Sequence stratigraphy, tectonics and hydrocarbon trap geometries of Middle Tertiary strata in the southern San Joaquin Basin, California

DOE Office of Scientific and Technical Information (OSTI.GOV)

Phillips, S.; Hewlett, J.S.; Bazeley, W.J.M.

1996-12-31

Tectonic evolution of the southern San Joaquin basin exerted a fundamental control on Cenozoic sequence boundary development, reservoir, source and seal facies distribution, and hydrocarbon trap development. Spatial and temporal variations in Tertiary sequence architecture across the basin reflect differences in eastside versus westside basin-margin geometries and deformation histories. Deposition of Tertiary sequences initiated in a forearc basin setting, bounded on the east by a ramp-margin adjacent to the eroded Sierran arc complex and on the west by the imbricated accretionary wedge of the Coast Ranges thrust. The major stages of Cenozoic basin evolution are: (1) Episodic compressional folding andmore » thrusting associated with oblique convergence of the Farallon and North American plates (Late Cretaceous to Oligocene), (2) localized folding and onset of basin subsidence related to Pacific Plate reorganization, microplate formation and rotation (Oligocene to Early Miocene), (3) transtensional faulting, folding basin subsidence associated with initiation of the San Andreas transform and continued microplate rotation (Micocene to Pliocene), and (4) compressional folding, extensional and strike- slip faulting related to evolution of the Pacific-North American transform boundary (Plio- Pleistocene). Complex stratigraphic relationships within Eocene to Middle Miocene rocks provide examples of tectonic influences on sequence architecture. These include development of: (1) Tectonically enhanced sequence boundaries (Early Eocene base Domengine unconformity) and local mid-sequence angular unconformities, (2) westside-derived syntectonic {open_quotes}lowstand{close_quotes} systems (Yokut/Turitella Silt wedge and Leda Sand/Cymric/Salt Creek wedge), (3) regional seals associated with subsidence-related transgressions (Round Mountain Silt), and (4) combination traps formed by structural inversion of distal lowstand delta reservoirs (e.g. Coalinga East Extension field).« less

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

PubMed Central

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

2013-01-01

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

Earthquake recurrence and risk assessment in circum-Pacific seismic gaps

USGS Publications Warehouse

Thatcher, W.

1989-01-01

THE development of the concept of seismic gaps, regions of low earthquake activity where large events are expected, has been one of the notable achievements of seismology and plate tectonics. Its application to long-term earthquake hazard assessment continues to be an active field of seismological research. Here I have surveyed well documented case histories of repeated rupture of the same segment of circum-Pacific plate boundary and characterized their general features. I find that variability in fault slip and spatial extent of great earthquakes rupturing the same plate boundary segment is typical rather than exceptional but sequences of major events fill identified seismic gaps with remarkable order. Earthquakes are concentrated late in the seismic cycle and occur with increasing size and magnitude. Furthermore, earthquake rup-ture starts near zones of concentrated moment release, suggesting that high-slip regions control the timing of recurrent events. The absence of major earthquakes early in the seismic cycle indicates a more complex behaviour for lower-slip regions, which may explain the observed cycle-to-cycle diversity of gap-filling sequences. ?? 1989 Nature Publishing Group.

Vegetation, climatic and floral changes at the Cretaceous-Tertiary boundary

USGS Publications Warehouse

Wolfe, J.A.; Upchurch, G.R.

1986-01-01

he western interior of North America has the only known non-marine sections that contain the iridium-rich clay interpreted as the Cretaceous-Tertiary (K-T) boundary1-7. Because vegetation and climate can be directly inferred from physiognomy of leaves8-15 and because leaf species typically represent low taxonomic categories, studies of leaf floras in these sections provide data on the effects of a terminal Cretaceous event on the land flora, vegetation and climate. A previous study based on detailed sampling of leaves and their dispersed cuticle16 in the Raton Basin provides a framework for interpretation of other leaf sequences over 20 degrees of latitude. We conclude that at the boundary there were: (1) High levels of extinction in the south and low levels in the north; (2) major ecological disruption followed by long-term vegetational changes that mimicked normal ecological succession; (3) a major increase in precipitation; and (4) a brief, low-temperature excursion, which supports models of an 'impact winter'. ?? 1986 Nature Publishing Group.

Turbulent boundary layers subjected to multiple curvatures and pressure gradients

NASA Technical Reports Server (NTRS)

Bandyopadhyay, Promode R.; Ahmed, Anwar

1993-01-01

The effects of abruptly applied cycles of curvatures and pressure gradients on turbulent boundary layers are examined experimentally. Two two-dimensional curved test surfaces are considered: one has a sequence of concave and convex longitudinal surface curvatures and the other has a sequence of convex and concave curvatures. The choice of the curvature sequences were motivated by a desire to study the asymmetric response of turbulent boundary layers to convex and concave curvatures. The relaxation of a boundary layer from the effects of these two opposite sequences has been compared. The effect of the accompaying sequences of pressure gradient has also been examined but the effect of curvature dominates. The growth of internal layers at the curvature junctions have been studied. Measurements of the Gortler and corner vortex systems have been made. The boundary layer recovering from the sequence of concave to convex curvature has a sustained lower skin friction level than in that recovering from the sequence of convex to concave curvature. The amplification and suppression of turbulence due to the curvature sequences have also been studied.

Disruption of Boundary Encoding During Sensorimotor Sequence Learning: An MEG Study.

PubMed

Michail, Georgios; Nikulin, Vadim V; Curio, Gabriel; Maess, Burkhard; Herrojo Ruiz, María

2018-01-01

Music performance relies on the ability to learn and execute actions and their associated sounds. The process of learning these auditory-motor contingencies depends on the proper encoding of the serial order of the actions and sounds. Among the different serial positions of a behavioral sequence, the first and last (boundary) elements are particularly relevant. Animal and patient studies have demonstrated a specific neural representation for boundary elements in prefrontal cortical regions and in the basal ganglia, highlighting the relevance of their proper encoding. The neural mechanisms underlying the encoding of sequence boundaries in the general human population remain, however, largely unknown. In this study, we examined how alterations of auditory feedback, introduced at different ordinal positions (boundary or within-sequence element), affect the neural and behavioral responses during sensorimotor sequence learning. Analysing the neuromagnetic signals from 20 participants while they performed short piano sequences under the occasional effect of altered feedback (AF), we found that at around 150-200 ms post-keystroke, the neural activities in the dorsolateral prefrontal cortex (DLPFC) and supplementary motor area (SMA) were dissociated for boundary and within-sequence elements. Furthermore, the behavioral data demonstrated that feedback alterations on boundaries led to greater performance costs, such as more errors in the subsequent keystrokes. These findings jointly support the idea that the proper encoding of boundaries is critical in acquiring sensorimotor sequences. They also provide evidence for the involvement of a distinct neural circuitry in humans including prefrontal and higher-order motor areas during the encoding of the different classes of serial order.

Seismic link at plate boundary

NASA Astrophysics Data System (ADS)

Ramdani, Faical; Kettani, Omar; Tadili, Benaissa

2015-06-01

Seismic triggering at plate boundaries has a very complex nature that includes seismic events at varying distances. The spatial orientation of triggering cannot be reduced to sequences from the main shocks. Seismic waves propagate at all times in all directions, particularly in highly active zones. No direct evidence can be obtained regarding which earthquakes trigger the shocks. The first approach is to determine the potential linked zones where triggering may occur. The second step is to determine the causality between the events and their triggered shocks. The spatial orientation of the links between events is established from pre-ordered networks and the adapted dependence of the spatio-temporal occurrence of earthquakes. Based on a coefficient of synchronous seismic activity to grid couples, we derive a network link by each threshold. The links of high thresholds are tested using the coherence of time series to determine the causality and related orientation. The resulting link orientations at the plate boundary conditions indicate that causal triggering seems to be localized along a major fault, as a stress transfer between two major faults, and parallel to the geothermal area extension.

Novel Single-Base Deletional Mutation in Major Intrinsic Protein (MIP) in Autosomal Dominant Cataract

PubMed Central

Geyer, David D.; Spence, M. Anne; Johannes, Meriam; Flodman, Pamela; Clancy, Kevin P.; Berry, Rebecca; Sparkes, Robert S.; Jonsen, Matthew D.; Isenberg, Sherwin J.; Bateman, J. Bronwyn

2006-01-01

PURPOSE To further elucidate the cataract phenotype, and identify the gene and mutation for autosomal dominant cataract (ADC) in an American family of European descent (ADC2) by sequencing the major intrinsic protein gene (MIP), a candidate based on linkage to chromosome 12q13. DESIGN Observational case series and laboratory experimental study. METHODS We examined two at-risk individuals in ADC2. We PCR-amplified and sequenced all four exons and all intron-exon boundaries of the MIP gene from genomic and cloned DNA in affected members to confirm one variant as the putative mutation. RESULTS We found a novel single deletion of nucleotide (nt) 3223 (within codon 235) in exon four, causing a frameshift that alters 41 of 45 subsequent amino acids and creates a premature stop codon. CONCLUSIONS We identified a novel single base pair deletion in the MIP gene and conclude that it is a pathogenic sequence alteration. PMID:16564824

Tectonic sequence stratigraphy, Early Permian Dry Mountain trough, east-central Nevada

DOE Office of Scientific and Technical Information (OSTI.GOV)

Snyder, W.S.; Gallegos, D.M.; Spinosa, C.

1991-06-01

The Early Permian Dry Mountain trough (DMT) of east-central Nevada is one of several tectonic basins and associated uplifts that developed along the continenetal margin during the latest Pennsylvanian-Early Permian Dry Mountain tectonic phase. The sequence stratigraphy reflects a combination of eustatic sea level changes and tectonic uplift or subsidence. Fewer than one to only a few million years separate the development of sequence boundaries within the DMT. At this scale, differences among published eustasy curves preclude their use as definitive tools to identify eustatically controlled sequence boundaries. Nevertheless, available data indicate several pulses of tectonism affected sedimentation within themore » DMT. The authors are attempting to develop criteria to distinguish tectonic from eustatic sequence boundaries. Detailed biostratigraphic data are required to provide an independent check on the correlation of sequence boundaries between measured sections. For example, the same age boundary may reflect tectonic uplift in one part of the basin and subsidence in another. The uplift may or may not result in subaerial exposure and erosion. For those boundaries that do not result from subaerial exposure, lithofacies and biofacies analyses are required to infer relative uplift (water depth decrease) or subsidence (water depth increase). There are inherent resolution limitations in both the paleontologic and sedimentologic methodologies. These limitations, combined with those of eustasy curves, dictate the preliminary nature of their results.« less

Albian to Santonian carbon isotope excursions and faunal extinctions in the Canadian Western Interior Sea: Recognition of eustatic sea-level controls on a forebulge setting

NASA Astrophysics Data System (ADS)

Schröder-Adams, Claudia J.; Herrle, Jens O.; Tu, Qiang

2012-12-01

The forebulge region of the Cretaceous Canadian Western Interior Sea (CWIS) was susceptible to subaerial exposure and marine erosion during sea level lowstands. The middle Albian to Santonian record as cored at Cold Lake, east-central Alberta, Canada documents numerous disconformities that are expressed in bioclastic concentration horizons and faunal extinctions and turnovers. Detailed comparison between a newly established δ13Corg. record measured on bulk sediment at Cold Lake and a combined δ13Ccarb. reference curve based on the Cretaceous English chalk and SE France hemipelagic marlstones highlights missing positive and negative δ13C excursions at the CWIS forebulge and thus missing sections that precisely corroborate with sequence boundaries. Disconformable boundaries correlate closely with global sea-level lowstands as established for the Cretaceous North Atlantic suggesting a pronounced eustatic influence on the CWIS forebulge setting. Sequence boundaries occur in the uppermost Middle Albian, lowermost Upper Albian, Albian/Cenomanian boundary, Cenomanian/Turonian boundary, middle Turonian to lower Coniacian and uppermost Middle Santonian, each followed by a positive δ13C excursion. Oceanic anoxic events 1d, 2 and 3 are recognized and linked to major faunal and floral assemblage changes. Of these the Albian/Cenomanian biotic turnover is the most severe in the CWIS marked by the total loss of Albian benthic foraminifera species. Causes of this benthic extinction might be linked to a period of anoxia (OAE 1d) during the latest Albian followed by sea-level controlled basin restriction.

