assembly Laboratory is a unique facility at NASA Langley Research Center used to investigate the robotic assembly of truss structures. Two special-purpose end-effectors have been used to assemble 102 truss members and 12 panels into an 8-meter diameter structure. One end-effector is dedicated to truss member insertion, while a second end-effector is used to install panels. Until recently, the robot motions required to construct the structure were developed iteratively using the facility hardware. Recent work at Langley has resulted in a compact machine vision system capable of providing position information relative to targets on the structure. Use of the vision system to guide the robot from an approach point 10 to 18 inches from the structure, offsetting model inaccuracies, permits robot motion based on calculated points as a first step toward use of preplanned paths from an automated path planner. This paper presents recent work at Langley highlighting the application of the machine vision system during truss member insertion.

  11. Automated Low-Cost Photogrammetry for Flexible Structure Monitoring

    NASA Astrophysics Data System (ADS)

    Wang, C. H.; Mills, J. P.; Miller, P. E.

    2012-07-01

    Structural monitoring requires instruments which can provide high precision and accuracy, reliable measurements at good temporal resolution and rapid processing speeds. Long-term campaigns and flexible structures are regarded as two of the most challenging subjects in monitoring engineering structures. Long-term monitoring in civil engineering is generally considered to be labourintensive and financially expensive and it can take significant effort to arrange the necessary human resources, transportation and equipment maintenance. When dealing with flexible structure monitoring, it is of paramount importance that any monitoring equipment used is able to carry out rapid sampling. Low cost, automated, photogrammetric techniques therefore have the potential to become routinely viable for monitoring non-rigid structures. This research aims to provide a photogrammetric solution for long-term flexible structural monitoring purposes. The automated approach was achieved using low-cost imaging devices (mobile phones) to replace traditional image acquisition stations and substantially reduce the equipment costs. A self-programmed software package was developed to deal with the hardware-software integration and system operation. In order to evaluate the performance of this low-cost monitoring system, a shaking table experiment was undertaken. Different network configurations and target sizes were used to determine the best configuration. A large quantity of image data was captured by four DSLR cameras and four mobile phone cameras respectively. These image data were processed using photogrammetric techniques to calculate the final results for the system evaluation.

  12. Automated analysis of fundamental features of brain structures.

    PubMed

    Lancaster, Jack L; McKay, D Reese; Cykowski, Matthew D; Martinez, Michael J; Tan, Xi; Valaparla, Sunil; Zhang, Yi; Fox, Peter T

    2011-12-01

    Automated image analysis of the brain should include measures of fundamental structural features such as size and shape. We used principal axes (P-A) measurements to measure overall size and shape of brain structures segmented from MR brain images. The rationale was that quantitative volumetric studies of brain structures would benefit from shape standardization as had been shown for whole brain studies. P-A analysis software was extended to include controls for variability in position and orientation to support individual structure spatial normalization (ISSN). The rationale was that ISSN would provide a bias-free means to remove elementary sources of a structure's spatial variability in preparation for more detailed analyses. We studied nine brain structures (whole brain, cerebral hemispheres, cerebellum, brainstem, caudate, putamen, hippocampus, inferior frontal gyrus, and precuneus) from the 40-brain LPBA40 atlas. This paper provides the first report of anatomical positions and principal axes orientations within a standard reference frame, in addition to "shape/size related" principal axes measures, for the nine brain structures from the LPBA40 atlas. Analysis showed that overall size (mean volume) for internal brain structures was preserved using shape standardization while variance was reduced by more than 50%. Shape standardization provides increased statistical power for between-group volumetric studies of brain structures compared to volumetric studies that control only for whole brain size. To test ISSN's ability to control for spatial variability of brain structures we evaluated the overlap of 40 regions of interest (ROIs) in a standard reference frame for the nine different brain structures before and after processing. Standardizations of orientation or shape were ineffective when not combined with position standardization. The greatest reduction in spatial variability was seen for combined standardizations of position, orientation and shape. These

  13. A screened automated structural search with semiempirical methods

    NASA Astrophysics Data System (ADS)

    Ota, Yukihiro; Ruiz-Barragan, Sergi; Machida, Masahiko; Shiga, Motoyuki

    2016-03-01

    We developed an interface program between a program suite for an automated search of chemical reaction pathways, GRRM, and a program package of semiempirical methods, MOPAC. A two-step structural search is proposed as an application of this interface program. A screening test is first performed by semiempirical calculations. Subsequently, a reoptimization procedure is done by ab initio or density functional calculations. We apply this approach to ion adsorption on cellulose. The computational efficiency is also shown for a GRRM search. The interface program is suitable for the structural search of large molecular systems for which semiempirical methods are applicable.

  14. Towards Automated Structure-Based NMR Resonance Assignment

    NASA Astrophysics Data System (ADS)

    Jang, Richard; Gao, Xin; Li, Ming

    We propose a general framework for solving the structure-based NMR backbone resonance assignment problem. The core is a novel 0-1 integer programming model that can start from a complete or partial assignment, generate multiple assignments, and model not only the assignment of spins to residues, but also pairwise dependencies consisting of pairs of spins to pairs of residues. It is still a challenge for automated resonance assignment systems to perform the assignment directly from spectra without any manual intervention. To test the feasibility of this for structure-based assignment, we integrated our system with our automated peak picking and sequence-based resonance assignment system to obtain an assignment for the protein TM1112 with 91% recall and 99% precision without manual intervention. Since using a known structure has the potential to allow one to use only N-labeled NMR data and avoid the added expense of using C-labeled data, we work towards the goal of automated structure-based assignment using only such labeled data. Our system reduced the assignment error of Xiong-Pandurangan-Bailey-Kellogg's contact replacement (CR) method, which to our knowledge is the most error-tolerant method for this problem, by 5 folds on average. By using an iterative algorithm, our system has the added capability of using the NOESY data to correct assignment errors due to errors in predicting the amino acid and secondary structure type of each spin system. On a publicly available data set for Ubiquitin, where the type prediction accuracy is 83%, we achieved 91% assignment accuracy, compared to the 59% accuracy that was obtained without correcting for typing errors.

  15. 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)

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

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

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

  17. Stratigraphic, structural and U-Pb geochronologic investigation of lower Paleozoic eugeoclinal strata in the Kootenay Arc, NE Washington and SE British Columbia

    SciTech Connect

    Smith, M.T.

    1990-01-01

    The Kootenay Arc in northwestern Washington and southeastern British Columbia is transitional between: (1) lower Paleozoic autochthonous miogeoclinal strata and Paleozoic to Mesozoic eugeoclinal terranes of uncertain paleogeographic affinity (e.g., the Quesnel terrane); and (2) areas where Devono-Mississippian tectonism was of a compressional nature, and areas in northern British Columbia and southern Yukon Territory where coeval deformation was evidently of an extensional nature. Stratigraphic, structural, and U-Pb geochronologic studies focussed primarily on portions of the Lardeau Group in the Trout Lake area in the northern Kootenay Arc and the Covada Group in the southern Kootenay Arc. As a result of these studies, the following concepts are proposed: (1) lower Paleozoic eugeoclinal strata can be correlated along the length of the Arc; (2) these strata are in fault contact with miogeoclinal strata along the length of the Arc; (3) a contractional event of pre-Mississippian and perhaps Devono-Mississippian age is recorded in the Kootenay Arc; (4) despite faulted contacts, the eugeoclinal strata are parautochthonous and derived from adjacent portions of North America; and (5) structures and stratigraphy in the Kootenay Arc are broadly correlative with those in the Roberts Mountains allochthon in central Nevada. Two important implications of this study are that: (1) through a series of stratigraphic linkages it can be demonstrated that the Quesnel terrane, a Mesozoic arc-related assemblage often regarded on the basis of faunal evidence to be exotic, is parautochthonous; and (2) the Antler Orogeny, often regarded as a localized disturbance, affected at least 1,200 km of the Cordilleran margin, and perhaps the entire Cordilleran margin.

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

    PubMed

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

    2012-04-01

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

  19. Towards automated crystallographic structure refinement with phenix.refine

    PubMed Central

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

    2012-01-01

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

  20. Automated extraction of chemical structure information from digital raster images

    PubMed Central

    Park, Jungkap; Rosania, Gus R; Shedden, Kerby A; Nguyen, Mandee; Lyu, Naesung; Saitou, Kazuhiro

    2009-01-01

    Background To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated. Results This paper aims to provide critical reviews for these systems and also report our recent development of ChemReader – a fully automated tool for extracting chemical structure diagrams in research articles and converting them into standard, searchable chemical file formats. Basic algorithms for recognizing lines and letters representing bonds and atoms in chemical structure diagrams can be independently run in sequence from a graphical user interface-and the algorithm parameters can be readily changed-to facilitate additional development specifically tailored to a chemical database annotation scheme. Compared with existing software programs such as OSRA, Kekule, and CLiDE, our results indicate that ChemReader outperforms other software systems on several sets of sample images from diverse sources in terms of the rate of correct outputs and the accuracy on extracting molecular substructure patterns. Conclusion The availability of ChemReader as a cheminformatic tool for extracting chemical structure information from digital raster images allows research and development groups to enrich their chemical structure databases by annotating the entries with published research articles. Based on its stable performance and high accuracy, ChemReader may be sufficiently accurate for annotating the chemical database with links to scientific research

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

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

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

  2. 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. PMID:25487359

  3. 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

  4. 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. PMID:25978453

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

    PubMed Central

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

    2015-01-01

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

  6. Automated 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.

  7. 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.

  8. 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, Jr.

    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

  9. 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 Appendix D to Part 360 Banks and Banking FEDERAL DEPOSIT INSURANCE CORPORATION REGULATIONS AND STATEMENTS OF GENERAL POLICY RESOLUTION AND RECEIVERSHIP RULES Pt. 360, App. D Appendix D to Part 360—Sweep/Automated Credit Account File Structure...

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. Upward-Facies Transition Analysis in Interpretation of Stratigraphic Sequence Within the Wetumpka Impact Structure, a Cretaceous marine impact in Alabama, USA

    NASA Astrophysics Data System (ADS)

    King, D. T.; Petruny, L. W.; Neathery, T. L.