Functional Requirements for Fab-7 Boundary Activity in the Bithorax Complex

PubMed Central

Wolle, Daniel; Cleard, Fabienne; Aoki, Tsutomu; Deshpande, Girish; Karch, Francois

2015-01-01

Chromatin boundaries are architectural elements that determine the three-dimensional folding of the chromatin fiber and organize the chromosome into independent units of genetic activity. The Fab-7 boundary from the Drosophila bithorax complex (BX-C) is required for the parasegment-specific expression of the Abd-B gene. We have used a replacement strategy to identify sequences that are necessary and sufficient for Fab-7 boundary function in the BX-C. Fab-7 boundary activity is known to depend on factors that are stage specific, and we describe a novel ∼700-kDa complex, the late boundary complex (LBC), that binds to Fab-7 sequences that have insulator functions in late embryos and adults. We show that the LBC is enriched in nuclear extracts from late, but not early, embryos and that it contains three insulator proteins, GAF, Mod(mdg4), and E(y)2. Its DNA binding properties are unusual in that it requires a minimal sequence of >65 bp; however, other than a GAGA motif, the three Fab-7 LBC recognition elements display few sequence similarities. Finally, we show that mutations which abrogate LBC binding in vitro inactivate the Fab-7 boundary in the BX-C. PMID:26303531

Seismic sequence stratigraphy of Miocene deposits related to eustatic, tectonic and climatic events, Cap Bon Peninsula, northeastern Tunisia

NASA Astrophysics Data System (ADS)

Gharsalli, Ramzi; Zouaghi, Taher; Soussi, Mohamed; Chebbi, Riadh; Khomsi, Sami; Bédir, Mourad

2013-09-01

The Cap Bon Peninsula, belonging to northeastern Tunisia, is located in the Maghrebian Alpine foreland and in the North of the Pelagian block. By its paleoposition, during the Cenozoic, in the edge of the southern Tethyan margin, this peninsula constitutes a geological entity that fossilized the eustatic, tectonic and climatic interactions. Surface and subsurface study carried out in the Cap Bon onshore area and surrounding offshore of Hammamet interests the Miocene deposits from the Langhian-to-Messinian interval time. Related to the basin and the platform positions, sequence and seismic stratigraphy studies have been conducted to identify seven third-order seismic sequences in subsurface (SM1-SM7), six depositional sequences on the Zinnia-1 petroleum well (SDM1-SDM6), and five depositional sequences on the El Oudiane section of the Jebel Abderrahmane (SDM1-SDM5). Each sequence shows a succession of high-frequency systems tract and parasequences. These sequences are separated by remarkable sequence boundaries and maximum flooding surfaces (SB and MFS) that have been correlated to the eustatic cycles and supercycles of the Global Sea Level Chart of Haq et al. (1987). The sequences have been also correlated with Sequence Chronostratigraphic Chart of Hardenbol et al. (1998), related to European basins, allows us to arise some major differences in number and in size. The major discontinuities, which limit the sequences resulted from the interplay between tectonic and climatic phenomena. It thus appears very judicious to bring back these chronological surfaces to eustatic and/or local tectonic activity and global eustatic and climatic controls.

Sequence stratigraphy of the Aux Vases Sandstone: A major oil producer in the Illinois basin

USGS Publications Warehouse

Leetaru, H.E.

2000-01-01

The Aux Vases Sandstone (Mississippian) has contributed between 10 and 25% of all the oil produced in Illinois. The Aux Vases is not only an important oil reservoir but is also an important source of groundwater, quarrying stone, and fluorspar. Using sequence stratigraphy, a more accurate stratigraphic interpretation of this economically important formation can be discerned and thereby enable more effective exploration for the resources contained therein. Previous studies have assumed that the underlying Spar Mountain, Karnak, and Joppa formations interfingered with the Aux Vases, as did the overlying Renault Limestone. This study demonstrates that these formations instead are separated by sequence boundaries; therefore, they are not genetically related to each other. A result of this sequence stratigraphic approach is the identification of incised valleys, paleotopography, and potential new hydrocarbon reservoirs in the Spar Mountain and Aux Vases. In eastern Illinois, the Aux Vases is bounded by sequence boundaries with 20 ft (6 m) of relief. The Aux Vases oil reservoir facies was deposited as a tidally influenced siliciclastic wedge that prograded over underlying carbonate-rich sediments. The Aux Vases sedimentary succession consists of offshore sediment overlain by intertidal and supratidal sediments. Low-permeability shales and carbonates typically surround the Aux Vases reservoir sandstone and thereby form numerous bypassed compartments from which additional oil can be recovered. The potential for new significant oil fields within the Aux Vases is great, as is the potential for undrained reservoir compartments within existing Aux Vases fields.

Sedimentary evolution of the Pliocene and Pleistocene Ebro margin, northeastern Spain

USGS Publications Warehouse

Alonso, B.; Field, M.E.; Gardner, J.V.; Maldonado, A.

1990-01-01

The Pliocene and Pleistocene deposits of the Spanish Ebro margin overlie a regional unconformity and contain a major disconformity. These unconformities, named Reflector M and Reflector G, mark the bases of two seismic sequences. Except for close to the upper boundary where a few small channel deposits are recognized, the lower sequence lacks channels. The upper sequence contains nine channel-levee complexes as well as base-of-slope aprons that represent the proximal part of the Valencia turbidite system. Diverse geometries and variations in seismic units distinguish shelf, slope, base-of-slope and basin-floor facies. Four events characterize the late Miocene to Pleistocene evolution of the Ebro margin: (a) formation of a paleodrainage system and an extensive erosion-to-depositional surface during the latest Miocene (Messinian), (b) deposition of hemipelagic units during the early Pliocene, (c) development of canyons during the late Pliocene to early Pleistocene, and (d) deposition of slope wedges, channel-levee complexes, and base-of-slope aprons alternating with hemipelagic deposition during the Pleistocene. Sea-level fluctuations influenced the evolution of the sedimentary sequences of the Ebro margin, but the major control was the sediment supply from the Ebro River. ?? 1990.

The Cretaceous-Tertiary boundary marine extinction and global primary productivity collapse

NASA Technical Reports Server (NTRS)

Zachos, J. C.; Arthus, M. A.; Dean, W. E.

1988-01-01

The extinction of marine phyto-and zoo-plankton across the K-T boundary has been well documented. Such an event may have resulted in decreased photosynthetic fixation of carbon in surface waters and a collapse of the food chain in the marine biosphere. Because the vertical and horizontal distribution of the carbon isotopic composition of total dissolved carton (TDC) in the modern ocean is controlled by the transfer of organic carbon from the surface to deep reservoirs, it follows that a major disruption of the marine biosphere would have had a major effect on the distribution of carbon isotopes in the ocean. Negative carbon isotope excursions have been identified at many marine K-T boundary sequences worldwide and are interpreted as a signal of decreased oceanic primary productivity. However, the magnitude, duration and consequences of this productivity crisis have been poorly constrained. On the basis of planktonic and benthic calcareous microfossil carbon isotope and other geochemical data from DSDP Site 577 located on the Shatsky Rise in the north-central Pacific, as well as other sites, researchers have been able to provide a reasonable estimate of the duration and magnitude of this event.

Functional Requirements for Fab-7 Boundary Activity in the Bithorax Complex.

PubMed

Wolle, Daniel; Cleard, Fabienne; Aoki, Tsutomu; Deshpande, Girish; Schedl, Paul; Karch, Francois

2015-11-01

Chromatin boundaries are architectural elements that determine the three-dimensional folding of the chromatin fiber and organize the chromosome into independent units of genetic activity. The Fab-7 boundary from the Drosophila bithorax complex (BX-C) is required for the parasegment-specific expression of the Abd-B gene. We have used a replacement strategy to identify sequences that are necessary and sufficient for Fab-7 boundary function in the BX-C. Fab-7 boundary activity is known to depend on factors that are stage specific, and we describe a novel ∼700-kDa complex, the late boundary complex (LBC), that binds to Fab-7 sequences that have insulator functions in late embryos and adults. We show that the LBC is enriched in nuclear extracts from late, but not early, embryos and that it contains three insulator proteins, GAF, Mod(mdg4), and E(y)2. Its DNA binding properties are unusual in that it requires a minimal sequence of >65 bp; however, other than a GAGA motif, the three Fab-7 LBC recognition elements display few sequence similarities. Finally, we show that mutations which abrogate LBC binding in vitro inactivate the Fab-7 boundary in the BX-C. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Seismic stratigraphy and structure of the Chukchi Borderland: implications for the opening of the Canada Basin

NASA Astrophysics Data System (ADS)

Ilhan, I.; Coakley, B.

2015-12-01

Interpretation of seismic reflection data from the western Chukchi Borderland has illuminated the structure and stratigraphy of the area. Basement rotated fault blocks are offset by two border fault systems (BFS1 and BFS2) and by secondary faults, striking curvilinear in the NW-SE direction, dipping to the NE. The BFS1 dissects the Chukchi Plateau into two first-order rotated blocks bounding two major sedimentary depocentres, the North Chukchi Basin and the Chukchi Plateau Central Basin. The BFS2, which has a larger offset than BFS1, forms the western boundary of the Northwind Basin. Much of the stratigraphy is controlled by sediment supply. The basins were starved early in their history, resulting in a limited syn-rift section. Substantial sediment accumulation in the Borderland appears to post-date large scale progradation of the depostional shelf edge across the Chukchi Shelf. Basin infill stratigraphies are subdivided into pre-rift, syn-rift, early-, middle-, late post-rift, and glacio-marine sequences (SB1-SB5). SB1 shows truncation of the remnants of the pre-rift strata below and onlap of the syn-rift sequence(s) above; the SB2 marks the termination of the rifting stage and is bounded by bi-directional onlap surface of the early post-rift strata above; the base of SB3 is an onlap surface marks the arrival of the prograding shelf margin sequence(s); the SB4 shows evidence of erosion at the base of the prograding late post-rift sequence(s); and the SB5 is an downloap surface marking the first arrival of the glacio-marine sediments eroded from the Chukchi Shelf. Two ages of the major sequence boundaries, the SB3 and SB4, can be directly tied to Popcorn and Crackerjack Chukchi Shelf well data, and the older ones, the end of rifting and the top of the pre-rift, are inferred based on stratigraphic observations. The stratigraphic relationship suggests that the Chukchi Borderland stratigraphy can be correlated in part to the Chukchi Shelf stratigraphy. The first and second-order rotated fault blocks and depositional history suggest that the Chukchi Borderland has been coupled to the Chukchi Shelf at least since the extension of the Borderland. Therefore we infer only small horizontal offsets between the Chukchi Borderland and the Chukchi Shelf, which have largely a shared geologic history.

The Triassic-Jurassic Boundary Event at the Paleo-Equator: Evidence for Global Change from Carbonate Sedimentology and Chemostratigraphy, Ras Al Khaimah, UAE.

NASA Astrophysics Data System (ADS)

Al-Suwaidi, A. H.; Steuber, T.; Suarez, M. B.; Ge, Y.

2015-12-01

The Triassic­-Jurassic (T-J) transition was a time of significant environmental perturbation typically associated with CAMP volcanism and is considered to be one of the six major extinction events in Earth's history. This event was associated with large perturbations of the global carbon cycle, as recorded in the isotopic composition of marine carbonate and bulk organic carbon. This has been elsewhere associated with widespread ocean acidification and a major disruption in marine carbonate production in neritic and pelagic environments. A carbon-isotope record from a paleo-equatorial carbonate platform exposed in Ras Al Khaimah, United Arab Emirates (UAE), shows continuous shallow-water carbonate sedimentation across the Triassic­-Jurassic boundary, in contrast with other boundary sections from higher latitudes, where carbonate sedimentation is typically discontinuous. δ13C shows a 4‰ negative excursion in both bulk organic carbon and carbonate carbon followed by a positive excursion. The boundary in Ras Al Khaimah, is placed at the base of a thick oolite unit overlying limestones with abundant and diverse Rhaetian reefal biota. Deposition of fossiliferous limestones in this location persisted into the uppermost Rhaetian and through the initial negative carbon-isotope excursion. While characteristic late Triassic biota with originally aragonitic mineralogy disappears at the boundary, aragonite persists as the inferred original mineralogy of the earliest Jurassic ooids and occasional skeletal bioclasts. The evidence presented herein suggest equatorial seawater of Tethys appears to have remained aragonite-supersaturated across the boundary and extinction event in contrast to higher latitude depositional sequences raising questions about how widespread ocean acidification was and in what conditions it may be favoured.