    2002-12-01

    During 1998, two core holes were drilled near the geographic center of the Wetumpka impact structure (32°, 31.2 min N; 86°, 10.4 min W), a 7.6 km diameter, Late Cretaceous complex impact structure located in Elmore County, Alabama. The core holes were located ~ 200 m apart and both penetrated ~ 200 m of unconsolidated material and rock. The structure-filling stratigraphy consists of two units. (1) A ~ 60 m-thick, unconsolidated, cross-stratified, red gravelly sand forms an upper (surficial) unit that comprises nearly all mappable terrain within Wetumpka's crystalline rim. (In some locales, this surficial unit contains mega-blocks of target rock several 100 m2 in area -- but not at the drill sites). (2) A ~ 140 m-thick lower unit of inter-bedded, impact-related lithologies, which are not exposed well at the surface. The order of lithologies in the lower unit differed between wells; and there were three main lithologies: (1) sandy breccia and sand units (most common); (2) impact breccias (containing shocked quartz in matrix); and (3) target rock blocks. The latter consisted of 1 to 10 m blocks of (a) schist or gneiss (i.e., deep crystalline basement) or (b) sedimentary strata (i.e., clayey sands and sandy clays of the Upper Cretaceous target layers -- Tuscaloosa Group, Eutaw Formation, and Mooreville Chalk). In order to understand better what the significance of the order of lithologies drilled in the two wells, we used a classical method for upward facies-transition analysis employed in sedimentary stratigraphy. The original method of R. C. Selley was used in this instance to help envision stratigraphic relationships among the structure-filling lithologies of the lower unit. This technique is a 'first-order Markov process' wherein 'the probability of the process being in a given state at a particular time may be deduced from knowledge of the immediately preceding state.' Upward facies-transition analysis applied to the lower unit's interbedded lithologies

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

    PubMed

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

    2012-06-01

    Automated structure verification using (1)H NMR data or a combination of (1)H and heteronuclear single-quantum correlation (HSQC) data is gaining more interest as a routine application for qualitative evaluation of large compound libraries produced by synthetic chemistry. The goal of this automated software method is to identify a manageable subset of compounds and data that require human review. In practice, the automated method will flag structure and data combinations that exhibit some inconsistency (i.e. strange chemical shifts, conflicts in multiplicity, or overestimated and underestimated integration values) and validate those that appear consistent. One drawback of this approach is that no automated system can guarantee that all passing structures are indeed correct structures. The major reason for this is that approaches using only (1)H or even (1)H and HSQC spectra often do not provide sufficient information to properly distinguish between similar structures. Therefore, current implementations of automated structure verification systems allow, in principle, false positive results. Presented in this work is a method that greatly reduces the probability of an automated validation system passing incorrect structures (i.e. false positives). This novel method was applied to automatically validate 127 non-proprietary compounds from several commercial sources. Presented also is the impact of this approach on false positive and false negative results. PMID:22549844

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

    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

  20. 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

  1. 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.

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

    PubMed Central

    2014-01-01

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

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

    SciTech Connect

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

    2012-04-01

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

  5. 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.

  6. 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.

  7. 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.

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

    PubMed

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

    2015-08-01

    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 (15)N-(1)H 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 score, for guiding model selection during the iterative NOE interpretation process, and (2) identifying incorrect NOESY cross peak assignments caused by errors in the NMR resonance assignment list. These improvements provide a more robust automated NOESY analysis program, ASDP, with the unique capability of being utilized with alternative structure generation and refinement programs including CYANA, CNS, and/or Rosetta. PMID:26081575

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

  10. 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.

  11. 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. PMID:18688764

  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. About the automated pattern creation of 3D jacquard double needle bed warp knitted structures

    NASA Astrophysics Data System (ADS)

    Renkens, W.; Kyosev, Y.

    2016-07-01

    Three dimensional structures can be produced on jacquard warp knitting machines with double needle bed. This work presents theoretical considerations about the modelling and simulation of these structures. After that a method is described, how to obtain production parameters from the simulation data. The analysis demonstrates, that the automated pattern creation of 3D structures is not always possible and not all mathematical solutions of the problem can be knittable.

  14. Automated Detection of Eruptive Structures for Solar Eruption Prediction

    NASA Astrophysics Data System (ADS)

    Georgoulis, Manolis K.

    2012-07-01

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

  15. Non-Uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination.

    PubMed

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

    2015-08-24

    High-resolution structure determination of small proteins in solution is one of the big assets of NMR spectroscopy in structural biology. Improvements in the 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 [(1)H,(1)H]-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

  16. Automated search of natively folded protein fragments for high-throughput structure determination in structural genomics.

    PubMed Central

    Kuroda, Y.; Tani, K.; Matsuo, Y.; Yokoyama, S.

    2000-01-01

    Structural genomic projects envision almost routine protein structure determinations, which are currently imaginable only for small proteins with molecular weights below 25,000 Da. For larger proteins, structural insight can be obtained by breaking them into small segments of amino acid sequences that can fold into native structures, even when isolated from the rest of the protein. Such segments are autonomously folding units (AFU) and have sizes suitable for fast structural analyses. Here, we propose to expand an intuitive procedure often employed for identifying biologically important domains to an automatic method for detecting putative folded protein fragments. The procedure is based on the recognition that large proteins can be regarded as a combination of independent domains conserved among diverse organisms. We thus have developed a program that reorganizes the output of BLAST searches and detects regions with a large number of similar sequences. To automate the detection process, it is reduced to a simple geometrical problem of recognizing rectangular shaped elevations in a graph that plots the number of similar sequences at each residue of a query sequence. We used our program to quantitatively corroborate the premise that segments with conserved sequences correspond to domains that fold into native structures. We applied our program to a test data set composed of 99 amino acid sequences containing 150 segments with structures listed in the Protein Data Bank, and thus known to fold into native structures. Overall, the fragments identified by our program have an almost 50% probability of forming a native structure, and comparable results are observed with sequences containing domain linkers classified in SCOP. Furthermore, we verified that our program identifies AFU in libraries from various organisms, and we found a significant number of AFU candidates for structural analysis, covering an estimated 5 to 20% of the genomic databases. Altogether, these

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

    NASA Technical Reports Server (NTRS)

    Harvey, Michael Stephen

    1993-01-01

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

  18. Development of a machine vision guidance system for automated assembly of space structures

    NASA Technical Reports Server (NTRS)

    Cooper, Eric G.; Sydow, P. Daniel

    1992-01-01

    The topics are presented in viewgraph form and include: automated structural assembly robot vision; machine vision requirements; vision targets and hardware; reflective efficiency; target identification; pose estimation algorithms; triangle constraints; truss node with joint receptacle targets; end-effector mounted camera and light assembly; vision system results from optical bench tests; and future work.

  19. 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.

  20. Volcano-stratigraphic and structural evolution of Brava Island (Cape Verde) based on 40Ar/ 39Ar, U-Th and field constraints

    NASA Astrophysics Data System (ADS)

    Madeira, José; Mata, João; Mourão, Cyntia; Brum da Silveira, António; Martins, Sofia; Ramalho, Ricardo; Hoffmann, Dirk L.

    2010-10-01

    Three volcano-stratigraphic units were identified at Brava Island in the Cape Verde Archipelago on the basis of field relationships, geologic mapping and 40Ar/ 39Ar and U-Th ages. The Lower Unit comprises a 2-to-3 Ma-old submarine volcanic sequence that represents the seamount stage. It is composed of nephelinitic/ankaramitic hyaloclastites and pillow lavas, which are cut by abundant co-genetic dikes. Plutonic rocks of an alkaline-carbonatite complex, which intruded the submarine sequence 1.8 to 1.3 Ma ago, constitute the Middle Unit. A major erosional surface developed between 1.3 and ~ 0.25 Ma. The post-erosional volcanism recorded in the Upper Unit started 0.25 Ma ago and is dominated by phonolitic magmatism. This phase is characterised by explosive phreato-magmatic and magmatic activity that produced block and ash flow, surge, and pyroclastic fall deposits and numerous phreato-magmatic craters. Effusive events are represented by lava domes and coulées. One peculiarity of Brava is the occurrence of carbonatites in both the plutonic complex and the post-erosional phase as extrusive volcanics. The intrusive carbonatites are younger than those occurring on Fogo, Santiago and Maio islands. Young (Upper Pleistocene to Holocene) extrusive carbonatites occurring in the late stages of volcanism are unknown in other Cape Verde islands. The occurrence of pillow lavas and hyaloclastites above the present sea level (up to 400 m) and raised Upper Pleistocene beaches indicates continuous uplift of Brava since the seamount stage. By dating raised marine markers, uplift rates were estimated at between 0.2 and 0.4 mm/a. The evolution of Brava was controlled by faults with directions similar to those described for Fogo, suggesting a common stress field. A detailed geological map (1/25,000) of Brava is presented.

  1. 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.

  2. SCOPmap: Automated assignment of protein structures to evolutionary superfamilies

    PubMed Central

    Cheek, Sara; Qi, Yuan; Krishna, S Sri; Kinch, Lisa N; Grishin, Nick V

    2004-01-01

    Background Inference of remote homology between proteins is very challenging and remains a prerogative of an expert. Thus a significant drawback to the use of evolutionary-based protein structure classifications is the difficulty in assigning new proteins to unique positions in the classification scheme with automatic methods. To address this issue, we have developed an algorithm to map protein domains to an existing structural classification scheme and have applied it to the SCOP database. Results The general strategy employed by this algorithm is to combine the results of several existing sequence and structure comparison tools applied to a query protein of known structure in order to find the homologs already classified in SCOP database and thus determine classification assignments. The algorithm is able to map domains within newly solved structures to the appropriate SCOP superfamily level with ~95% accuracy. Examples of correctly mapped remote homologs are discussed. The algorithm is also capable of identifying potential evolutionary relationships not specified in the SCOP database, thus helping to make it better. The strategy of the mapping algorithm is not limited to SCOP and can be applied to any other evolutionary-based classification scheme as well. SCOPmap is available for download. Conclusion The SCOPmap program is useful for assigning domains in newly solved structures to appropriate superfamilies and for identifying evolutionary links between different superfamilies. PMID:15598351

  3. 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

  4. Fully automated high-quality NMR structure determination of small 2H-enriched proteins

    PubMed Central

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

    2010-01-01

    Determination of high-quality small protein structures by nuclear magnetic resonance (NMR) methods generally requires acquisition and analysis of an extensive set of structural constraints. The process generally demands extensive backbone and sidechain resonance assignments, and weeks or even months of data collection and interpretation. Here we demonstrate rapid and high-quality protein NMR structure generation using CS-Rosetta with a perdeuterated protein sample made at a significantly reduced cost using new bacterial culture condensation methods. Our strategy provides the basis for a high-throughput approach for routine, rapid, high-quality structure determination of small proteins. As an example, we demonstrate the determination of a high-quality 3D structure of a small 8 kDa protein, E. coli cold shock protein A (CspA), using <4 days of data collection and fully automated data analysis methods together with CS-Rosetta. The resulting CspA structure is highly converged and in excellent agreement with the published crystal structure, with a backbone RMSD value of 0.5 Å, an all atom RMSD value of 1.2 Å to the crystal structure for well-defined regions, and RMSD value of 1.1 Å to crystal structure for core, non-solvent exposed sidechain atoms. Cross validation of the structure with 15N- and 13C-edited NOESY data obtained with a perdeuterated 15N, 13C-enriched 13CH3 methyl protonated CspA sample confirms that essentially all of these independently-interpreted NOE-based constraints are already satisfied in each of the 10 CS-Rosetta structures. By these criteria, the CS-Rosetta structure generated by fully automated analysis of data for a perdeuterated sample provides an accurate structure of CspA. This represents a general approach for rapid, automated structure determination of small proteins by NMR. PMID:20734145

  5. 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.