Of dups and dinos: evolution at the K/Pg boundary.

PubMed

Lohaus, Rolf; Van de Peer, Yves

2016-04-01

Fifteen years into sequencing entire plant genomes, more than 30 paleopolyploidy events could be mapped on the tree of flowering plants (and many more when also transcriptome data sets are considered). While some genome duplications are very old and have occurred early in the evolution of dicots and monocots, or even before, others are more recent and seem to have occurred independently in many different plant lineages. Strikingly, a majority of these duplications date somewhere between 55 and 75 million years ago (mya), and thus likely correlate with the K/Pg boundary. If true, this would suggest that plants that had their genome duplicated at that time, had an increased chance to survive the most recent mass extinction event, at 66mya, which wiped out a majority of plant and animal life, including all non-avian dinosaurs. Here, we review several processes, both neutral and adaptive, that might explain the establishment of polyploid plants, following the K/Pg mass extinction. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

DETERMINATION OF ELASTIC WAVE VELOCITY AND RELATIVE HYPOCENTER LOCATIONS USING REFRACTED WAVES. II. APPLICATION TO THE HAICHENG, CHINA, AFTERSHOCK SEQUENCE.

USGS Publications Warehouse

Shedlock, Kaye M.; Jones, Lucile M.; Ma, Xiufang

1985-01-01

The authors located the aftershocks of the February 4, 1975 Haicheng, China, aftershock sequence using an arrival time difference (ATD) simultaneous inversion method for determining the near-source (in situ) velocity and the location of the aftershocks with respect to a master event. The aftershocks define a diffuse zone, 70 km multiplied by 25 km, trending west-northwest, perpendicular to the major structural trend of the region. The main shock and most of the large aftershocks have strike-slip fault plane solutions. The preferred fault plane strikes west-northwest, and the inferred sense of motion is left-lateral. The entire Haicheng earthauake sequence appears to have been the response of an intensely faulted range boundary to a primarily east-west crustal compression and/or north-south extension.

Seismic interpretation and thrust tectonics of the Amadeus Basin, central Australia, along the BMR regional seismic line

NASA Astrophysics Data System (ADS)

Shaw, Russell D.; Korsch, Russell J.; Wright, C.; Goleby, B. R.

At the northern margin of the Amadeus Basin the monoclinal upturn (the MacDonnell Homocline) is interpreted to be the result of rotation and limited back-thrusting of the sedimentary sequence in front of a southerly-directed, imbricate basement thrust-wedge. This thrust complex is linked at depth to the crust-cutting Redbank Thrust Zone. In the northern part of the basin immediately to the south, regional seismic reflection profiling across the Missionary Plain shows a sub-horizontal, north-dipping, parautochthonous sedimentary sequence between about 8.5 km and 12.0 km thick. This sedimentary sequence shows upturning only at the northern and southern extremities, and represents an unusual, relatively undeformed region between converging thrust systems. In this intervening region, the crust appears to have been tilted downwards and northwards in response to the upthrusting to the north. Still farther to the south, the vertical uplift of the southern hanging wall of the Gardiner Thrust is about 6 km. Seismic reflection profiling in the region immediately south of the Gardiner Thrust indicates repetition of the sedimentary sequence. At the far end of the profile, in the Kernot Range, an imbricate thrust system fans ahead of a ramp-flat thrust pair. This thrust system (the Kernot Range Thrust System) occurs immediately north of an aeromagnetic domain boundary which marks the southern limit of a central ridge region characterized by thin Palaeozoic sedimentary cover and shallow depths to magnetic basement. A planar seismic event, imaged to a depth of at least 18 km, may correspond to the same boundary and is interpreted as a pre-basin Proterozoic thrust. Overall, the structure in the shallow sedimentary section in the central-southern region of the Amadeus Basin indicates that north-directed thrusting during the Dovonian-Carboniferous Alice Springs Orogeny was thin-skinned. During this orogeny an earlier thrust system, formed during the Petermann Ranges Orogeny and precursor orogenies in the Late Proterozoic, was reactivated with Proterozoic salt deposits localising the decollement zone. The Alice Springs Orogeny also reactivated a major mid Proterozoic province boundary in the basement to the north of the basin, resulting in major thrust movement at the northern basin margin.

Tracking tumor boundary in MV-EPID images without implanted markers: A feasibility study.

PubMed

Zhang, Xiaoyong; Homma, Noriyasu; Ichiji, Kei; Takai, Yoshihiro; Yoshizawa, Makoto

2015-05-01

To develop a markerless tracking algorithm to track the tumor boundary in megavoltage (MV)-electronic portal imaging device (EPID) images for image-guided radiation therapy. A level set method (LSM)-based algorithm is developed to track tumor boundary in EPID image sequences. Given an EPID image sequence, an initial curve is manually specified in the first frame. Driven by a region-scalable energy fitting function, the initial curve automatically evolves toward the tumor boundary and stops on the desired boundary while the energy function reaches its minimum. For the subsequent frames, the tracking algorithm updates the initial curve by using the tracking result in the previous frame and reuses the LSM to detect the tumor boundary in the subsequent frame so that the tracking processing can be continued without user intervention. The tracking algorithm is tested on three image datasets, including a 4-D phantom EPID image sequence, four digitally deformable phantom image sequences with different noise levels, and four clinical EPID image sequences acquired in lung cancer treatment. The tracking accuracy is evaluated based on two metrics: centroid localization error (CLE) and volume overlap index (VOI) between the tracking result and the ground truth. For the 4-D phantom image sequence, the CLE is 0.23 ± 0.20 mm, and VOI is 95.6% ± 0.2%. For the digital phantom image sequences, the total CLE and VOI are 0.11 ± 0.08 mm and 96.7% ± 0.7%, respectively. In addition, for the clinical EPID image sequences, the proposed algorithm achieves 0.32 ± 0.77 mm in the CLE and 72.1% ± 5.5% in the VOI. These results demonstrate the effectiveness of the authors' proposed method both in tumor localization and boundary tracking in EPID images. In addition, compared with two existing tracking algorithms, the proposed method achieves a higher accuracy in tumor localization. In this paper, the authors presented a feasibility study of tracking tumor boundary in EPID images by using a LSM-based algorithm. Experimental results conducted on phantom and clinical EPID images demonstrated the effectiveness of the tracking algorithm for visible tumor target. Compared with previous tracking methods, the authors' algorithm has the potential to improve the tracking accuracy in radiation therapy. In addition, real-time tumor boundary information within the irradiation field will be potentially useful for further applications, such as adaptive beam delivery, dose evaluation.

Tracking tumor boundary in MV-EPID images without implanted markers: A feasibility study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Xiaoyong, E-mail: xiaoyong@ieee.org; Homma, Noriyasu, E-mail: homma@ieee.org; Ichiji, Kei, E-mail: ichiji@yoshizawa.ecei.tohoku.ac.jp

2015-05-15

Purpose: To develop a markerless tracking algorithm to track the tumor boundary in megavoltage (MV)-electronic portal imaging device (EPID) images for image-guided radiation therapy. Methods: A level set method (LSM)-based algorithm is developed to track tumor boundary in EPID image sequences. Given an EPID image sequence, an initial curve is manually specified in the first frame. Driven by a region-scalable energy fitting function, the initial curve automatically evolves toward the tumor boundary and stops on the desired boundary while the energy function reaches its minimum. For the subsequent frames, the tracking algorithm updates the initial curve by using the trackingmore » result in the previous frame and reuses the LSM to detect the tumor boundary in the subsequent frame so that the tracking processing can be continued without user intervention. The tracking algorithm is tested on three image datasets, including a 4-D phantom EPID image sequence, four digitally deformable phantom image sequences with different noise levels, and four clinical EPID image sequences acquired in lung cancer treatment. The tracking accuracy is evaluated based on two metrics: centroid localization error (CLE) and volume overlap index (VOI) between the tracking result and the ground truth. Results: For the 4-D phantom image sequence, the CLE is 0.23 ± 0.20 mm, and VOI is 95.6% ± 0.2%. For the digital phantom image sequences, the total CLE and VOI are 0.11 ± 0.08 mm and 96.7% ± 0.7%, respectively. In addition, for the clinical EPID image sequences, the proposed algorithm achieves 0.32 ± 0.77 mm in the CLE and 72.1% ± 5.5% in the VOI. These results demonstrate the effectiveness of the authors’ proposed method both in tumor localization and boundary tracking in EPID images. In addition, compared with two existing tracking algorithms, the proposed method achieves a higher accuracy in tumor localization. Conclusions: In this paper, the authors presented a feasibility study of tracking tumor boundary in EPID images by using a LSM-based algorithm. Experimental results conducted on phantom and clinical EPID images demonstrated the effectiveness of the tracking algorithm for visible tumor target. Compared with previous tracking methods, the authors’ algorithm has the potential to improve the tracking accuracy in radiation therapy. In addition, real-time tumor boundary information within the irradiation field will be potentially useful for further applications, such as adaptive beam delivery, dose evaluation.« less

Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing.

PubMed

Thauvin-Robinet, Christel; Franco, Brunella; Saugier-Veber, Pascale; Aral, Bernard; Gigot, Nadège; Donzel, Anne; Van Maldergem, Lionel; Bieth, Eric; Layet, Valérie; Mathieu, Michèle; Teebi, Ahmad; Lespinasse, James; Callier, Patrick; Mugneret, Francine; Masurel-Paulet, Alice; Gautier, Elodie; Huet, Frédéric; Teyssier, Jean-Raymond; Tosi, Mario; Frébourg, Thierry; Faivre, Laurence

2009-02-01

Oral-facial-digital type I syndrome (OFDI) is characterised by an X-linked dominant mode of inheritance with lethality in males. Clinical features include facial dysmorphism with oral, dental and distal abnormalities, polycystic kidney disease and central nervous system malformations. Considerable allelic heterogeneity has been reported within the OFD1 gene, but DNA bi-directional sequencing of the exons and intron-exon boundaries of the OFD1 gene remains negative in more than 20% of cases. We hypothesized that genomic rearrangements could account for the majority of the remaining undiagnosed cases. Thus, we took advantage of two independent available series of patients with OFDI syndrome and negative DNA bi-directional sequencing of the exons and intron-exon boundaries of the OFD1 gene from two different European labs: 13/36 cases from the French lab; 13/95 from the Italian lab. All patients were screened by a semiquantitative fluorescent multiplex method (QFMPSF) and relative quantification by real-time PCR (qPCR). Six OFD1 genomic deletions (exon 5, exons 1-8, exons 1-14, exons 10-11, exons 13-23 and exon 17) were identified, accounting for 5% of OFDI patients and for 23% of patients with negative mutation screening by DNA sequencing. The association of DNA direct sequencing, QFMPSF and qPCR detects OFD1 alteration in up to 85% of patients with a phenotype suggestive of OFDI syndrome. Given the average percentage of large genomic rearrangements (5%), we suggest that dosage methods should be performed in addition to DNA direct sequencing analysis to exclude the involvement of the OFD1 transcript when there are genetic counselling issues. (c) 2008 Wiley-Liss, Inc.

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

NASA Astrophysics Data System (ADS)

Yang, Wan; Kominz, Michelle A.

2003-01-01

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

Facies analysis and sequence stratigraphic framework of upper Campanian strata (Neslen and Mount Garfield formations, Bluecastle Tongue of the Castlegate sandstone, and Mancos shale), Eastern Book cliffs, Colorado and Utah

USGS Publications Warehouse

Kirschbaum, Mark A.; Hettinger, Robert D.