  6. 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.

  7. 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.

  8. 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

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

    NASA Technical Reports Server (NTRS)

    Arpasi, Dale J.; Cole, Gary L.

    1987-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Arpasi, Dale J.; Cole, Gary L.

    1987-01-01

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

  11. 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.

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

    SciTech Connect

    Foley, M.G.

    1991-02-01

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

  13. 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.

  14. Implicitly modelled stratigraphic surfaces using generalized interpolation

    NASA Astrophysics Data System (ADS)

    Hillier, Michael; de Kemp, Eric; Schetselaar, Ernst

    2016-06-01

    Stratigraphic surfaces implicitly modelled using a generalized interpolation approach in various geological settings is presented to demonstrate its modelling capabilities and limitations. The generalized interpolation approach provides a useful mathematical framework in modelling continuous surfaces from scattered data consisting of the following geological constraints: contact locations and planar orientations. Examples are presented to show the effectiveness of the method in generating plausible representations of geological structures in sparse data environments. One of the major advantages of implicit surface modelling has long been claimed as its ability to model geometries with arbitrary topology. It is, however, demonstrated that this is in fact a disadvantage in robustly generating geologically realistic surfaces in structurally complex domains with a known topology.

  15. 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.

  16. 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. PMID:21288193

  17. 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.

  18. Stratigraphic modeling of sedimentary basins

    SciTech Connect

    Aigner, T. ); Lawrence, D.T. )

    1990-11-01

    A two-dimensional stratigraphic forward model has been successfully applied and calibrated in clastic, carbonate, and mixed clastic/carbonate regimes. Primary input parameters are subsidence, sea level, volume of clastics, and carbonate growth potential. Program output includes sequence geometries, facies distribution lithology distribution, chronostratigraphic plots, burial history plots, thermal and maturity histories, and crossplots. The program may be used to predict reservoir distribution, to constrain interpretations of well and seismic data, to rapidly test exploration scenarios in frontier basins, and to evaluate the fundamental controls on observed basin stratigraphy. Applications to data sets from Main Pass (US Gulf Coast), Offshore Sarawak (Malaysia), Rub'al Khali basin (Oman), Paris basin (France), and Baltimore Canyon (US East Coast) demonstrate that the program can be used to simulate stratigraphy on a basin-wide scale as well as on the scale of individual prospects.

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

    PubMed

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

    2015-12-01

    ProMOL, a plugin for the PyMOL molecular graphics system, is a structure-based protein function prediction tool. ProMOL includes a set of routines for building motif templates that are used for screening query structures for enzyme active sites. Previously, each motif template was generated manually and required supervision in the optimization of parameters for sensitivity and selectivity. We developed an algorithm and workflow for the automation of motif building and testing routines in ProMOL. The algorithm uses a set of empirically derived parameters for optimization and requires little user intervention. The automated motif generation algorithm was first tested in a performance comparison with a set of manually generated motifs based on identical active sites from the same 112 PDB entries. The two sets of motifs were equally effective in identifying alignments with homologs and in rejecting alignments with unrelated structures. A second set of 296 active site motifs were generated automatically, based on Catalytic Site Atlas entries with literature citations, as an expansion of the library of existing manually generated motif templates. The new motif templates exhibited comparable performance to the existing ones in terms of hit rates against native structures, homologs with the same EC and Pfam designations, and randomly selected unrelated structures with a different EC designation at the first EC digit, as well as in terms of RMSD values obtained from local structural alignments of motifs and query structures. This research is supported by NIH grant GM078077. PMID:26573864

  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. COMPUTER AUTOMATED STUDY OF THE STRUCTURE-MUTAGENICITY RELATIONSHIPS OF NON-FUSED-RING NITROARENES AND RELATED COMPOUNDS

    EPA Science Inventory

    A quantitative structure-activity analysis of the mutagenicity of non-fused ring nitroaromatic compounds is reported. The analysis is performed on the basis of substructural fragment descriptors according to a recently developed methodology acronymed CASE (Computer Automated Stru...

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

    NASA Technical Reports Server (NTRS)

    Ascoli, Edward P.; Prueger, George H.

    1995-01-01

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

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

    PubMed

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

    2016-07-01

    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

  4. 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

  5. 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

  6. 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.

  7. A fully automated trabecular bone structural analysis tool based on T2* -weighted magnetic resonance imaging.

    PubMed

    Kraiger, Markus; Martirosian, Petros; Opriessnig, Peter; Eibofner, Frank; Rempp, Hansjoerg; Hofer, Michael; Schick, Fritz; Stollberger, Rudolf

    2012-03-01

    One major source affecting the precision of bone structure analysis in quantitative magnetic resonance imaging (qMRI) is inter- and intraoperator variability, inherent in delineating and tracing regions of interest along longitudinal studies. In this paper an automated analysis tool, featuring bone marrow segmentation, region of interest generation, and characterization of cancellous bone of articular joints is presented. In evaluation studies conducted at the knee joint the novel analysis tool significantly decreased the standard error of measurement and improved the sensitivity in detecting minor structural changes. It further eliminated the need of time-consuming user interaction, and thereby increasing reproducibility. PMID:21862288

  8. Automated Real-Space Refinement of Protein Structures Using a Realistic Backbone Move Set

    PubMed Central

    Haddadian, Esmael J.; Gong, Haipeng; Jha, Abhishek K.; Yang, Xiaojing; DeBartolo, Joe; Hinshaw, James R.; Rice, Phoebe A.; Sosnick, Tobin R.; Freed, Karl F.

    2011-01-01

    Crystals of many important biological macromolecules diffract to limited resolution, rendering accurate model building and refinement difficult and time-consuming. We present a torsional optimization protocol that is applicable to many such situations and combines Protein Data Bank-based torsional optimization with real-space refinement against the electron density derived from crystallography or cryo-electron microscopy. Our method converts moderate- to low-resolution structures at initial (e.g., backbone trace only) or late stages of refinement to structures with increased numbers of hydrogen bonds, improved crystallographic R-factors, and superior backbone geometry. This automated method is applicable to DNA-binding and membrane proteins of any size and will aid studies of structural biology by improving model quality and saving considerable effort. The method can be extended to improve NMR and other structures. Our backbone score and its sequence profile provide an additional standard tool for evaluating structural quality. PMID:21843481

  9. 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.

  10. 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.

  11. Stratigraphic evidence for shear in structural development of the Triassic Levant margin: New borehole data on the epicontinental to deep marine transition in Israel

    NASA Astrophysics Data System (ADS)

    Korngreen, D.; Benjamini, C.

    2013-04-01

    Triassic tectonic movements that include shear along a significant portion of the Levant margin, are evidenced from microfacies analysis of material recovered from the Asher-Atlit 1, Ga'ash-2, Meged-2, Devora-2 and Ramalla-1 onshore boreholes. Seismic studies showed that structural lineaments attributed to early Mesozoic extension underlie coastal and central Israel, trending NE-SW beneath southern Israel and sub-parallel to the then- extensional Palmyride basin of Syria. A more curved trend, approximately NNW-SSE, lies to the north beneath central Israel. Coast-parallel sedimentary domains formed above these lineaments, which constitute the newly formed passive margin of the Levant coast in the Triassic. The sedimentary history of these domains indicates that some were linked to each other, and others disconnected. The relative vertical movement between one domain and another is explained by activation of transpressional and trans-tensional shear movements on the underlying curved faults. These subordinate vertical movements also created the discontinuous barriers and small subsiding basins that separate the epicontinental sedimentary domain from the open Tethys, causing partial restriction necessary for the intermittent development of thick evaporites in the internal domains, alternating with a regionally suppressed carbonate system. This zone is here named the Onshore Levant Margin Shear Zone (OLMSZ). Shear was invoked theoretically in a number of models for the tectonic evolution of the eastern Mediterranean as part of a Neotethyan opening system. This paper provides rock-based evidence for such shear applicable to 20% of the eastern Levant margin in the Triassic.

  12. 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.

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

    SciTech Connect

    Fenglei Li

    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

  14. PDB_REDO: automated re-refinement of X-ray structure models in the PDB.

    PubMed

    Joosten, Robbie P; Salzemann, Jean; Bloch, Vincent; Stockinger, Heinz; Berglund, Ann-Charlott; Blanchet, Christophe; Bongcam-Rudloff, Erik; Combet, Christophe; Da Costa, Ana L; Deleage, Gilbert; Diarena, Matteo; Fabbretti, Roberto; Fettahi, Géraldine; Flegel, Volker; Gisel, Andreas; Kasam, Vinod; Kervinen, Timo; Korpelainen, Eija; Mattila, Kimmo; Pagni, Marco; Reichstadt, Matthieu; Breton, Vincent; Tickle, Ian J; Vriend, Gert

    2009-06-01

    Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour. PMID:22477769

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

    PubMed

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

    2016-04-15

    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

  16. 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

  17. Stratigraphic Relationships on Husband Hill, Mars

    NASA Astrophysics Data System (ADS)

    Cole, S. B.; Watters, W. A.; Squyres, S. W.

    2011-03-01

    We measure bedding plane orientations of outcrops on Cumberland Ridge in the Columbia Hills. Our measurements are consistent with the hypotheses that the outcrops (1) form a stratigraphic section, and (2) drape the Husband Hill edifice.

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

    PubMed

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

    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. PMID:26561914

  19. 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.

  20. 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.

  1. 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.

  2. PAP-LMPCR for improved, allele-specific footprinting and automated chromatin fine structure analysis

    PubMed Central

    Ingram, R.; Gao, C.; LeBon, J.; Liu, Q.; Mayoral, R. J.; Sommer, S. S.; Hoogenkamp, M.; Riggs, A. D.; Bonifer, C.

    2008-01-01

    The analysis of chromatin fine structure and transcription factor occupancy of differentially expressed genes by in vivo footprinting and ligation-mediated-PCR (LMPCR) is a powerful tool to understand the impact of chromatin on gene expression. However, as with all PCR-based techniques, the accuracy of the experiments has often been reduced by sequence similarities and the presence of GC-rich or repeat sequences, and some sequences are completely refractory to analysis. Here we describe a novel method, pyrophosphorolysis activated polymerization LMPCR or PAP-LMPCR, which is capable of generating accurate and reproducible footprints specific for individual alleles and can read through sequences previously not accessible for analysis. In addition, we have adapted this technique for automation, thus enabling the simultaneous and rapid analysis of chromatin structure at many different genes. PMID:18208840

  3. 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

  4. Automated assignment of MS/MS cleavable cross-links in protein 3D-structure analysis.

    PubMed

    Götze, Michael; Pettelkau, Jens; Fritzsche, Romy; Ihling, Christian H; Schäfer, Mathias; Sinz, Andrea

    2015-01-01

    CID-MS/MS cleavable cross-linkers hold an enormous potential for an automated analysis of cross-linked products, which is essential for conducting structural proteomics studies. The created characteristic fragment ion patterns can easily be used for an automated assignment and discrimination of cross-linked products. To date, there are only a few software solutions available that make use of these properties, but none allows for an automated analysis of cleavable cross-linked products. The MeroX software fills this gap and presents a powerful tool for protein 3D-structure analysis in combination with MS/MS cleavable cross-linkers. We show that MeroX allows an automatic screening of characteristic fragment ions, considering static and variable peptide modifications, and effectively scores different types of cross-links. No manual input is required for a correct assignment of cross-links and false discovery rates are calculated. The self-explanatory graphical user interface of MeroX provides easy access for an automated cross-link search platform that is compatible with commonly used data file formats, enabling analysis of data originating from different instruments. The combination of an MS/MS cleavable cross-linker with a dedicated software tool for data analysis provides an automated workflow for 3D-structure analysis of proteins. MeroX is available at www.StavroX.com . PMID:25261217

  5. 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. PMID:24391363

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

    PubMed Central

    Ishikawa, Yoshinobu

    2013-01-01

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

  7. Automated structure modeling of large protein assemblies using crosslinks as distance restraints.

    PubMed

    Ferber, Mathias; Kosinski, Jan; Ori, Alessandro; Rashid, Umar J; Moreno-Morcillo, María; Simon, Bernd; Bouvier, Guillaume; Batista, Paulo Ricardo; Müller, Christoph W; Beck, Martin; Nilges, Michael

    2016-06-01

    Crosslinking mass spectrometry is increasingly used for structural characterization of multisubunit protein complexes. Chemical crosslinking captures conformational heterogeneity, which typically results in conflicting crosslinks that cannot be satisfied in a single model, making detailed modeling a challenging task. Here we introduce an automated modeling method dedicated to large protein assemblies ('XL-MOD' software is available at http://aria.pasteur.fr/supplementary-data/x-links) that (i) uses a form of spatial restraints that realistically reflects the distribution of experimentally observed crosslinked distances; (ii) automatically deals with ambiguous and/or conflicting crosslinks and identifies alternative conformations within a Bayesian framework; and (iii) allows subunit structures to be flexible during conformational sampling. We demonstrate our method by testing it on known structures and available crosslinking data. We also crosslinked and modeled the 17-subunit yeast RNA polymerase III at atomic resolution; the resulting model agrees remarkably well with recently published cryoelectron microscopy structures and provides additional insights into the polymerase structure. PMID:27111507

  8. 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

  9. 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.

  10. A structural study of cyanotrichite from Dachang by conventional and automated electron diffraction

    NASA Astrophysics Data System (ADS)

    Ventruti, Gennaro; Mugnaioli, Enrico; Capitani, Giancarlo; Scordari, Fernando; Pinto, Daniela; Lausi, Andrea

    2015-09-01

    The crystal structure of cyanotrichite, having general formula Cu4Al2(SO4)(OH)12·2H2O, from the Dachang deposit (China) was studied by means of conventional transmission electron microscopy, automated electron diffraction tomography (ADT) and synchrotron X-ray powder diffraction (XRPD). ADT revealed the presence of two different cyanotrichite-like phases. The same phases were also recognized in the XRPD pattern, allowing the perfect indexing of all peaks leading, after refinement to the following cell parameters: (1) a = 12.417(2) Å, b = 2.907(1) Å, c = 10.157(1) Å and β = 98.12(1); (2) a = 12.660(2) Å, b = 2.897(1) Å, c = 10.162(1) Å and β = 92.42(1)°. Only for the former phase, labeled cyanotrichite-98, a partial structure, corresponding to the [Cu4Al2(OH){12/2+}] cluster, was obtained ab initio by direct methods in space group C2/ m on the basis of electron diffraction data. Geometric and charge-balance considerations allowed to reach the whole structure model for the cyanotrichite-98 phase. The sulfate group and water molecule result to be statistically disordered over two possible positions, but keeping the average structure consistent with the C-centering symmetry, in agreement with ADT results.

  11. Automated identification of RNA 3D modules with discriminative power in RNA structural alignments.

    PubMed

    Theis, Corinna; Höner Zu Siederdissen, Christian; Hofacker, Ivo L; Gorodkin, Jan

    2013-12-01

    Recent progress in predicting RNA structure is moving towards filling the 'gap' in 2D RNA structure prediction where, for example, predicted internal loops often form non-canonical base pairs. This is increasingly recognized with the steady increase of known RNA 3D modules. There is a general interest in matching structural modules known from one molecule to other molecules for which the 3D structure is not known yet. We have created a pipeline, metaRNAmodules, which completely automates extracting putative modules from the FR3D database and mapping of such modules to Rfam alignments to obtain comparative evidence. Subsequently, the modules, initially represented by a graph, are turned into models for the RMDetect program, which allows to test their discriminative power using real and randomized Rfam alignments. An initial extraction of 22 495 3D modules in all PDB files results in 977 internal loop and 17 hairpin modules with clear discriminatory power. Many of these modules describe only minor variants of each other. Indeed, mapping of the modules onto Rfam families results in 35 unique locations in 11 different families. The metaRNAmodules pipeline source for the internal loop modules is available at http://rth.dk/resources/mrm. PMID:24005040

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. The Upgrade Programme for the Structural Biology beamlines at the European Synchrotron Radiation Facility - High throughput sample evaluation and automation

    NASA Astrophysics Data System (ADS)

    Theveneau, P.; Baker, R.; Barrett, R.; Beteva, A.; Bowler, M. W.; Carpentier, P.; Caserotto, H.; de Sanctis, D.; Dobias, F.; Flot, D.; Guijarro, M.; Giraud, T.; Lentini, M.; Leonard, G. A.; Mattenet, M.; McCarthy, A. A.; McSweeney, S. M.; Morawe, C.; Nanao, M.; Nurizzo, D.; Ohlsson, S.; Pernot, P.; Popov, A. N.; Round, A.; Royant, A.; Schmid, W.; Snigirev, A.; Surr, J.; Mueller-Dieckmann, C.

    2013-03-01

    Automation and advances in technology are the key elements in addressing the steadily increasing complexity of Macromolecular Crystallography (MX) experiments. Much of this complexity is due to the inter-and intra-crystal heterogeneity in diffraction quality often observed for crystals of multi-component macromolecular assemblies or membrane proteins. Such heterogeneity makes high-throughput sample evaluation an important and necessary tool for increasing the chances of a successful structure determination. The introduction at the ESRF of automatic sample changers in 2005 dramatically increased the number of samples that were tested for diffraction quality. This "first generation" of automation, coupled with advances in software aimed at optimising data collection strategies in MX, resulted in a three-fold increase in the number of crystal structures elucidated per year using data collected at the ESRF. In addition, sample evaluation can be further complemented using small angle scattering experiments on the newly constructed bioSAXS facility on BM29 and the micro-spectroscopy facility (ID29S). The construction of a second generation of automated facilities on the MASSIF (Massively Automated Sample Screening Integrated Facility) beam lines will build on these advances and should provide a paradigm shift in how MX experiments are carried out which will benefit the entire Structural Biology community.

  18. 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. PMID:19552372

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    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.

  1. Automated Assignment of MS/MS Cleavable Cross-Links in Protein 3D-Structure Analysis

    NASA Astrophysics Data System (ADS)

    Götze, Michael; Pettelkau, Jens; Fritzsche, Romy; Ihling, Christian H.; Schäfer, Mathias; Sinz, Andrea

    2015-01-01

    CID-MS/MS cleavable cross-linkers hold an enormous potential for an automated analysis of cross-linked products, which is essential for conducting structural proteomics studies. The created characteristic fragment ion patterns can easily be used for an automated assignment and discrimination of cross-linked products. To date, there are only a few software solutions available that make use of these properties, but none allows for an automated analysis of cleavable cross-linked products. The MeroX software fills this gap and presents a powerful tool for protein 3D-structure analysis in combination with MS/MS cleavable cross-linkers. We show that MeroX allows an automatic screening of characteristic fragment ions, considering static and variable peptide modifications, and effectively scores different types of cross-links. No manual input is required for a correct assignment of cross-links and false discovery rates are calculated. The self-explanatory graphical user interface of MeroX provides easy access for an automated cross-link search platform that is compatible with commonly used data file formats, enabling analysis of data originating from different instruments. The combination of an MS/MS cleavable cross-linker with a dedicated software tool for data analysis provides an automated workflow for 3D-structure analysis of proteins. MeroX is available at www.StavroX.com .

  2. 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. PMID:24710340

  3. 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.

  4. Automated cerebellar lobule segmentation with application to cerebellar structural analysis in cerebellar disease.

    PubMed

    Yang, Zhen; Ye, Chuyang; Bogovic, John A; Carass, Aaron; Jedynak, Bruno M; Ying, Sarah H; Prince, Jerry L

    2016-02-15

    The cerebellum plays an important role in both motor control and cognitive function. Cerebellar function is topographically organized and diseases that affect specific parts of the cerebellum are associated with specific patterns of symptoms. Accordingly, delineation and quantification of cerebellar sub-regions from magnetic resonance images are important in the study of cerebellar atrophy and associated functional losses. This paper describes an automated cerebellar lobule segmentation method based on a graph cut segmentation framework. Results from multi-atlas labeling and tissue classification contribute to the region terms in the graph cut energy function and boundary classification contributes to the boundary term in the energy function. A cerebellar parcellation is achieved by minimizing the energy function using the α-expansion technique. The proposed method was evaluated using a leave-one-out cross-validation on 15 subjects including both healthy controls and patients with cerebellar diseases. Based on reported Dice coefficients, the proposed method outperforms two state-of-the-art methods. The proposed method was then applied to 77 subjects to study the region-specific cerebellar structural differences in three spinocerebellar ataxia (SCA) genetic subtypes. Quantitative analysis of the lobule volumes shows distinct patterns of volume changes associated with different SCA subtypes consistent with known patterns of atrophy in these genetic subtypes. PMID:26408861

  5. Automated Foveola Localization in Retinal 3D-OCT Images Using Structural Support Vector Machine Prediction

    PubMed Central

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

    2013-01-01

    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. PMID:23285565

  6. 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.