2004-01-01

Facies and sequence-stratigraphic analysis identifies six high-resolution sequences within upper Campanian strata across about 120 miles of the Book Cliffs in western Colorado and eastern Utah. The six sequences are named after prominent sandstone units and include, in ascending order, upper Sego sequence, Neslen sequence, Corcoran sequence, Buck Canyon/lower Cozzette sequence, upper Cozzette sequence, and Cozzette/Rollins sequence. A seventh sequence, the Bluecastle sequence, is present in the extreme western part of the study area. Facies analysis documents deepening- and shallowing- upward successions, parasequence stacking patterns, downlap in subsurface cross sections, facies dislocations, basinward shifts in facies, and truncation of strata.All six sequences display major incision into shoreface deposits of the Sego Sandstone and sandstones of the Corcoran and Cozzette Members of the Mount Garfield Formation. The incised surfaces represent sequence-boundary unconformities that allowed bypass of sediment to lowstand shorelines that are either attached to the older highstand shorelines or are detached from the older highstand shorelines and located southeast of the main study area. The sequence boundary unconformities represent valley incisions that were cut during successive lowstands of relative sea level. The overlying valley-fill deposits generally consist of tidally influenced strata deposited during an overall base level rise. Transgressive surfaces can be traced or projected over, or locally into, estuarine deposits above and landward of their associated shoreface deposits. Maximum flooding surfaces can be traced or projected landward from offshore strata into, or above, coastal-plain deposits. With the exception of the Cozzette/Rollins sequence, the majority of coal-bearing coastal-plain strata was deposited before maximum flooding and is therefore within the transgressive systems tracts. Maximum flooding was followed by strong progradation of parasequences and low preservation potential of coastal-plain strata within the highstand systems tract. The large incised valleys, lack of transgressive retrogradational parasequences, strong progradational nature of highstand parasequences, and low preservation of coastal-plain strata in the highstand systems tracts argue for relatively low accommodation space during deposition of the Sego, Corcoran, and Cozzette sequences. The Buck Canyon/Cozzette and Cozzette/Rollins sequences contrast with other sequences in that the preservation of retrogradational parasequences and the development of large estuaries coincident with maximum flooding indicate a relative increase in accommodation space during deposition of these strata. Following maximum flooding, the Buck Canyon/Cozzette sequence follows the pattern of the other sequences, but the Cozzette/Rollins sequence exhibits a contrasting offlapping pattern with development of offshore clinoforms that downlap and eventually parallel its maximum flooding surface. This highstand systems tract preserves a thick coal-bearing section where the Rollins Sandstone Member of the Mount Garfield Formation parasequences prograde out of the study area, stepping up as much as 800 ft stratigraphically over a distance of about 90 miles. This progradational stacking pattern indicates a higher accommodation space and increased sedimentation rate compared to the previous sequences.

The Boundary Function Method. Fundamentals

NASA Astrophysics Data System (ADS)

Kot, V. A.

2017-03-01

The boundary function method is proposed for solving applied problems of mathematical physics in the region defined by a partial differential equation of the general form involving constant or variable coefficients with a Dirichlet, Neumann, or Robin boundary condition. In this method, the desired function is defined by a power polynomial, and a boundary function represented in the form of the desired function or its derivative at one of the boundary points is introduced. Different sequences of boundary equations have been set up with the use of differential operators. Systems of linear algebraic equations constructed on the basis of these sequences allow one to determine the coefficients of a power polynomial. Constitutive equations have been derived for initial boundary-value problems of all the main types. With these equations, an initial boundary-value problem is transformed into the Cauchy problem for the boundary function. The determination of the boundary function by its derivative with respect to the time coordinate completes the solution of the problem.

Depositional systems and stratigraphy of Paleozoic and Lower Mesozoic rocks in outcrop, Tassili region, southwest Algeria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hertig, S.P.; Tye, R.S.; Coffield, D.Q.

1991-08-01

Paleozoic to Lower Mesozoic strata of the southeastern Algerian Tassili are traditionally subdivided by regionally extensive unconformities such as the Pan African, Taconic, Caledonian, and Hercynian. Using outcrop data from southeastern Algeria, this classic approach is modified by reinterpreting the genesis of these unconformities and rock sequences. Five prominent sequences, defined within the Paleozoic and lower Mesozoic section, usually consist of a succession of lowstand, transgressive, and highstand system tracts separated by sequence boundaries or transgressive surfaces. The Pan-African, Taconic, Caledonian, and Hercynian unconformities are sequence boundaries. Important sequence boundaries also occur within the Ordovician and Silurian sections. These sequencesmore » correlate with subsurface data in the Illizi basin and provide a framework for renewed exploration in the subsurface of the Algerian Sahara, where more than 30 billion bbl of recoverable oil and oil equivalent have been generated and trapped.« less

Perceiving the writing sequence of Chinese characters: an ERP investigation.

PubMed

Qiu, Yinchen; Zhou, Xiaolin

2010-04-01

The neural dynamics in perceiving well-learned sequences and its modulation by task demand were investigated in this study in which participants were asked to observe stroke-by-stroke display of Chinese characters composed of two radicals while their brain activity was monitored with the event-related potential (ERP) technique. Experiment 1 used an accuracy judgment task that would draw participants' attention to the violation of the writing sequence whereas Experiment 2 required participants to judge the completion of the display and thus the more automatic aspects of sequence processing could be revealed. In Experiment 1, the within-radical boundary reversal produced bilateral posterior N2 enhancement and the cross-boundary reversal elicited a left N2 effect and right posterior N2 reduction on the critical stroke. Both types of reversal elicited P3 effects on the critical stroke and sustained negativity effects on the following stroke, with the size being larger for the cross-boundary reversal. In Experiment 2, in addition to the P3 effects, the within-boundary reversal elicited a left posterior N2 effect and the cross-boundary reversal elicited right posterior N2 reduction on the critical stroke. Moreover, on the following stroke, the cross-boundary reversal elicited a right N2 effect and both types of reversal elicited sustained positivity effects. These findings demonstrate that native Chinese readers use their sequential knowledge to predict upcoming strokes in perceiving the writing of characters and to construct appropriate representations for the action sequence regardless of whether such predictions and constructions are required by the task. Copyright 2009 Elsevier Inc. All rights reserved.

Stratigraphy and sedimentology of the K/T boundary deposit in Haiti

NASA Technical Reports Server (NTRS)

Carey, S.; Sigurdsson, H.; Dhondt, S.; Espindola, J. M.

1993-01-01

The K/T boundary sequence is exposed in uplifted carbonate sediments of the southwest peninsula of Haiti. It is found at 15 localities within the Beloc formation, a sequence of limestone and marls interpreted as a monoclinal nappe structure thrust to the north. This tectonic deformation has affected the K/T boundary deposit to varying degrees. In some cases the less competent K/T deposit has acted as a slip plane leading to extensive shearing of the boundary layer, as well as duplication of the section. The presence of glassy tektites, shocked quartz, and an Ir anomaly directly link the deposit to a bolide impact. Stratigraphic and sedimentological features of the tripartite sequence indicate that it was formed by deposition from ballistic fallout of coarse tektites, emplacement of particle gravity flows and fine grained fallout of widely dispersed impact ejecta.

Evolution of Modern Birds Revealed by Mitogenomics: Timing the Radiation and Origin of Major Orders

PubMed Central

Pacheco, M. Andreína; Battistuzzi, Fabia U.; Lentino, Miguel; Aguilar, Roberto F.; Kumar, Sudhir; Escalante, Ananias A.

2011-01-01

Mitochondrial (mt) genes and genomes are among the major sources of data for evolutionary studies in birds. This places mitogenomic studies in birds at the core of intense debates in avian evolutionary biology. Indeed, complete mt genomes are actively been used to unveil the phylogenetic relationships among major orders, whereas single genes (e.g., cytochrome c oxidase I [COX1]) are considered standard for species identification and defining species boundaries (DNA barcoding). In this investigation, we study the time of origin and evolutionary relationships among Neoaves orders using complete mt genomes. First, we were able to solve polytomies previously observed at the deep nodes of the Neoaves phylogeny by analyzing 80 mt genomes, including 17 new sequences reported in this investigation. As an example, we found evidence indicating that columbiforms and charadriforms are sister groups. Overall, our analyses indicate that by improving the taxonomic sampling, complete mt genomes can solve the evolutionary relationships among major bird groups. Second, we used our phylogenetic hypotheses to estimate the time of origin of major avian orders as a way to test if their diversification took place prior to the Cretaceous/Tertiary (K/T) boundary. Such timetrees were estimated using several molecular dating approaches and conservative calibration points. Whereas we found time estimates slightly younger than those reported by others, most of the major orders originated prior to the K/T boundary. Finally, we used our timetrees to estimate the rate of evolution of each mt gene. We found great variation on the mutation rates among mt genes and within different bird groups. COX1 was the gene with less variation among Neoaves orders and the one with the least amount of rate heterogeneity across lineages. Such findings support the choice of COX 1 among mt genes as target for developing DNA barcoding approaches in birds. PMID:21242529

No major stratigraphic gap exists near the Middle-Upper Pennsylvanian (Desmoinesian-Missourian) boundary in North America

USGS Publications Warehouse

Falcon-Lang, H. J.; Heckel, P.H.; DiMichele, W.A.; Blake, B.M.; Easterday, C.R.; Eble, C.F.; Elrick, S.; Gastaldo, Robert A.; Greb, S.F.; Martino, R.L.; John, Nelson W.; Pfefferkorn, H.W.; Phillips, T.L.; Rosscoe, S.J.

2011-01-01

Interregional correlation of the marine zones of major cyclothems between North America and eastern Europe does not support assertions that a major stratigraphic gap exists between the traditional regional Desmoinesian and Missourian stages in North America. Such a gap was previously proposed to explain an abrupt change in megafloral assemblages in the northern Appalachian Basin and by extension across all of North America. Conodont-based correlation from the essentially complete low-shelf Midcontinent succession (distal from the highstand shoreline), through the mid-shelf Illinois Basin, to the high shelf of the Appalachian Basin (proximal to highstand shoreline) demonstrates that all major ???400 kyr cyclothem groupings in the Midcontinent are recognizable in the Illinois Basin. In the Appalachian Basin, however, the grouping at the base of the Missourian is represented only by paleosols and localized coal. The immediately preceding grouping was removed very locally by paleovalley incision, as is evident at the 7-11 Mine, Columbiana County, Ohio, from which the original megafloral data were derived. At the few localities where incised paleodrainage exists, there may be a gap of ???1000 kyr, but a gap of no more than ???600 kyr occurs elsewhere in the Appalachian Basin at that level and its magnitude progressively decreases westward into the Illinois (???300 kyr) and Midcontinent (<200 kyr) Basins. Thus, while a gap is present near the Desmoinesian-Missourian boundary in North America, it is typically more than an order of magnitude smaller than that originally proposed and is similar to the gaps inferred at sequence boundaries between cyclothems at many horizons in the Pennsylvanian of North America. Copyright ?? 2011, SEPM.

Stratigraphic architecture and gamma ray logs of deeper ramp carbonates (Upper Jurassic, SW Germany)

NASA Astrophysics Data System (ADS)

Pawellek, T.; Aigner, T.

2003-07-01

The objective of this paper is to contribute to the development of sequence stratigraphic models for extensive epicontinental carbonate systems deposited over cratonic areas. Epicontinental carbonates of the SW German Upper Jurassic were analysed in terms of microfacies, sedimentology and sequence stratigraphy based on 2.5 km of core, 70 borehole gamma ray logs and 24 quarries. Facies analysis revealed six major facies belts across the deeper parts of the carbonate ramp, situated generally below fair-weather wave base, and mostly below average storm wave base but in the reach of occasional storm events. Observed stratigraphic patterns differ in some aspects from widely published sequence stratigraphic models: Elementary sedimentary cycles are mostly more or less symmetrical and are, thus, referred to as "genetic sequences" or "genetic units" [AAAPG Bull. 55 (1971) 1137; Frazier, D.E., 1974. Depositional episodes: their relationship to the Quaternary stratigraphic framework in the northwestern portion of the Gulf Basin. University of Texas, Austin, Bureau of Economic Geology Geologicalo Circular 71-1; AAPG Bull. 73 (1989) 125; Galloway, W.E., Hobday, D.K., 1996. Terrigenous Clastic Depositional Systems. 489 pp., Springer; Cross, T.A., Baker, M.R., Chapin, M.S., Clark, M.S., Gardner, M.H., Hanson, M.S., Lessenger, M.A., Little, L.D., McDonough, K.J., Sonnenfeld, M.D., Valasek, D.W., Williams, M.R., Witter, D.N., 1993. Applications of high-resolution sequence stratigraphy to reservoir analysis. Edition Technip 1993, 11-33; Bull. Cent. Rech. Explor. Prod. Elf-Aquitaine 16 (1992) 357; Homewood, P., Mauriaud, P., Lafont, F., 2000. Best practices in sequence stratigraphy. Elf EP Mem. 25, 81 pp.; Homewood, P., Eberli, G.P., 2000. Genetic stratigraphy on the exploration and production scales. Elf EP Mem. 24, 290 pp.], in contrast to the asymmetrical, shallowing-upward "parasequences" of the EXXON approach. Neither sequence boundaries nor maximum flooding surfaces could be clearly delineated. Cycle boundaries are generally not represented by sharp stratal surfaces but are always transitional and, thus, referred to as "turnarounds" [Nor. Pet. Soc. Spec. Publ. 8 (1998) 171]. Several types of genetic sequences were delineated. Both major types of facies and sequences show characteristic gamma ray log signatures. Based on the cycle stacking and the gamma ray patterns, a hierarchy of sequences was recognized, probably driven in part by 100,000- and 400,000-year Milankovitch signals. The cyclicity allowed regional correlations across various depositional environments such as sponge-microbial bioherms and coeval basins. The basin-wide correlation revealed evidence for a subtle clinoform-type stratigraphic architecture along very gentle slopes, rather than a so far assumed simple "layer cake" pattern.