  7. Structural and Functional Relationships in Glaucoma Using Standard Automated Perimetry and the Humphrey Matrix

    PubMed Central

    Park, Seong Bae; Nam, Yoon Pyo; Sung, Kyung Rim

    2009-01-01

    Purpose To evaluate and compare correlations between structural and functional loss in glaucoma as assessed by optical coherence tomography (OCT), scanning laser polarimetry (GDx VCC, as this was the model used in this study), standard automated perimetry (SAP), and the Humphrey Matrix (Matrix). Methods Ninety glaucomatous eyes identified with SAP and 112 eyes diagnosed using Matrix were independently classified into six subgroups, either S1/M1 (MD>-6dB), S2/M2 (-12structural and functional defects when assessed using OCT and GDx VCC. These correlations were weaker in the Matrix subgroups, especially in the early stages of glaucoma. PMID:19794944

  8. Automated artery-venous classification of retinal blood vessels based on structural mapping method

    NASA Astrophysics Data System (ADS)

    Joshi, Vinayak S.; Garvin, Mona K.; Reinhardt, Joseph M.; Abramoff, Michael D.

    2012-03-01

    Retinal blood vessels show morphologic modifications in response to various retinopathies. However, the specific responses exhibited by arteries and veins may provide a precise diagnostic information, i.e., a diabetic retinopathy may be detected more accurately with the venous dilatation instead of average vessel dilatation. In order to analyze the vessel type specific morphologic modifications, the classification of a vessel network into arteries and veins is required. We previously described a method for identification and separation of retinal vessel trees; i.e. structural mapping. Therefore, we propose the artery-venous classification based on structural mapping and identification of color properties prominent to the vessel types. The mean and standard deviation of each of green channel intensity and hue channel intensity are analyzed in a region of interest around each centerline pixel of a vessel. Using the vector of color properties extracted from each centerline pixel, it is classified into one of the two clusters (artery and vein), obtained by the fuzzy-C-means clustering. According to the proportion of clustered centerline pixels in a particular vessel, and utilizing the artery-venous crossing property of retinal vessels, each vessel is assigned a label of an artery or a vein. The classification results are compared with the manually annotated ground truth (gold standard). We applied the proposed method to a dataset of 15 retinal color fundus images resulting in an accuracy of 88.28% correctly classified vessel pixels. The automated classification results match well with the gold standard suggesting its potential in artery-venous classification and the respective morphology analysis.

  9. 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.

  10. New Software for Plotting and Analyzing Stratigraphic Data

    NASA Astrophysics Data System (ADS)

    Lewis, K. W.; Keeler, T. L.; Maloof, A. C.

    2011-02-01

    Stratigraphy, the study of layering in rock, ice, and sediment records, lies at the heart of the geological sciences. The lithology, grain size, and texture of layered successions, along with a host of measurable geochemical and geophysical parameters, record information about past environmental and geographic conditions. Despite the importance of stratigraphic records to Earth history, there is a dearth of accessible, user-friendly open-source software for generating stratigraphic plots and analyzing stratigraphic data. Often, stratigraphic logs and associated geochemical and geophysical data are assembled and plotted manually using multiple software packages. The integrated stratigraphic data can then be cumbersome to analyze quantitatively.

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

    PubMed Central

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

    2013-01-01

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

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

    SciTech Connect

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

    2007-01-19

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

  13. STASSAGE: A FORTRAN program to decode stratigraphic ages from the international IGBADAT database

    NASA Astrophysics Data System (ADS)

    Al-Mishwat, Ali T.

    1997-04-01

    STASSAGE is a FORTRAN program designed to decode stratigraphic age data contained within the international igneous rock database IGBADAT, and databases with similar structure. The algorithm decodes and translates stratigraphic information and retrieves rock samples falling within a desired stratigraphic age or a stratigraphic age interval, as specified in a search condition, along with petrographic, geochemical, mineralogic, and other ancillary data pertaining to these specimens. Program core operation involves two basic steps: decoding and translation, followed by search, comparison, and retrieval. The search engine in the program utilizes a system of stratigraphic figure-of-merit (SFOM) numbers and the principle of inclusiveness. The SFOM number system assigns to every recognized stratigraphic age a numerical value that is largest for oldest ages and smallest for youngest ones. The Principle of Inclusiveness states that " All Belongs to One and One Contains All", meaning that all ages in lower-rank stratigraphic age divisions are included in higher-rank age divisions containing them, and that a higher-rank age division contains in it all of its lower-rank component ages. In order to select specimens satisfying some given search criteria, search algorithms invoke the principle of inclusiveness and use extensive alphanumeric string comparisons that apply simple greater-than and lessthan Boolean algebra operators to the SFOM numbers to decode abbreviated IGBA age nouns. Samples screened by the search filter are saved in an output file, along with their full specimen descriptions for further analysis. Optionally, the program provides the facility to recast retrieved data of such samples into blank-delimited spreadsheets which are compatible with most spreadsheet programs.

  14. Stratigraphic Paleobiology of the Taranto Area

    NASA Astrophysics Data System (ADS)

    Scarponi, Daniele; Angeletti, Lorenzo; Taviani, Marco; Huntley, John Warren; Amorosi, Alessandro; Negri, Alessandra; Battista Vai, Gian

    2015-04-01

    The area surrounding Taranto, Italy is chronostratigraphically very important, as it is one of the few areas in the world where Upper Pleistocene marine successions are well exposed, easily accessible, and relatively thick. Several outcrops in this area were investigated as suitable marine sections for defining the Late Pleistocene GSSP. At these locations, the late Pleistocene bathymetric history of the Taranto area was depicted using macrobenthic assemblages from a network of outcrops and cores. Outcrops at Pontile, Fronte, and Garitta, along with two cores drilled at Cimino and Cantoro were densely sampled to conduct quantitatively-derived paleobathymetric reconstructions. These deposits yielded relatively diverse mollusk associations (> 250 species and > 9.000 specimens distributed among 55 samples), dominated by extant mollusk species of known bathymetric distribution. Multiple analytical approaches were applied to the macrobenthic dataset in a comparative fashion: (i) direct calibration by weighted averaging of taxa with known preferred depth recovered in a sample, (ii) posteriori-calibrated ordination (DCA) using bathymetric data of key extant taxa. These analyses were conducted at both species and genus level. Regardless of the choice of the analytical method, mollusk assemblages yielded bathymetric trends congruent with previous qualitative and semi-quantitative paleoecological and stratigraphic analyses: the bathymetric range of sampled deposits is bracketed between 140 and 0 meters. Secondly, macrobenthos-derived proxies provided an improved characterization of the marine deposits in terms of sample bathymetry and by discriminating shallowing-upward (regressive) trends from deepening-upward (transgressive) tendencies. Thirdly, mollusk-derived bathymetric inferences suggest spatial bathymetric gradients that are coherent with the morphology of the study area. In conclusion, the results provided an improved characterization of coastal depositional facies

  15. 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.

  16. Alaskan Peninsula Cenozoic stratigraphy: stratigraphic sequences and current research

    SciTech Connect

    Allison, R.C.; Armentrout, J.M.

    1985-04-01

    Geology of the Alaska Peninsula-Island Arc and Continental Margin, by C.A. Burk, is the principal reference for stratigraphic studies on the Alaska Peninsula. Burk mapped the Phanerozoic stratigraphy and provided a geologic history and structural interpretation of the area between Wide Bay and Unimak Island. Cenozoic rocks were mapped as three unconformity-bounded sequences. Recognition of specific formations was difficult due to similarity of lithofacies, isolated outcrops, rapid facies changes, and alteration and burial by young volcanics. Consequently, megafossil assemblages were relied upon to facilitate correlations between study areas. The three unconformity-bounded Cenozoic sequences are: (1) the Paleogene Beaver Bay Group consisting of three formations: the dominantly nonmarine Tolstoi Formation, the dominantly marine Stepovak Formation, and the volcanic Meshik Formation. Current work suggests these units are at least in part coeval facies of late Paleocene through Oligocene age. (2) The Neogene Bear Lake Formation consisting of the lower Unga Conglomerate Member and an unnamed upper member. Rapid facies changes and incorrect reports of fossil occurrence have resulted in confusion of stratigraphic relationships within this sequence of middle to late Miocene age. (3) A late Neogene informally defined upper sequence consisting of interbedded marginal marine, coastal-plain, and volcanic facies. Current work suggests this sequence is Pliocene through Pleistocene in age.

  17. Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments

    PubMed Central

    Kuszewski, John J.; Thottungal, Robin Augustine; Schwieters, Charles D.; Clore, G. Marius

    2008-01-01

    We report substantial improvements to the previously introduced automated NOE assignment and structure determination protocol known as PASD. The improved protocol includes extensive analysis of input spectral data to create a low-resolution contact map of residues expected to be close in space. This map is used to obtain reasonable initial guesses of NOE assignment likelihoods which are refined during subsequent structure calculations. Information in the contact map about which residues are predicted to not be close in space is applied via conservative repulsive distance restraints which are used in early phases of the structure calculations. In comparison with the previous protocol, the new protocol requires significantly less computation time. We show results of running the new PASD protocol on six proteins and demonstrate that useful assignment and structural information is extracted on proteins of more than 220 residues. We show that useful assignment information can be obtained even in the case in which a unique structure cannot be determined. PMID:18668206

  18. Europa's Northern Trailing Hemisphere: Lineament Stratigraphic Framework

    NASA Technical Reports Server (NTRS)

    Figueredo, P. H.; Hare, T.; Ricq, E.; Strom, K.; Greeley, R.; Tanaka, K.; Senske, D.

    2004-01-01

    Knowledge of the global distribution of Europan geologic units in time and space is a necessary step for the synthesis of the results of the Galileo mission and in preparation for future exploration (namely, by JIMO) of the satellite. We have initiated the production of the first Global Geological Map of Europa. As a base map, we use the recently published global photomosaic of Europa (U.S.G.S. Map I-2757) and additional Galileo SSI images at their original resolution. The map is being produced entirely on GIS format for analysis and combination with other datasets [1]. One of the main objectives of this project is to establish a global stratigraphic framework for Europa. In the absence of a well-developed cratering record, this goal will be achieved using the satellite s global network of lineaments (ridges, ridge complexes and bands; cf. [2]). Here we present the preliminary stratigraphic framework synthesized from the sequence of lineaments derived for the northern trailing hemisphere of Europa (Figure 1, below), and we discuss its significance and some emerging implications.

  19. 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

  20. 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. PMID:25190042

  1. 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.

  2. Hierarchical construction of stratigraphic elements in surface-based reservoir models

    NASA Astrophysics Data System (ADS)

    Wang, Y.; Xu, S.; Mukerji, T.

    2013-12-01

    We present a surface-based simulation algorithm connecting stratigraphic hierarchy with surface-based reservoir models through statistical metrics. Geostatistical simulation algorithms provide tools for modeling spatial complexity and the resulting uncertainties for energy resource assessments. As a new family within a wide array of stochastic geological models, surface-based models and rule-based algorithms effectively represent stratigraphic responses to geological events in both time and space by assigning depositional and erosional surfaces with predefined geometries and rules. Recent advances in surface-based modeling focus on simulating morphological evolution of deep-water depositional systems and constraining models to available well and seismic data. However, especially in deep-water plays, scarce well data can only bring information about local stratal features rather than relatively general information such as hierarchy or organization, when these features are below seismic resolution. Without such information, surface-based models lack geological realism and may not be reliable even when conditioned to data. Our proposed surface-based simulation algorithm links stratigraphic hierarchy with surface-based reservoir modeling through spatial statistical tools. Ripley's K-function is used to quantitatively describe the stratigraphic distribution patterns of channel deposits. We also use the compensation index metric for quantifying the strength of compensational stacking in stratigraphic elements. These two metrics help us to extract information about sedimentary hierarchy and element organization from a set of experimental strata, and bridge physical tank experiments with numerical models. We utilize these two geostatistical metrics in conjunction with a surface-based simulation algorithm to 1) integrate clustering and compensational stacking patterns of channel deposits into reservoir modeling 2) make numerical models represent a stratigraphic hierarchical

  3. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  5. Spectral stratigraphy: multispectral remote sensing as a stratigraphic tool, Wind River/Big Horn basin, Wyoming

    SciTech Connect

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

    1987-05-01

    Stratigraphic and structural analyses of the Wind River and Big Horn basins areas of central Wyoming are in progress. One result has been the development of a new approach to stratigraphic and structural analysis that uses photogeologic and spectral interpretation of multispectral image data to remotely characterize the attitude, thickness, and lithology of strata. New multispectral systems that have only been available since 1982 are used with topographic data to map upper paleozoic and Mesozoic strata exposed on the southern margin of the Bighorn Mountains. Thematic Mapper (TM) satellite data together with topographic data are used to map lithologic contacts, measure dip and strike, and develop a stratigraphic column that is correlated with conventional surface and subsurface sections. Aircraft-acquired Airborne Imaging Spectrometer and Thermal Infrared Multispectral Scanner data add mineralogical information to the TM column, including the stratigraphic distribution of quartz, calcite, dolomite, montmorillonite, and gypsum. Results illustrate an approach that has general applicability in other geologic investigations that could benefit from remotely acquired information about areal variations in attitude, sequence, thickness, and lithology of strata exposed at the Earth's surface. Application of their methods elsewhere is limited primarily by availability of multispectral and topographic data and quality of bedrock exposures.

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

    NASA Astrophysics Data System (ADS)

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

    2010-04-01

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

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

    PubMed

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

    2015-04-01

    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

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

    2016-03-01

    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.

  15. 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.

  16. 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.

  17. Automated retrieval of forest structure variables based on multi-scale texture analysis of VHR satellite imagery

    NASA Astrophysics Data System (ADS)

    Beguet, Benoit; Guyon, Dominique; Boukir, Samia; Chehata, Nesrine

    2014-10-01

    The main goal of this study is to design a method to describe the structure of forest stands from Very High Resolution satellite imagery, relying on some typical variables such as crown diameter, tree height, trunk diameter, tree density and tree spacing. The emphasis is placed on the automatization of the process of identification of the most relevant image features for the forest structure retrieval task, exploiting both spectral and spatial information. Our approach is based on linear regressions between the forest structure variables to be estimated and various spectral and Haralick's texture features. The main drawback of this well-known texture representation is the underlying parameters which are extremely difficult to set due to the spatial complexity of the forest structure. To tackle this major issue, an automated feature selection process is proposed which is based on statistical modeling, exploring a wide range of parameter values. It provides texture measures of diverse spatial parameters hence implicitly inducing a multi-scale texture analysis. A new feature selection technique, we called Random PRiF, is proposed. It relies on random sampling in feature space, carefully addresses the multicollinearity issue in multiple-linear regression while ensuring accurate prediction of forest variables. Our automated forest variable estimation scheme was tested on Quickbird and Pléiades panchromatic and multispectral images, acquired at different periods on the maritime pine stands of two sites in South-Western France. It outperforms two well-established variable subset selection techniques. It has been successfully applied to identify the best texture features in modeling the five considered forest structure variables. The RMSE of all predicted forest variables is improved by combining multispectral and panchromatic texture features, with various parameterizations, highlighting the potential of a multi-resolution approach for retrieving forest structure

  18. 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. PMID:26064644

  19. 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

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

    PubMed Central

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

    2015-01-01

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

  1. 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.

  2. 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.

  3. Fully Automated and Robust Tracking of Transient Waves in Structured Anatomies Using Dynamic Programming.

    PubMed

    Akkus, Zeynettin; Bayat, Mahdi; Cheong, Mathew; Viksit, Kumar; Erickson, Bradley J; Alizad, Azra; Fatemi, Mostafa

    2016-10-01

    Tissue stiffness is often linked to underlying pathology and can be quantified by measuring the mechanical transient transverse wave speed (TWS) within the medium. Time-of-flight methods based on correlation of the transient signals or tracking of peaks have been used to quantify the TWS from displacement maps obtained with ultrasound pulse-echo techniques. However, it is challenging to apply these methods to in vivo data because of tissue inhomogeneity, noise and artifacts that produce outliers. In this study, we introduce a robust and fully automated method based on dynamic programming to estimate TWS in tissues with known geometries. The method is validated using ultrasound bladder vibrometry data from an in vivo study. We compared the results of our method with those of time-of-flight techniques. Our method performs better than time-of-flight techniques. In conclusion, we present a robust and accurate TWS detection method that overcomes the difficulties of time-of-flight methods. PMID:27425150

  4. 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.

  5. 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

  6. 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.

  7. Automated Feature Extraction and Hydrocode Modeling of Impact Related Structures on Mars: Preliminary Report

    NASA Astrophysics Data System (ADS)

    Plesko, C. S.; Asphaug, E.; Brumby, S. P.; Gisler, G. R.

    2003-07-01

    A systematic, combined modeling and observation effort to correlate Martian impact structures craters and their regional aftermaths to the impactors, impact processes and target geologies responsible.

  8. 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.

  9. Automated wind load characterization of wind turbine structures by embedded model updating

    NASA Astrophysics Data System (ADS)

    Swartz, R. Andrew; Zimmerman, Andrew T.; Lynch, Jerome P.

    2010-04-01

    The continued development of renewable energy resources is for the nation to limit its carbon footprint and to enjoy independence in energy production. Key to that effort are reliable generators of renewable energy sources that are economically competitive with legacy sources. In the area of wind energy, a major contributor to the cost of implementation is large uncertainty regarding the condition of wind turbines in the field due to lack of information about loading, dynamic response, and fatigue life of the structure expended. Under favorable circumstances, this uncertainty leads to overly conservative designs and maintenance schedules. Under unfavorable circumstances, it leads to inadequate maintenance schedules, damage to electrical systems, or even structural failure. Low-cost wireless sensors can provide more certainty for stakeholders by measuring the dynamic response of the structure to loading, estimating the fatigue state of the structure, and extracting loading information from the structural response without the need of an upwind instrumentation tower. This study presents a method for using wireless sensor networks to estimate the spectral properties of a wind turbine tower loading based on its measured response and some rudimentary knowledge of its structure. Structural parameters are estimated via model-updating in the frequency domain to produce an identification of the system. The updated structural model and the measured output spectra are then used to estimate the input spectra. Laboratory results are presented indicating accurate load characterization.

  10. A hybrid computational-experimental approach for automated crystal structure solution

    NASA Astrophysics Data System (ADS)

    Meredig, Bryce; Wolverton, C.

    2013-02-01

    Crystal structure solution from diffraction experiments is one of the most fundamental tasks in materials science, chemistry, physics and geology. Unfortunately, numerous factors render this process labour intensive and error prone. Experimental conditions, such as high pressure or structural metastability, often complicate characterization. Furthermore, many materials of great modern interest, such as batteries and hydrogen storage media, contain light elements such as Li and H that only weakly scatter X-rays. Finally, structural refinements generally require significant human input and intuition, as they rely on good initial guesses for the target structure. To address these many challenges, we demonstrate a new hybrid approach, first-principles-assisted structure solution (FPASS), which combines experimental diffraction data, statistical symmetry information and first-principles-based algorithmic optimization to automatically solve crystal structures. We demonstrate the broad utility of FPASS to clarify four important crystal structure debates: the hydrogen storage candidates MgNH and NH3BH3; Li2O2, relevant to Li-air batteries; and high-pressure silane, SiH4.

  11. 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

  12. 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.

  13. Comparison of the bacterial community structure within the equine hindgut and faeces using Automated Ribosomal Intergenic Spacer Analysis (ARISA).

    PubMed

    Sadet-Bourgeteau, S; Philippeau, C; Dequiedt, S; Julliand, V

    2014-12-01

    The horse's hindgut bacterial ecosystem has often been studied using faecal samples. However few studies compared both bacterial ecosystems and the validity of using faecal samples may be questionable. Hence, the present study aimed to compare the structure of the equine bacterial community in the hindgut (caecum, right ventral colon) and faeces using a fingerprint technique known as Automated Ribosomal Intergenic Spacer Analysis (ARISA). Two DNA extraction methods were also assessed. Intestinal contents and faeces were sampled 3 h after the morning meal on four adult fistulated horses fed meadow hay and pelleted concentrate. Irrespective of the intestinal segment, Principal Component Analysis of ARISA profiles showed a strong individual effect (P<0.0001). However, across the study, faecal bacterial community structure significantly (P<0.001) differed from those of the caecum and colon, while there was no difference between the two hindgut communities. The use of a QIAamp(®) DNA Stool Mini kit increased the quality of DNA extracted irrespective of sample type. The differences observed between faecal and hindgut bacterial communities challenge the use of faeces as a representative for hindgut activity. Further investigations are necessary to compare bacterial activity between the hindgut and faeces in order to understand the validity of using faecal samples. PMID:25075719

  14. 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.

  15. 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.

  16. 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.

  17. A method for automated determination of the crystal structures from X-ray powder diffraction data

    SciTech Connect

    Hofmann, D. W. M. Kuleshova, L. N.