Sequence stratigraphy of the Maastrichtian-Paleocene succession at the Dakhla Oasis, Western Desert, Egypt

NASA Astrophysics Data System (ADS)

Hewaidy, Abdel Galil A.; Farouk, Sherif; Bazeen, Youssef S.

2017-12-01

The Maastrichtian-Paleocene succession at the Dakhla Oasis is marked by the presence of a typical Nile Valley Facies represented by the Dakhla and Tarawan formations in Edmonstone and Qur El Malik sections in the central and western parts of the oasis, while a mixed Nile Valley and Garra Al-Arbain facies represented by Dakhla, Kurkur and Tarawan formations in Teneida section in the eastern part of the oasis adjacent to the Abu Tartur Plateau. These sections were examined for their foraminiferal contents, lithologic characters and stratigraphic boundaries. The distribution of foraminifera in the studied sections is variable and inconstant, as the planktonics are concentrated only at certain levels, which may be considered as a time intervals of transgression and maximum flooding surfaces. Eight planktonic biozones are distinguished in this work; of theses two are of Maastrichtain age and six are of Paleocene age. Eight 3rd order depositional sequences are recognized in the studied Maastrichtian-Paleocene succession based on the time stratigraphic boundaries released from the planktonic foraminifera and sea level changes which are released from the paleoecologic interpretations. The distinguished sequences are subdivided into their systems tracts based on the paleobathymetric interpretations of P/B% and benthic biofacies analysis. These sequences are bounded by eight sequence boundaries (SB A - SB H) represented by unconformity surfaces and depositional hiatuses. The correlation of the sequence boundaries of the established depositional sequences with the eustatic sea level curve, suggesting that these depositional sequences were resulted from the interplay of eustatic sea-level changes and local tectonic activities.

Cenozoic global sea level, sequences, and the New Jersey transect: Results from coastal plain and continental slope drilling

USGS Publications Warehouse

Miller, K.G.; Mountain, Gregory S.; Browning, J.V.; Kominz, M.; Sugarman, P.J.; Christie-Blick, N.; Katz, M.E.; Wright, J.D.

1998-01-01

The New Jersey Sea Level Transect was designed to evaluate the relationships among global sea level (eustatic) change, unconformity-bounded sequences, and variations in subsidence, sediment supply, and climate on a passive continental margin. By sampling and dating Cenozoic strata from coastal plain and continental slope locations, we show that sequence boundaries correlate (within ??0.5 myr) regionally (onshore-offshore) and interregionally (New Jersey-Alabama-Bahamas), implicating a global cause. Sequence boundaries correlate with ??18O increases for at least the past 42 myr, consistent with an ice volume (glacioeustatic) control, although a causal relationship is not required because of uncertainties in ages and correlations. Evidence for a causal connection is provided by preliminary Miocene data from slope Site 904 that directly link ??18O increases with sequence boundaries. We conclude that variation in the size of ice sheets has been a primary control on the formation of sequence boundaries since ~42 Ma. We speculate that prior to this, the growth and decay of small ice sheets caused small-amplitude sea level changes (<20 m) in this supposedly ice-free world because Eocene sequence boundaries also appear to correlate with minor ??18O increases. Subsidence estimates (backstripping) indicate amplitudes of short-term (million-year scale) lowerings that are consistent with estimates derived from ??18O studies (25-50 m in the Oligocene-middle Miocene and 10-20 m in the Eocene) and a long-term lowering of 150-200 m over the past 65 myr, consistent with estimates derived from volume changes on mid-ocean ridges. Although our results are consistent with the general number and timing of Paleocene to middle Miocene sequences published by workers at Exxon Production Research Company, our estimates of sea level amplitudes are substantially lower than theirs. Lithofacies patterns within sequences follow repetitive, predictable patterns: (1) coastal plain sequences consist of basal transgressive sands overlain by regressive highstand silts and quartz sands; and (2) although slope lithofacies variations are subdued, reworked sediments constitute lowstand deposits, causing the strongest, most extensive seismic reflections. Despite a primary eustatic control on sequence boundaries, New Jersey sequences were also influenced by changes in tectonics, sediment supply, and climate. During the early to middle Eocene, low siliciclastic and high pelagic input associated with warm climates resulted in widespread carbonate deposition and thin sequences. Late middle Eocene and earliest Oligocene cooling events curtailed carbonate deposition in the coastal plain and slope, respectively, resulting in a switch to siliciclastic sedimentation. In onshore areas, Oligocene sequences are thin owing to low siliciclastic and pelagic input, and their distribution is patchy, reflecting migration or progradation of depocenters; in contrast, Miocene onshore sequences are thicker, reflecting increased sediment supply, and they are more complete downdip owing to simple tectonics. We conclude that the New Jersey margin provides a natural laboratory for unraveling complex interactions of eustasy, tectonics, changes in sediment supply, and climate change.

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

USGS Publications Warehouse

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

1997-01-01

This Field Excursion will visit outcrops of the fluvial-deltaic Upper Cretaceous (Turonian) Ferron Sandstone Member of the Mancos Shale, known as the Last Chance delta or Upper Ferron Sandstone. This field guide and the field stops will outline the architecture and depositional sequence stratigraphy of the Upper Ferron Sandstone clastic wedge and explore the stratigraphic positions and compositions of major coal zones. The implications of the architecture and stratigraphy of the Ferron fluvial-deltaic complex for coal and coalbed methane resources will be discussed. Early works suggested that the southwesterly derived deltaic deposits of the the upper Ferron Sandstone clastic wedge were a Type-2 third-order depositional sequence, informally called the Ferron Sequence. These works suggested that the Ferron Sequence is separated by a type-2 sequence boundary from the underlying 3rd-order Hyatti Sequence, which has its sediment source from the northwest. Within the 3rd-order depositional sequence, the deltaic events of the Ferron clastic wedge, recognized as parasequence sets, appear to be stacked into progradational, aggradational, and retrogradational patterns reflecting a generally decreasing sediment supply during an overall slow sea-level rise. The architecture of both near-marine facies and non-marine fluvial facies exhibit well defined trends in response to this decrease in available sediment. Recent studies have concluded that, unless coincident with a depositional sequence boundary, regionally extensive coal zones occur at the tops of the parasequence sets within the Ferron clastic wedge. These coal zones consist of coal seams and their laterally equivalent fissile carbonaceous shales, mudstones, and siltstones, paleosols, and flood plain mudstones. Although the compositions of coal zones vary along depositional dip, the presence of these laterally extensive stratigraphic horizons, above parasequence sets, provides a means of correlating and defining the tops of depositional parasequence sets in both near-marine and non-marine parts of fluvial-deltaic depositional sequences. Ongoing field studies, based on this concept of coal zone stratigraphy, and detailed stratigraphic mapping, have documented the existence of at least 12 parasequence sets within the Last Chance delta clastic wedge. These parasequence sets appear to form four high frequency, 4th-order depositional sequences. The dramatic erosional unconformities, associated with these 4th-order sequence boundaries, indicate that there was up to 20-30 m of erosion, signifying locally substantial base-level drops. These base-level drops were accompanied by a basin ward shift in paleo-shorelines by as much as 5-7 km. These 4th-order Upper Ferron Sequences are superimposed on the 3rd-order sea-level rise event and the 3rd-order, sediment supply/accommodation space driven, stratigraphie architecture of the Upper Ferron Sandstone. The fluvial deltaic architecture shows little response to these 4th-order sea-level events. Coal zones generally thicken landward relative to the mean position of the landward pinch-out of the underlying parasequence set, but after some distance landward, they decrease in thickness. Coal zones also generally thin seaward relative to the mean position of the landward pinch-out of the underlying parasequence set. The coal is thickest in the region between this landward pinch-out and the position of maximum zone thickness. Data indicate that the proportion of coal in the coal zone decreases progressively landward from the landward pinch-out. The effects of differential compaction and differences in original pre-peat swamp topography have the effect of adding perturbations to the general trends. These coal zone systematics have major impact on approaches to exploration and production, and the resource accessment of both coal and coalbed methane.

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

NASA Astrophysics Data System (ADS)

Yoshida, S.

2000-11-01

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

MHz-Rate NO PLIF Imaging in a Mach 10 Hypersonic Wind Tunnel

NASA Technical Reports Server (NTRS)

Jiang, N.; Webster, M.; Lempert, Walter R.; Miller, J. D.; Meyer, T. R.; Danehy, Paul M.

2010-01-01

NO PLIF imaging at repetition rates as high as 1 MHz is demonstrated in the NASA Langley 31 inch Mach 10 hypersonic wind tunnel. Approximately two hundred time correlated image sequences, of between ten and twenty individual frames, were obtained over eight days of wind tunnel testing spanning two entries in March and September of 2009. The majority of the image sequences were obtained from the boundary layer of a 20 flat plate model, in which transition was induced using a variety of cylindrical and triangular shaped protuberances. The high speed image sequences captured a variety of laminar and transitional flow phenomena, ranging from mostly laminar flow, typically at lower Reynolds number and/or in the near wall region of the model, to highly transitional flow in which the temporal evolution and progression of characteristic streak instabilities and/or corkscrew-shaped vortices could be clearly identified. A series of image sequences were also obtained from a 20 compression ramp at a 10 angle of attack in which the temporal dynamics of the characteristic separated flow was captured in a time correlated manner.

Provenance and sequence architecture of the Middle-Late Eocene Gehannam and Birket Qarun formations at Wadi Al Hitan, Fayum Province, Egypt

NASA Astrophysics Data System (ADS)

Anan, Tarek; El Shahat, Adam

2014-12-01

The Middle-Upper Eocene Gehannam and Birket Qarun formations at Wadi Al Hitan (Valley of Whales) in Fayum Province of Egypt are dominated by marine siliciclastic sediments. Sedimentation took place in synclinal basins that were inherited from the Late Cretaceous tectonism. The siliciclastic sediments accumulated in low energy open shallow marine shelf. Most of the siliciclastics are heavily bioturbated by Thalassinoides. The abundance of unstable and moderately stable heavy minerals suggests that the Middle-Upper Eocene clastics were largely derived from the weathered regolith of the exhumed basement rocks of the Red Sea mountains. The ultrastable heavies were mainly recycled from positive landmass that bound the Eocene basins. Two sequence boundaries were observed in the studied succession. The first boundary lies within a rhizolith bearing-sandstone unit that occurs at the boundary between the Gehannam and Birket Qarun formations. The second sequence boundary occurs within the upper part of the Birket Qarun Formation, in a shale horizon bioturbated by Thalassinoides. Three 3rd order depositional sequences were recognized. These sequences may be formed due to tectonic activity that started in the Late Cretaceous and may be rejuvenated again during the Eocene time. Also emergence activities that were active during the Eocene led to the formation of the picked sequences by changing relative sea level. The recorded systems tracts are transgressive systems tract (TST), highstand systems tract (HST), and falling-stage systems tract (FSST).

The terminal Permian in European Russia: Vyaznikovian Horizon, Nedubrovo Member, and Permian-Triassic boundary

NASA Astrophysics Data System (ADS)

Lozovsky, V. R.; Balabanov, Yu. P.; Karasev, E. V.; Novikov, I. V.; Ponomarenko, A. G.; Yaroshenko, O. P.

2016-07-01

The comprehensive analysis of the data obtained on terrestrial vertebrata, ostracods, entomologic fauna, megaflora, and microflora in deposits of the Vyaznikovian Horizon and Nedubrovo Member, as well as the paleomagnetic data measured in enclosing rocks, confirms heterogeneity of these deposits. Accordingly, it is necessary to distinguish these two stratons in the terminal Permian of the East European Platform. The combined sequence of Triassic-Permian boundary deposits in the Moscow Syneclise, which is considered to be the most complete sequence in the East European Platform, is as follows (from bottom upward): Vyatkian deposits; Vyaznikovian Horizon, including Sokovka and Zhukovo members; Nedubrovo Member (Upper Permian); Astashikha and Ryabi members of the Vokhmian Horizon (Lower Triassic). None of the sequences of Permian-Triassic boundary deposits known in the area of study characterizes this sequence in full volume. In the north, the Triassic deposits are underlain by the Nedubrovo Member; in the south (the Klyazma River basin), the sections are underlain by the Vyaznikovian Horizon. The Permian-Triassic boundary adopted in the General Stratigraphic Scale of Russia for continental deposits of the East European platform (the lower boundary of the Astashikha Member) is more ancient than the one adopted in the International Stratigraphic Chart. The same geological situation is observed in the German Basin and other localities where Triassic continental deposits are developed. The ways of solving this problem are discussed in this article.

Overview of the Kinematics of the Salton Trough and Northern Gulf of California

NASA Astrophysics Data System (ADS)

Stock, J. M.

2016-12-01

In the Salton Trough and Northern Gulf of California, transtensional rifting is leading to full continental plate breakup, as a major continental block is being transferred to an oceanic plate. Since at least 6 Ma this region has taken up most of the plate boundary slip between the Pacific and North America plates at this latitude. We review the structural history of plate separation, as constrained by many recent studies of present and past fault configurations, seismicity, and basin development as seen from geology and geophysics. Modern activity in the USA is dominated by NW-striking strike-slip faults (San Andreas, San Jacinto, Elsinore), and subsidiary NE-striking faults. There is an equally broad zone in Mexico (faults from the Mexicali Valley to the Colorado River Delta and bounding the Laguna Salada basin), including active low-angle detachment faults. In both areas, shifts in fault activity are indicated by buried faults and exhumed or buried earlier basin strata. Seismicity defines 3 basin segments in the N Gulf: Consag-Wagner, Upper Delfin, and Lower Delfin, but localization is incomplete. These basins occupy a broad zone of modern deformation, lacking single transform faults, although major strike-slip faults formed in the surrounding continental area. The off-boundary deformation on the western side of the plate boundary has changed with time, as seen by Holocene and Quaternary faults controlling modern basins in the Gulf Extensional Province of NE Baja California, and stranded Pliocene continental and marine basin strata in subaerial fault blocks. The eastern side of the plate boundary, in the shallow northeastern Gulf, contains major NW-striking faults that may have dominated the earlier (latest Miocene-early Pliocene) kinematics. The Sonoran coastal plain likely buries additional older faults and basin sequences; further studies here are needed to refine models of the earlier structural development of this sector. Despite > 250 km of plate separation, and production of new crustal area in these segments of the plate boundary, the deformation is not considered to be fully localized because some occurs outside the region of new crustal formation. Similar scenarios may need to be considered when evaluating continent-ocean transitions in other rift systems.

Phylogenetic diversity of Flavobacteria isolated from the North Sea on solid media.

PubMed

Hahnke, Richard L; Harder, Jens

2013-10-01

Flavobacteria are abundant in the North Sea, an epeiric sea on the continental shelf of Europe. However, this abundance has so far not been reflected by the number of strains in culture collections. In this study, Flavobacteria were isolated from pelagic and benthic samples, such as seawater, phytoplankton, sediment and its porewater, and from surfaces of animals and seaweeds on agar plates with a variety of carbon sources. Dilution cultivation with a new medium, incubation at low temperatures and with long incubation times, and colony screening by a Flavobacteria-Cytophagia-specific PCR detecting 16S rRNA gene sequences led to a collection of phylogenetically diverse strains. Two strains affiliated with Flammeovirgaceae and seven strains affiliated with Cyclobacteriaceae, whereas within the Flavobacteriaceae 20 isolated strains presumably represented seven novel candidate genera and 355 strains affiliated with 26 of 80 validly described marine Flavobacteriaceae genera, based on a genus boundary of 95.0% 16S rRNA gene sequence identity. The majority of strains (276) affiliated with 37 known species in 16 genera (based on a boundary of 98.7% 16S rRNA gene sequence identity), whereas 79 strains likely represented 42 novel species in 22 established Flavobacteriaceae genera. Pigmentation, iridescence, gliding motility, agar lysis, and flexirubin as a chemical marker supported the taxonomy at the species level. This study demonstrated the culturability on solid medium of phylogenetically diverse Flavobacteria originating from the North Sea. Copyright © 2013 Elsevier GmbH. All rights reserved.

The geological history of Northeast Syrtis Major, Mars

NASA Astrophysics Data System (ADS)

Bramble, Michael S.; Mustard, John F.; Salvatore, Mark R.

2017-09-01

As inferred from orbital spectroscopic data, Northeast Syrtis Major bears considerable mineral diversity that spans the Noachian-Hesperian boundary despite its small geographic area. In this study we use observations from the High Resolution Imaging Science Experiment, supplemented with Context Camera imagery, to characterize and map the lateral extent of geomorphic units in Northeast Syrtis Major, and constrain the geomorphic context of the orbital-identified mineral signatures. Using recent observations, we confirm previous mineralogy identified with the Compact Reconnaissance Imaging Spectrometer for Mars, and greatly extend the lateral extent of visible to near-infrared investigation utilizing the greater coverage. Analysis of Thermal Emission Imaging System observations reveals further physical properties and distribution of the geomorphic units. The stratigraphy, which spans the Noachian-Hesperian boundary, displays significant morphological heterogeneity at the decameter scale, but it is unifiable under five distinct geomorphic units. Our paired morphological and mineralogical analysis allows us to construct a detailed geological history of Northeast Syrtis Major. Several geological events that occurred in Northeast Syrtis Major-including the formation of the post-Isidis crust, the emplacement of an olivine-rich unit, the formation of sulfate minerals, and the emplacement of the Syrtis Major Volcanics-can be related to regional and global processes constraining the local chronology. Other mineralogical indicators, particularly the formation of Al-phyllosilicates, are difficult to place in the temporal sequence. They are observed in isolated patches on the post-Isidis crust, not as a distinct stratigraphic unit as observed elsewhere in Nili Fossae, suggesting their formation via isolated leaching or through alteration of initial compositional heterogeneities within the crust. Exposures of an olivine-rich unit are intermittently observed to form quasi-circular landforms, suggestive of emplacement in circular depressions, which may indicate a period of cratering between the formation of the Isidis basin and the deposition of the olivine-rich unit. We identify and discuss intriguing large linear features of the olivine-rich unit, reminiscent of dyke-fed volcanism, that have raised bounding ridges suggestive of contact metamorphism with the crust. We compile, review, and discuss many of the outstanding questions and running hypotheses relevant to our mapping area. A synthesis of our geomorphic mapping with recent literature reveals a well-defined geological history with extensive aqueous activity at Northeast Syrtis Major that is amassed in a stratigraphic sequence spanning a time likely greater than 250 million years of geological history. Our geomorphic and spectral analyses confirm that Northeast Syrtis Major exhibits considerable geomorphic and mineralogic diversity within a relatively small geographic area that is representative of the geologic processes occurring throughout the broader Nili Fossae region during the Noachian and Hesperian. Northeast Syrtis Major adds to this sequence by exposing the diverse environmental history of this region as observed through the presence of alteration minerals not present in this fidelity or proximity elsewhere in Nili Fossae.

Intrinsic sequence specificity of the Cas1 integrase directs new spacer acquisition

PubMed Central

Rollie, Clare; Schneider, Stefanie; Brinkmann, Anna Sophie; Bolt, Edward L; White, Malcolm F

2015-01-01

The adaptive prokaryotic immune system CRISPR-Cas provides RNA-mediated protection from invading genetic elements. The fundamental basis of the system is the ability to capture small pieces of foreign DNA for incorporation into the genome at the CRISPR locus, a process known as Adaptation, which is dependent on the Cas1 and Cas2 proteins. We demonstrate that Cas1 catalyses an efficient trans-esterification reaction on branched DNA substrates, which represents the reverse- or disintegration reaction. Cas1 from both Escherichia coli and Sulfolobus solfataricus display sequence specific activity, with a clear preference for the nucleotides flanking the integration site at the leader-repeat 1 boundary of the CRISPR locus. Cas2 is not required for this activity and does not influence the specificity. This suggests that the inherent sequence specificity of Cas1 is a major determinant of the adaptation process. DOI: http://dx.doi.org/10.7554/eLife.08716.001 PMID:26284603

Computer constructed imagery of distant plasma interaction boundaries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grenstadt, E.W.; Schurr, H.D.; Tsugawa, R.K.

1982-01-01

Computer constructed sketches of plasma boundaries arising from the interaction between the solar wind and the magnetosphere can serve as both didactic and research tools. In particular, the structure of the earth's bow shock can be represented as a nonuniform surfce according to the instantaneous orientation of the IMF, and temporal changes in structural distribution can be modeled as a sequence of sketches based on observed sequences of spacecraft-based measurements. Viewed rapidly, such a sequence of sketches can be the basis for representation of plasma processes by computer animation.

Stratigraphy and conodont biostratigraphy of the uppermost Carboniferous and Lower Permian from the North American Midcontinent

USGS Publications Warehouse

Boardman, Darwin R.; Wardlaw, Bruce R.; Nestell, Merlynd K.

2009-01-01

Part A The uppermost Wabaunsee, Admire, Council Grove, and lower Chase Groups of Kansas, Oklahoma, and Nebraska are placed into three third-order depositional sequences: a Gzhelian late-highstand sequence set, a Council Grove transgressive and highstand sequence set, and a Chase transgressive sequence set. Sequences are defined by bounding maximum-exposure surfaces and are placed within the zone of exposure surfaces (typically, stacked paleosols). Conodonts are abundant in open-marine deposits and most marine units have a differing and characteristic faunal make-up. Eleven species are described as new: Streptognathodus binodosus, S. denticulatus, S. elongianus, S. florensis, S. lineatus, S. nevaensis, S. postconstrictus, S. postelongatus, S. robustus, S. translinearis, and S. trimilus. Part B Maximum-marine flooding levels and marine-condensed sections from uppermost Carboniferous and Lower Permian fourth-order (0.1-1 m.y.) depositional sequences of the North American midcontinent reveal a rich stratigraphic succession of species of Streptognathodus and Sweetognathus conodonts that permits high-precision correlation of the Carboniferous-Permian boundary as well as the Asselian-Sakmarian and Sakmarian-Artinskian boundaries. Eleven new species of Streptognathodus are described: Streptognathodus binodosus, S. denticulatus, S. elongianus, S. florensis, S. lineatus, S. nevaensis, S. postconstrictus, S. postelongatus, S. robustus, S. translinearis, and S. trimilus. Seventeen species are redescribed and clarified and include Streptognathodus alius, S. barskovi, S. bellus, S. brownvillensis, S. conjunctus, S. constrictus, S. elongatus, S. farmeri, S. flexuosus, S. fuchengensis, S. fusus, S. invaginatus, S. isolatus, S. longissimus, S. minacutus, S. nodulinearis, and S. wabaunsensis. The correlated level of the Carboniferous-Permian boundary is recognized in the lower part of the Red Eagle Depositional Sequence based on the introduction of Streptognathodus isolatus Chernykh, Ritter, and Wardlaw; Streptognathodus minacutus Barskov and Reimers; Streptognathodus invaginatus Reshetkova and Chernykh; Streptognathodus fuchengensis Zhao; and Streptognathodus nodulinearis Reshetkova and Chernykh. The correlated Carboniferous-Permian boundary occurs in the depositional sequence that represents the maximum-marine highstand of the Council Grove Composite Third Order Sequence. This level represents a significant marine-flooding event that should be correlatable in numerous shelfal sections throughout the world. Although the Asselian-Sakmarian boundary has not been rigorously defined, Sweetognathus merrilli has been informally utilized as a Sakmarian indicator. Due to the ecologically controlled distribution of species of Sweetognathus, we prefer to use a species of Streptognathodus as a defining species. We propose that Streptognathodus barskovi (Kozur) Reshetkova be considered as a potentially defining or ancillary defining species for the Sakmarian Stage. In the North American midcontinent, Streptognathodus barskovi appears in the same depositional sequence with Sweetognathus merrilli in the Eiss (Lower Bader) Depositional Sequence. Historically, Sweetognathus whitei has been used to mark the Sakmarian-Artinskian boundary. In our succession Sweetognathus whitei and Streptognathodus florensis appear in the basal part of the Barneston Depositional Sequence. We suggest that Streptognathodus florensis be further investigated as a possible defining or ancillary defining taxon for the base of the Artinskian Stage. This depositional sequence also forms the maximum-marine highstand of the Chase Third-Order Composite Depositional Sequence suggesting that this level is a significant marine-flooding event that should be widely traceable in numerous shelfal sections.