    2006-05-15

    An algorithm is proposed for determining the crystal structure of compounds. In the framework of this algorithm, X-ray powder diffraction patterns are compared using a new similarity index. Unlike the indices traditionally employed in X-ray powder diffraction analysis, the new similarity index can be applied even in the case of overlapping peaks and large differences in unit cell parameters. The capabilities of the proposed procedure are demonstrated by solving the crystal structures of a number of organic pigments (PY111, PR181, Me-PR170)

  18. Automated assignment of NMR chemical shifts based on a known structure and 4D spectra.

    PubMed

    Trautwein, Matthias; Fredriksson, Kai; Möller, Heiko M; Exner, Thomas E

    2016-08-01

    Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is the basis for a number of applications, like chemical shift perturbation mapping and studies on the dynamics of proteins. This assignment is not a trivial task even if a 3D protein structure is known and needs almost as much effort as the assignment for structure prediction if performed manually. We present here a new algorithm based solely on 4D [(1)H,(15)N]-HSQC-NOESY-[(1)H,(15)N]-HSQC spectra which is able to assign a large percentage of chemical shifts (73-82 %) unambiguously, demonstrated with proteins up to a size of 250 residues. For the remaining residues, a small number of possible assignments is filtered out. This is done by comparing distances in the 3D structure to restraints obtained from the peak volumes in the 4D spectrum. Using dead-end elimination, assignments are removed in which at least one of the restraints is violated. Including additional information from chemical shift predictions, a complete unambiguous assignment was obtained for Ubiquitin and 95 % of the residues were correctly assigned in the 251 residue-long N-terminal domain of enzyme I. The program including source code is available at https://github.com/thomasexner/4Dassign . PMID:27484442

  19. Combining Structure and Sequence Information Allows Automated Prediction of Substrate Specificities within Enzyme Families

    PubMed Central

    Röttig, Marc; Rausch, Christian; Kohlbacher, Oliver

    2010-01-01

    An important aspect of the functional annotation of enzymes is not only the type of reaction catalysed by an enzyme, but also the substrate specificity, which can vary widely within the same family. In many cases, prediction of family membership and even substrate specificity is possible from enzyme sequence alone, using a nearest neighbour classification rule. However, the combination of structural information and sequence information can improve the interpretability and accuracy of predictive models. The method presented here, Active Site Classification (ASC), automatically extracts the residues lining the active site from one representative three-dimensional structure and the corresponding residues from sequences of other members of the family. From a set of representatives with known substrate specificity, a Support Vector Machine (SVM) can then learn a model of substrate specificity. Applied to a sequence of unknown specificity, the SVM can then predict the most likely substrate. The models can also be analysed to reveal the underlying structural reasons determining substrate specificities and thus yield valuable insights into mechanisms of enzyme specificity. We illustrate the high prediction accuracy achieved on two benchmark data sets and the structural insights gained from ASC by a detailed analysis of the family of decarboxylating dehydrogenases. The ASC web service is available at http://asc.informatik.uni-tuebingen.de/. PMID:20072606

  20. 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…

  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

    2015-01-01

    This paper describes a new low-cost means to detect and locate mechanical impacts (collisions) on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing) the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach. PMID:26029951

  2. Automated antibody structure prediction using Accelrys tools: Results and best practices

    PubMed Central

    Fasnacht, Marc; Butenhof, Ken; Goupil-Lamy, Anne; Hernandez-Guzman, Francisco; Huang, Hongwei; Yan, Lisa

    2014-01-01

    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. Proteins 2014; 82:1583–1598. © 2014 The Authors. Proteins published by Wiley Periodicals, Inc. PMID:24833271

  3. 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

  4. A graphical software system to present stratigraphic information of surveyed sections

    NASA Astrophysics Data System (ADS)

    Sprenger, Antoinette; ten Kate, Warner G.

    Stratigraphic sections are the foundation of many regional stratigraphic analyses. The Pascal program STRATCOLUMN is designed specifically as an aid to produce a graphical presentation of litho- and biostratigraphic data of a geologic section or a core. It is useful in a wide variety of geologic settings. The layout of the plot is highly flexible. In general it consists of a header, an explanation, a lithological column, and a series of adjacent columns filled with additional information. The stratigraphic layer, defined by a set of characteristics, is the fundamental element from which the lithological column is constructed. Text and data observed in the field or in the laboratory, are expressed in additional columns according to a variety of graphical layouts. Notations of lithotypes, icons of fossils, sedimentary and biogenic structures correspond as much as possible to conventional symbolism. Many are available by default in the program, but the system provides the user with ways to construct his own single or composite lithotype notations and icons. The present version of the program runs under NOS/BE operating system on a CDC CYBER mainframe. Only elementary graphic routines of CALCOMP are used, making the program adaptable to other computer environments. Free formatting throughout simplifies the structure of the input files. Large plots are produced economically, because all selected features are stored dynamically.

  5. Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments.

    PubMed

    Akhmedov, Murodzhon; Çatay, Bülent; Apaydın, Mehmet Serkan

    2015-12-01

    Nuclear Magnetic Resonance (NMR) Spectroscopy is an important technique that allows determining protein structure in solution. An important problem in protein structure determination using NMR spectroscopy is the mapping of peaks to corresponding amino acids, also known as the assignment problem. Structure-Based Assignment (SBA) is an approach to solve this problem using a template structure that is homologous to the target. Our previously developed approach Nuclear Vector Replacement-Binary Integer Programming (NVR-BIP) computed the optimal solution for small proteins, but was unable to solve the assignments of large proteins. NVR-Ant Colony Optimization (ACO) extended the applicability of the NVR approach for such proteins. One of the input data utilized in these approaches is the Nuclear Overhauser Effect (NOE) data. NOE is an interaction observed between two protons if the protons are located close in space. These protons could be amide protons, protons attached to the alpha-carbon atom in the backbone of the protein, or side chain protons. NVR only uses backbone protons. In this paper, we reformulate the NVR-BIP model to distinguish the type of proton in NOE data and use the corresponding proton coordinates in the extended formulation. In addition, the threshold value over interproton distances is set in a standard manner for all proteins by extracting the NOE upper bound distance information from the data. We also convert NOE intensities into distance thresholds. Our new approach thus handles the NOE data correctly and without manually determined parameters. We accordingly adapt NVR-ACO solution methodology to these changes. Computational results show that our approaches obtain optimal solutions for small proteins. For the large proteins our ant colony optimization-based approach obtains promising results. PMID:26260854

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. CHEM-PATH-TRACKER: An automated tool to analyze chemical motifs in molecular structures.

    PubMed

    Ribeiro, João V; Cerqueira, N M F S A; Fernandes, Pedro A; Ramos, Maria J

    2014-07-01

    In this article, we propose a method for locating functionally relevant chemical motifs in protein structures. The chemical motifs can be a small group of residues or structure protein fragments with highly conserved properties that have important biological functions. However, the detection of chemical motifs is rather difficult because they often consist of a set of amino acid residues separated by long, variable regions, and they only come together to form a functional group when the protein is folded into its three-dimensional structure. Furthermore, the assemblage of these residues is often dependent on non-covalent interactions among the constituent amino acids that are difficult to detect or visualize. To simplify the analysis of these chemical motifs and give access to a generalized use for all users, we developed chem-path-tracker. This software is a VMD plug-in that allows the user to highlight and reveal potential chemical motifs requiring only a few selections. The analysis is based on atoms/residues pair distances applying a modified version of Dijkstra's algorithm, and it makes possible to monitor the distances of a large pathway, even during a molecular dynamics simulation. This tool turned out to be very useful, fast, and user-friendly in the performed tests. The chem-path-tracker package is distributed as an independent platform and can be found at http://www.fc.up.pt/PortoBioComp/database/doku.php?id=chem-path-tracker. PMID:24775806

  12. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations

    PubMed Central

    Dolinsky, Todd J.; Czodrowski, Paul; Li, Hui; Nielsen, Jens E.; Jensen, Jan H.; Klebe, Gerhard; Baker, Nathan A.

    2007-01-01

    Real-world observable physical and chemical characteristics are increasingly being calculated from the 3D structures of biomolecules. Methods for calculating pKa values, binding constants of ligands, and changes in protein stability are readily available, but often the limiting step in computational biology is the conversion of PDB structures into formats ready for use with biomolecular simulation software. The continued sophistication and integration of biomolecular simulation methods for systems- and genome-wide studies requires a fast, robust, physically realistic and standardized protocol for preparing macromolecular structures for biophysical algorithms. As described previously, the PDB2PQR web server addresses this need for electrostatic field calculations (Dolinsky et al., Nucleic Acids Research, 32, W665–W667, 2004). Here we report the significantly expanded PDB2PQR that includes the following features: robust standalone command line support, improved pKa estimation via the PROPKA framework, ligand parameterization via PEOE_PB charge methodology, expanded set of force fields and easily incorporated user-defined parameters via XML input files, and improvement of atom addition and optimization code. These features are available through a new web interface (http://pdb2pqr.sourceforge.net/), which offers users a wide range of options for PDB file conversion, modification and parameterization. PMID:17488841

  13. Digital tabulation of stratigraphic data from oil and gas wells in Cuyama Valley and surrounding areas, central California

    USGS Publications Warehouse

    Sweetkind, Donald S.; Bova, Shiera C.; Langenheim, V.E.; Shumaker, Lauren E.; Scheirer, Daniel S.

    2013-01-01

    Stratigraphic information from 391 oil and gas exploration wells from Cuyama Valley, California, and surrounding areas are herein compiled in digital form from reports that were released originally in paper form. The Cuyama Basin is located within the southeasternmost part of the Coast Ranges and north of the western Transverse Ranges, west of the San Andreas fault. Knowledge of the location and elevation of stratigraphic tops of formations throughout the basin is a first step toward understanding depositional trends and the structural evolution of the basin through time, and helps in understanding the slip history and partitioning of slip on San Andreas and related faults.

  14. 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.

  15. 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.

  16. 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.