Periodic sequence of stabilized wave segments in an excitable medium

NASA Astrophysics Data System (ADS)

Zykov, V. S.; Bodenschatz, E.

2018-03-01

Numerical computations show that a stabilization of a periodic sequence of wave segments propagating through an excitable medium is possible only in a restricted domain within the parameter space. By application of a free-boundary approach, we demonstrate that at the boundary of this domain the parameter H introduced in our Rapid Communication is constant. We show also that the discovered parameter predetermines the propagation velocity and the shape of the wave segments. The predictions of the free-boundary approach are in good quantitative agreement with results from numerical reaction-diffusion simulations performed on the modified FitzHugh-Nagumo model.

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

USGS Publications Warehouse

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

2001-01-01

A high-resolution chronostratigraphy has been developed for Miocene shallow-water carbonate strata in the Cabo de Gata region of SE Spain for evaluation of local, regional and global factors that controlled platform architecture prior to and during the Messinian salinity crisis. Paleomagnetic data were collected from strata at three localities. Mean natural remanent magnetization (NRM) ranges between 1.53 ?? 10-8 and 5.2 ?? 10-3 Am2/kg. Incremental thermal and alternating field demagnetization isolated the characteristic remanent magnetization (ChRM). Rock magnetic studies show that the dominant magnetic mineral is magnetite, but mixtures of magnetite and hematite occur. A composite chronostratigraphy was derived from five stratigraphic sections. Regional stratigraphic data, biostratigraphic data, and an 40Ar/39Ar date of 8.5 ?? 0.1 Ma, for an interbedded volcanic flow, place the strata in geomagnetic polarity Chrons C4r to C3r. Sequence-stratigraphic and diagenetic evidence indicate a major unconformity at the base of depositional sequence (DS)3 that contains a prograding reef complex, suggesting that approximately 250 000 yr of record (Subchrons C3Br.2r to 3Br.1r) are missing near the Messinian-Tortonian boundary. Correlation to the GPTS shows that the studied strata represent five third- to fourth-order DSs. Basal units are temperate to subtropical ramps (DS1A, DS1B, DS2); these are overlain by subtropical to tropical reefal platforms (DS3), which are capped by subtropical to tropical cyclic carbonates (Terminal Carbonate Complex, TCC). Correlation of the Cabo de Gata record to the Melilla area of Morocco, and the Sorbas basin of Spain indicate that early - Late Tortonian ramp strata from these areas are partially time-equivalent. Similar strata are extensively developed in the Western Mediterranean and likely were influenced by a cool climate or influx of nutrients during an overall rise in global sea-level. After ramp deposition, a sequence boundary (SB3) in Cabo de Gata correlates with a sequence boundary in Morocco and a published third-order eustatic fall suggesting at least a partial eustatic control for the sequence boundary. Coral reefs began to develop earlier in Cabo de Gata than at Melilla or Sorbas, arguing for local factors affecting this major environmental transition. Later Messinian reefs (DS3) from all areas are time-equivalent, suggesting a regional or global control on their formation. Some Halimeda-rich horizons in the Western Mediterranean are not time-equivalent event strata as hypothesized by others. Correlation of the relative sea-level curve for the fringing reef complex (DS3) with a published eustatic curve suggests at least a partial third-order global eustatic control for the highstand part of the sequence. Downstepping DS3 reefs and initial subaerial exposure of earlier DS3 reef strata approximately correlate with initiation of a series of subaerial unconformities in the South Pacific. The longer-term relative fall in sea-level during DS3 downstepping reef progradation does not correlate with a published third-order eustatic fall. Eustatic sea-level fluctuations may have been associated with initiation of the Mediterranean Messinian salinity crisis, but the longer-term fall may have been linked to tectonic uplift in the Mediterranean region. Widespread distribution of 'TCC-style' cycles of approximately the same age suggests a regional (Western Mediterranean) or global control on sea-level change responsible for TCC cycles. In addition, four subaerial exposure-capped TCC cycles may correlate with similar subaerial unconformities in the South Pacific, suggesting at least a partial eustatic control on TCC cyclicity. The high rates of relative sea-level change needed to generate a minimum of 25-30 m sea-level changes associated with each cycle are consistent with glacio-eustacy along with rapid evaporitic drawdown in the Mediterranean. ?? 2001 Elsevier Science B.V. All rights reserved.

Watershed boundaries and geographic isolation: patterns of diversification in cutthroat trout from western North America.

PubMed

Loxterman, Janet L; Keeley, Ernest R

2012-03-19

For wide-ranging species, intraspecific variation can occur as a result of reproductive isolation from local adaptive differences or from physical barriers to movement. Cutthroat trout (Oncorhynchus clarkii), a widely distributed fish species from North America, has been divided into numerous putative subspecies largely based on its isolation in different watersheds. In this study, we examined mtDNA sequence variation of cutthroat trout to determine the major phylogenetic lineages of this polytypic species. We use these data as a means of testing whether geographic isolation by watershed boundaries can be a primary factor organizing intraspecific diversification. We collected cutthroat trout from locations spanning almost the entire geographic range of this species and included samples from all major subspecies of cutthroat trout. Based on our analyses, we reveal eight major lineages of cutthroat trout, six of which correspond to subspecific taxonomy commonly used to describe intraspecific variation in this species. The Bonneville cutthroat trout (O. c. utah) and Yellowstone cutthroat trout (O. c. bouvieri) did not form separate monophyletic lineages, but instead formed an intermixed clade. We also document the geographic distribution of a Great Basin lineage of cutthroat trout; a group typically defined as Bonneville cutthroat trout, but it appears more closely related to the Colorado River lineage of cutthroat trout. Our study indicates that watershed boundaries can be an organizing factor isolating genetic diversity in fishes; however, historical connections between watersheds can also influence the template of isolation. Widely distributed species, like cutthroat trout, offer an opportunity to assess where historic watershed connections may have existed, and help explain the current distribution of biological diversity across a landscape.

Watershed boundaries and geographic isolation: patterns of diversification in cutthroat trout from western North America

PubMed Central

2012-01-01

Background For wide-ranging species, intraspecific variation can occur as a result of reproductive isolation from local adaptive differences or from physical barriers to movement. Cutthroat trout (Oncorhynchus clarkii), a widely distributed fish species from North America, has been divided into numerous putative subspecies largely based on its isolation in different watersheds. In this study, we examined mtDNA sequence variation of cutthroat trout to determine the major phylogenetic lineages of this polytypic species. We use these data as a means of testing whether geographic isolation by watershed boundaries can be a primary factor organizing intraspecific diversification. Results We collected cutthroat trout from locations spanning almost the entire geographic range of this species and included samples from all major subspecies of cutthroat trout. Based on our analyses, we reveal eight major lineages of cutthroat trout, six of which correspond to subspecific taxonomy commonly used to describe intraspecific variation in this species. The Bonneville cutthroat trout (O. c. utah) and Yellowstone cutthroat trout (O. c. bouvieri) did not form separate monophyletic lineages, but instead formed an intermixed clade. We also document the geographic distribution of a Great Basin lineage of cutthroat trout; a group typically defined as Bonneville cutthroat trout, but it appears more closely related to the Colorado River lineage of cutthroat trout. Conclusion Our study indicates that watershed boundaries can be an organizing factor isolating genetic diversity in fishes; however, historical connections between watersheds can also influence the template of isolation. Widely distributed species, like cutthroat trout, offer an opportunity to assess where historic watershed connections may have existed, and help explain the current distribution of biological diversity across a landscape. PMID:22429757

Cambro-ordovician sea-level fluctuations and sequence boundaries: The missing record and the evolution of new taxa

USGS Publications Warehouse

Lehnert, O.; Miller, J.F.; Leslie, Stephen A.; Repetski, J.E.; Ethington, Raymond L.

2005-01-01

The evolution of early Palaeozoic conodont faunas shows a clear connection to sea-level changes. One way that this connection manifests itself is that thick successions of carbonates are missing beneath major sequence boundaries due to karstification and erosion. From this observation arises the question of how many taxa have been lost from different conodont lineages in these incomplete successions. Although many taxa suffered extinction due to the environmental stresses associated with falling sea-levels, some must have survived in these extreme conditions. The number of taxa missing in the early Palaeozoic tropics always will be unclear, but it will be even more difficult to evaluate the missing record in detrital successions of higher latitudes. A common pattern in the evolution of Cambrian-Ordovician conodont lineages is appearances of new species at sea-level rises and disappearances at sea-level drops. This simple picture can be complicated by intervals that consistently have no representatives of a particular lineage, even after extensive sampling of the most complete sections. Presumably the lineages survived in undocumented refugia. In this paper, we give examples of evolution in Cambrian-Ordovician shallowmarine conodont faunas and highlight problems of undiscovered or truly missing segments of lineages. ?? The Palaeontological Association.

Divisions of geologic time-major chronostratigraphic and geochronologic units

USGS Publications Warehouse

,

2010-01-01

Effective communication in the geosciences requires consistent uses of stratigraphic nomenclature, especially divisions of geologic time. A geologic time scale is composed of standard stratigraphic divisions based on rock sequences and is calibrated in years. Over the years, the development of new dating methods and the refinement of previous methods have stimulated revisions to geologic time scales. Advances in stratigraphy and geochronology require that any time scale be periodically updated. Therefore, Divisions of Geologic Time, which shows the major chronostratigraphic (position) and geochronologic (time) units, is intended to be a dynamic resource that will be modified to include accepted changes of unit names and boundary age estimates. This fact sheet is a modification of USGS Fact Sheet 2007-3015 by the U.S. Geological Survey Geologic Names Committee.

Proterozoic crustal boundary in the southern part of the Illinois Basin

USGS Publications Warehouse

Heigold, P.C.; Kolata, Dennis R.

1993-01-01

Recently acquired COCORP and proprietary seismic reflection data in the southern part of the Illinois Basin, combined with other geological and geophysical data, indicate that a WNW-trending Proterozoic terrane boundary (40 km wide) lies within basement. The boundary is characterized by the termination of subhorizontal Proterozoic reflectors and associated diffraction patterns along a line coinciding with the major magnetic lineament in this region (South Central Magnetic Lineament). North of the boundary, where reflectors thought to represent a sequence of layered Proterozoic rocks in the upper crust are widespread and as much as 11 km thick, total magnetic intensity values are relatively high, suggesting layers of rock with high magnetic susceptibility. To the south, the Proterozoic rocks are acoustically transparent on seismic reflection sections and total magnetic intensity values are relatively low. Moreover, relatively high Bouguer gravity anomaly values to the south may be caused by a dense, altered, lower crustal layer similar to that interpreted from deep seismic refraction studies to underlie the northern Mississippi Embayment. The boundary lies along the projected trend of the northern margin of the Early Proterozoic Central Plains orogen and we suggest that it marks the convergent margin of this orogen. Reactivation of the boundary and the associated zone of weakness during late Paleozoic times apparently resulted in structural deformation in the southern part of the Illinois Basin, including movement along the Cottage Grove Fault System and Ste. Genevieve Fault Zone and igneous activity at Hicks Dome. In addition to the role played by this crustal boundary in the evolution of the Illinois Basin, its location between the Wabash Valley Seismic Zone to the northeast and the New Madrid Seismic Zone to the southwest may be a significant factor in present-day seismicity. ?? 1993.