  17. Informatics in radiology: automated structured reporting of imaging findings using the AIM standard and XML.

    PubMed

    Zimmerman, Stefan L; Kim, Woojin; Boonn, William W

    2011-01-01

    Quantitative and descriptive imaging data are a vital component of the radiology report and are frequently of paramount importance to the ordering physician. Unfortunately, current methods of recording these data in the report are both inefficient and error prone. In addition, the free-text, unstructured format of a radiology report makes aggregate analysis of data from multiple reports difficult or even impossible without manual intervention. A structured reporting work flow has been developed that allows quantitative data created at an advanced imaging workstation to be seamlessly integrated into the radiology report with minimal radiologist intervention. As an intermediary step between the workstation and the reporting software, quantitative and descriptive data are converted into an extensible markup language (XML) file in a standardized format specified by the Annotation and Image Markup (AIM) project of the National Institutes of Health Cancer Biomedical Informatics Grid. The AIM standard was created to allow image annotation data to be stored in a uniform machine-readable format. These XML files containing imaging data can also be stored on a local database for data mining and analysis. This structured work flow solution has the potential to improve radiologist efficiency, reduce errors, and facilitate storage of quantitative and descriptive imaging data for research. PMID:21357413

  18. Automated structure extraction and XML conversion of life science database flat files.

    PubMed

    Philippi, Stephan; Köhler, Jacob

    2006-10-01

    In the light of the increasing number of biological databases, their integration is a fundamental prerequisite for answering complex biological questions. Database integration, therefore, is an important area of research in bioinformatics. Since most of the publicly available life science databases are still exclusively exchanged by means of proprietary flat files, database integration requires parsers for very different flat file formats. Unfortunately, the development and maintenance of database specific flat file parsers is a nontrivial and time-consuming task, which takes considerable effort in large-scale integration scenarios. This paper introduces heuristically based concepts for automatic structure extraction from life science database flat files. On the basis of these concepts the FlatEx prototype is developed for the automatic conversion of flat files into XML representations. PMID:17044405

  19. 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.

  20. 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.

  1. Application of Hadamard spectroscopy to automated structure verification in high-throughput NMR.

    PubMed

    Ruan, Ke; Yang, Shengtian; Van Sant, Karey A; Likos, John J

    2009-08-01

    Combined verification using 1-D proton and HSQC has been proved to be quite successful; the acquisition time of HSQC spectra, however, can be limiting in its high-throughput applications. The replacement with Hadamard HSQC can significantly enhance the throughput. We hereby propose a protocol to optimize the grouping of the predicted carbon chemical shifts from the proposed structure and the associated Hadamard frequencies and bandwidths. The resulting Hadamard HSQC spectra compare favorably with their Fourier-transformed counterparts, and have demonstrated to perform equivalently in terms of combined verification, but with several fold enhancement in throughput, as illustrated for 21 commercial available molecules and 16 prototypical drug compounds. Further improvement of the verification accuracy can be achieved by the cross validation from Hadamard TOCSY, which can be acquired without much sacrifice in throughput. PMID:19496061

  2. Automated segmentation of intramacular layers in Fourier domain optical coherence tomography structural images from normal subjects

    PubMed Central

    Zhang, Xusheng; Yousefi, Siavash; An, Lin

    2012-01-01

    Abstract. Segmentation of optical coherence tomography (OCT) cross-sectional structural images is important for assisting ophthalmologists in clinical decision making in terms of both diagnosis and treatment. We present an automatic approach for segmenting intramacular layers in Fourier domain optical coherence tomography (FD-OCT) images using a searching strategy based on locally weighted gradient extrema, coupled with an error-removing technique based on statistical error estimation. A two-step denoising preprocess in different directions is also employed to suppress random speckle noise while preserving the layer boundary as intact as possible. The algorithms are tested on the FD-OCT volume images obtained from four normal subjects, which successfully identify the boundaries of seven physiological layers, consistent with the results based on manual determination of macular OCT images. PMID:22559689

  3. Stratigraphic relationships and geologic history depicted by computer mapping

    SciTech Connect

    Jones, T.A.; Johnson, C.R.

    1983-09-01

    The construction of detailed contour maps showing forms and relationships of stratigraphic horizons has become increasingly important in exploration and production. A complete depiction of geology must include known geometric relationships (onlap, offlap, truncation, etc) among the various stratigraphic horizons, as well as depths to horizons and thickness of intervals. Preorogenic and pre-erosional forms should be restored as part of the geologic history. A large geographic area that includes many stratigraphic horizons with several periods of diastrophism and erosion usually involves so many data that use of the computer is necessary. Unfortunately, many computer-generated maps and cross sections do not include such relationships and restorations. Most computer mapping programs generate grids of interpolated data that are used for drawing contour maps. Procedures to generate grids that show the configurations of horizons at various stages of geologic development, as well as providing estimates of the pre-erosional forms, are straightforward, and are not significantly different from manuel methods.

  4. Automated grid generation from models of complex geologic structure and stratigraphy

    SciTech Connect

    Gable, C.; Trease, H.; Cherry, T.

    1996-04-01

    The construction of computational grids which accurately reflect complex geologic structure and stratigraphy for flow and transport models poses a formidable task. With an understanding of stratigraphy, material properties and boundary and initial conditions, the task of incorporating this data into a numerical model can be difficult and time consuming. Most GIS tools for representing complex geologic volumes and surfaces are not designed for producing optimal grids for flow and transport computation. We have developed a tool, GEOMESH, for generating finite element grids that maintain the geometric integrity of input volumes, surfaces, and geologic data and produce an optimal (Delaunay) tetrahedral grid that can be used for flow and transport computations. GEOMESH also satisfies the constraint that the geometric coupling coefficients of the grid are positive for all elements. GEOMESH generates grids for two dimensional cross sections, three dimensional regional models, represents faults and fractures, and has the capability of including finer grids representing tunnels and well bores into grids. GEOMESH also permits adaptive grid refinement in three dimensions. The tools to glue, merge and insert grids together demonstrate how complex grids can be built from simpler pieces. The resulting grid can be utilized by unstructured finite element or integrated finite difference computational physics codes.

  5. Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability.

    PubMed

    Goldenzweig, Adi; Goldsmith, Moshe; Hill, Shannon E; Gertman, Or; Laurino, Paola; Ashani, Yacov; Dym, Orly; Unger, Tamar; Albeck, Shira; Prilusky, Jaime; Lieberman, Raquel L; Aharoni, Amir; Silman, Israel; Sussman, Joel L; Tawfik, Dan S; Fleishman, Sarel J

    2016-07-21

    Upon heterologous overexpression, many proteins misfold or aggregate, thus resulting in low functional yields. Human acetylcholinesterase (hAChE), an enzyme mediating synaptic transmission, is a typical case of a human protein that necessitates mammalian systems to obtain functional expression. We developed a computational strategy and designed an AChE variant bearing 51 mutations that improved core packing, surface polarity, and backbone rigidity. This variant expressed at ∼2,000-fold higher levels in E. coli compared to wild-type hAChE and exhibited 20°C higher thermostability with no change in enzymatic properties or in the active-site configuration as determined by crystallography. To demonstrate broad utility, we similarly designed four other human and bacterial proteins. Testing at most three designs per protein, we obtained enhanced stability and/or higher yields of soluble and active protein in E. coli. Our algorithm requires only a 3D structure and several dozen sequences of naturally occurring homologs, and is available at http://pross.weizmann.ac.il. PMID:27425410

  6. 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

  7. Polar Layered Deposits: Preliminary Stratigraphic Assessment from MGS Observations

    NASA Technical Reports Server (NTRS)

    Murray, B. C.; Byrne, S.; Danielson, G. E.; Herkenhoff, K. E.; Soderblom, L. A.; Zuber, M. T.

    2000-01-01

    Global and hemispheric climatic, volcanic and impact events that modulated the formation of the Martian polar layered deposits can be revealed by detailed stratigraphic analyses of well-exposed sequences of those layers. Complete three-dimensional Mars Orbiting Laser Altimeter (MOLA) topography of the north and south polar deposits is now available, and very abundant Mars Orbiter Camera (MOC) imagery that is well calibrated is becoming available. This paper presents an assessment of the polar stratigraphic potential based on observations from Mars Global Surveyor (MGS) mapping cycles through M7. Additional information can be found in the original extended abstract.

  8. 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.

  9. Process automation

    SciTech Connect

    Moser, D.R.

    1986-01-01

    Process automation technology has been pursued in the chemical processing industries and to a very limited extent in nuclear fuel reprocessing. Its effective use has been restricted in the past by the lack of diverse and reliable process instrumentation and the unavailability of sophisticated software designed for process control. The Integrated Equipment Test (IET) facility was developed by the Consolidated Fuel Reprocessing Program (CFRP) in part to demonstrate new concepts for control of advanced nuclear fuel reprocessing plants. A demonstration of fuel reprocessing equipment automation using advanced instrumentation and a modern, microprocessor-based control system is nearing completion in the facility. This facility provides for the synergistic testing of all chemical process features of a prototypical fuel reprocessing plant that can be attained with unirradiated uranium-bearing feed materials. The unique equipment and mission of the IET facility make it an ideal test bed for automation studies. This effort will provide for the demonstration of the plant automation concept and for the development of techniques for similar applications in a full-scale plant. A set of preliminary recommendations for implementing process automation has been compiled. Some of these concepts are not generally recognized or accepted. The automation work now under way in the IET facility should be useful to others in helping avoid costly mistakes because of the underutilization or misapplication of process automation. 6 figs.

  10. Exploration for stratigraphic traps in a foreland basin using a sequence stratigraphic simulation: Examples from the Eocene/Oligocene of the Apure-Llanos basin, Venezuela

    SciTech Connect

    Reistroffer, J.; Levine, P.A.; Kendall, C.G.; Finno, A.

    1996-12-31

    Foreland basin depositional sequences provide a sensitive record of the interaction between tectonism, eustatic sea level fluctuations, and sedimentation rates. Interplay between these controlling factors creates sedimentary geometries which are unique to this tectonic setting and form excellent stratigraphic hydrocarbon traps. Incised valley fill deposits, {open_quote}forced regression{close_quote} deposits, and combination structure-stratigraphic traps are the predominant reservoir types. In an effort to extend our understanding of the development of these traps, the sequence stratigraphy of a regional seismic transact through the Apure-Llanos basin was simulated. From the Late Eocene through Oligocene, the Apure-Llanos basin was Characterized by multiple phases of compression and a southeast migrating depocenter. Sands of the Mirador and Carbonera formations, which onlap the Arauca Arch to the southeast, were shed from the Guyana craton and were Cannibalized from sediments along the deformation front to the northwest. These sands comprise the principal reservoirs in the study area. Shales of the Leon Formation, which act as a regional seal, were deposited during rapid flexural subsidence and eustatic sea level rise during the early Oligocene. The Arauca Arch acted as a focal mechanism for east and southeast migrating hydrocarbons. Simulation results predict an important stratigraphic pinchout of the Mirador Formation sands against the Arauca Arch, which correlates with the Arauca Reid in Colombia to the southwest. Also, modeling indicates that minimal Tertiary oil production In the La Victoria Field to the east is due to the lack of an adequate seal. Our results provide a conceptual model which predicts hydrocarbon reservoir and seal relationships in a foreland basin setting with limited data control.