Terrestrial ecosystem collapse associated to the K-Pg boundary and dinosaur extinction: palynological evidences

NASA Astrophysics Data System (ADS)

Bercovici, A.; Vajda, V.; Lyson, T. R.; Chester, S. G. B.; Sargis, E. J.; Pearson, D. A.; Joyce, W. G.

2012-04-01

We report here the discovery of the stratigraphically youngest in situ dinosaur specimen. This ceratopsian brow horn was found in southeastern Montana, in the Western Interior of the United States in a poorly rooted, silty mudstone floodplain deposit and only 13 centimeters below the palynologically defined K-Pg boundary. The boundary is identified using three criteria: 1) substantial decrease in diversity and abundance of Cretaceous pollen and spore taxa that completely disappear from the palynological record a few meters above the boundary, 2) the presence of a "fern spike", and 3) palynostratigraphical correlation to a nearby section where primary extraterrestrial impact markers are present (e.g., iridium anomaly, spherules and shocked quartz). The palynological record in the rock sequence immediately following the K-Pg boundary consistently indicates a sudden and major loss of the Cretaceous components across the North American record. During this rapid decline, the palynological assemblages are dominated by freshwater ferns (Azolla) and algae (usually Pediastrum sp. and Penetetrapites sp.) indicating generalized flooding in the area. The onset of the Paleocene sedimentation is subsequently announced by the presence of variegated beds, multiple lignite seams and small scale meandering river systems, starting with palynological associations that attest for reworking and erosion. The destabilization of terrestrial ecosystems is coincident with the markers of the K-Pg boundary, supporting a catastrophic event taking place over a very short duration. The in situ ceratopsian brow horn demonstrates that a gap devoid of non-avian dinosaur fossils in the last meters of the Cretaceous is artificial and thus inconsistent with the hypothesis that non-avian dinosaurs were extinct prior to the K-Pg boundary asteroid impact event.

Depositional framework and sequence stratigraphic aspects of the Coniacian Santonian mixed siliciclastic/carbonate Matulla sediments in Nezzazat and Ekma blocks, Gulf of Suez, Egypt

NASA Astrophysics Data System (ADS)

El-Azabi, M. H.; El-Araby, A.

2007-04-01

Superb outcrops of mixed siliciclastic/carbonate rocks mark the Coniacian-Santonian Matulla Formation exposed in Nezzazat and Ekma blocks, west central Sinai. They are built up of various lithofacies that reflect minor fluctuations in relative sea-level from lower intertidal to slightly deep subtidal settings. Relying on the facies characteristics and stratal geometries, the siliciclastic rocks are divided into seven depositional facies, including beach foreshore laminated sands, upper shoreface cross-bedded sandstone, lower shoreface massive bioturbated and wave-rippled sandstones, shallow subtidal siltstone and deep subtidal shale/claystone. The carbonate rocks comprise lower intertidal lime-mudstone, floatstone and dolostone, shallow subtidal skeletal shoal of oyster rudstone/bioclastic grainstone, and shoal margin packstone. Oolitic grain-ironstone and ferribands are partially intervened the facies types. Deposition has taken place under varied conditions of restricted, partly open marine circulation, low to high wave energy and normal to raised salinity during alternating periods of abundant and ceased clastic supply. The facies types are arranged into asymmetric upward-shallowing cycles that record multiple small-scale transgressive-regressive events. Lime-mudstone and sandstone normally terminate the regressive events. Four sequence boundaries marking regional relative sea-level falls divide the Matulla Formation into three stratigraphic units. These boundaries are Turonian/Coniacian, intra-Coniacian, Coniacian/Santonian and Santonian/Campanian. They do not fit with those sequence boundaries proposed in Haq et al.'s global eustatic curves (1988) except for the sea-level fall associated with the intra-Coniacian boundary. Other sequence boundaries have resulted from regional tectonic impact of the Syrian Arc Fold System that has been initiated in north Egypt during the Latest Turonian-Coniacian. These boundaries enclose three well-defined 3rd order depositional sequences; their enclosing shallowing-upward cycles (i.e. parasequences) record the 4th order relative sea-level fluctuations. 34 and 20 parasequence sets, in the order of a few meters to tens of meters thick, mark the Matulla sequences in Nezzazat and Ekma blocks respectively. Each sequence shows an initial phase of rapid sea-level rise with retrogradational sets, followed by lowering sea-level and progradation/aggradation of the parasequence sets. The transgressive deposits display predominance of deep subtidal lagoonal facies, while highstand deposits show an increase in siliciclastic and carbonate facies with the progressive decrease of lagoonal facies. The sedimentary patterns and environments suggest that the regional, partly eustatic sea-level (i.e. intra-Coniacian) changes controlled the overall architecture of the sequence distribution, whereas changes in the clastic input controlled the variations in facies associations within each depositional sequence.

Sequence stratigraphy of the Lower Cenomanian Bahariya Formation, Bahariya Oasis, Western Desert, Egypt

NASA Astrophysics Data System (ADS)

Catuneanu, O.; Khalifa, M. A.; Wanas, H. A.

2006-08-01

The Lower Cenomanian Bahariya Formation corresponds to a second-order depositional sequence that formed within a continental shelf setting under relatively low-rate conditions of positive accommodation (< 200 m during 3-6 My). This overall trend of base-level rise was interrupted by three episodes of base-level fall that resulted in the formation of third-order sequence boundaries. These boundaries are represented by subaerial unconformities (replaced or not by younger transgressive wave ravinement surfaces), and subdivide the Bahariya Formation into four third-order depositional sequences. The construction of the sequence stratigraphic framework of the Bahariya Formation is based on the lateral and vertical changes between shelf, subtidal, coastal and fluvial facies, as well as on the nature of contacts that separate them. The internal (third-order) sequence boundaries are associated with incised valleys, which explain (1) significant lateral changes in the thickness of incised valley fill deposits, (2) the absence of third-order highstand and even transgressive systems tracts in particular areas, and (3) the abrupt facies shifts that may occur laterally over relatively short distances. Within each sequence, the concepts of lowstand, transgressive and highstand systems tracts are used to explain the observed lateral and vertical facies variability. This case study demonstrates the usefulness of sequence stratigraphic analysis in understanding the architecture and stacking patterns of the preserved rock record, and helps to identify 13 stages in the history of base-level changes that marked the evolution of the Bahariya Oasis region during the Early Cenomanian.

Structure of A-C Type Intervariant Interface in Nonmodulated Martensite in a Ni-Mn-Ga Alloy.

PubMed

Ouyang, S; Yang, Y Q; Han, M; Xia, Z H; Huang, B; Luo, X; Zhao, G M; Chen, Y X

2016-07-06

The structure of A-C type intervariant interface in nonmodulated martensite in the Ni54Mn25Ga21 alloy was studied using high resolution transmission electron microscopy. The A-C interface is between the martensitic variants A and C, each of which has a nanoscale substructure of twin-related lamellae. According to their different thicknesses, the nanoscale lamellae in each variant can be classified into major and minor lamellae. It is the boundaries between these lamellae in different variants that constitute the A-C interface, which is thus composed of major-major, minor-minor, and major-minor lamellar boundaries. The volume fraction of the minor lamellae, λ, plays an important role in the structure of A-C interfaces. For major-major and minor-minor lamellar boundaries, they are symmetrical or asymmetrical tilt boundaries; for major-minor boundary, as λ increases, it changes from a symmetrical tilt boundary to two asymmetrical microfacets. Moreover, both lattice and misfit dislocations were observed in the A-C interfaces. On the basis of experimental observations and dislocation theory, we explain how different morphologies of the A-C interface are formed and describe the formation process of the A-C interfaces from λ ≈ 0 to λ ≈ 0.5 in terms of dislocation-boundary interaction, and we infer that low density of interfacial dislocations would lead to high mobility of the A-C interface.

A Lower-Crust or Mantle Source for Mineralizing Fluids Beneath the Olympic Dam IOCG Deposit, Australia: New Evidence From Magnetotelluric Sounding

NASA Astrophysics Data System (ADS)

Heinson, G.

2005-12-01

The iron-oxide-copper-gold (IOCG) Olympic Dam (OD) deposit, situated along the margin of the Proterozoic Gawler Craton, South Australia, is the world's largest uranium deposit, and sixth largest copper deposit; it also contains significant reserves of gold, silver and rare-earth elements (REE). Gaining a better understanding of the mechanisms for genesis of the economic mineralisation is fundamental for defining exploration models in similar crustal-settings. To delineate crustal structures that may constrain mineral system fluid pathways, coincident deep crustal seismic and magnetotelluric (MT) transects were obtained along a 220 km section that crosses OD and the major crustal boundaries. We present results from 58 long-period (10-104 s) MT sites, with site spacing of 5 to 10 km. A 2D inversion of all MT data to a depth of 100 km shows four notable features: (a) sedimentary cover sequences with low resistivity (<20 Ω.m) thicken to 10 km towards the northern cover sequences of the Adelaide Rift Complex; (b) a northeast-dipping crustal boundary separates a highly resistive (>1000 Ω.m) Archaean crustal core, from a more conductive crust to the north (typically <500 Ω.m); (c) to the north of OD, the crust to about 20 km is quite resistive (~1000 Ω.m), but the lower crust is much more conductive (<100 Ω.m); and (d) beneath OD, we image a low-resistivity region (<100 Ω.m) throughout the crust, coincident with a seismically transparent region. We argue that the cause of the low-resistivity and low-reflectivity region beneath OD may be due to the upward movement of crustal-volatiles that have deposited conductive graphite mineralisation along grain boundaries, simultaneously annihilating acoustic impedance boundaries. The source of the volatiles may be from the mantle-degassing or retrograde metamorphism of the lower crust associated with Proterozoic crustal deformation.

The May 29 2008 earthquake aftershock sequence within the South Iceland Seismic Zone: Fault locations and source parameters of aftershocks

NASA Astrophysics Data System (ADS)

Brandsdottir, B.; Parsons, M.; White, R. S.; Gudmundsson, O.; Drew, J.

2010-12-01

The mid-Atlantic plate boundary breaks up into a series of segments across Iceland. The South Iceland Seismic Zone (SISZ) is a complex transform zone where left-lateral E-W shear between the Reykjanes Peninsula Rift Zone and the Eastern Volcanic Zone is accommodated by bookshelf faulting along N-S lateral strike-slip faults. The SISZ is also a transient feature, migrating sideways in response to the southward propagation of the Eastern Volcanic Zone. Sequences of large earthquakes (M > 6) lasting from days to years and affecting most of the seismic zone have occurred repeatedly in historical time (last 1100 years), separated by intervals of relative quiescence lasting decades to more than a century. On May 29 2008, a Mw 6.1 earthquake struck the western part of the South Iceland Seismic Zone, followed within seconds by a slightly smaller event on a second fault ~5 km further west. Aftershocks, detected by a temporal array of 11 seismometers and three permanent Icelandic Meteorological Office stations were located using an automated Coalescence Microseismic Mapping technique. The epicenters delineate two major and several smaller N-S faults as well as an E-W zone of activity stretching further west into the Reykjanes Peninsula Rift Zone. Fault plane solutions show both right lateral and oblique strike slip mechanisms along the two major N-S faults. The aftershocks deepen from 3-5 km in the north to 8-9 km in the south, suggesting that the main faults dip southwards. The faulting is interpreted to be driven by the local stress due to transform motion between two parallel segments of the divergent plate boundary crossing Iceland.

A conserved segmental duplication within ELA.

PubMed

Brinkmeyer-Langford, C L; Murphy, W J; Childers, C P; Skow, L C

2010-12-01

The assembled genomic sequence of the horse major histocompatibility complex (MHC) (equine lymphocyte antigen, ELA) is very similar to the homologous human HLA, with the notable exception of a large segmental duplication at the boundary of ELA class I and class III that is absent in HLA. The segmental duplication consists of a ∼ 710 kb region of at least 11 repeated blocks: 10 blocks each contain an MHC class I-like sequence and the helicase domain portion of a BAT1-like sequence, and the remaining unit contains the full-length BAT1 gene. Similar genomic features were found in other Perissodactyls, indicating an ancient origin, which is consistent with phylogenetic analyses. Reverse-transcriptase PCR (RT-PCR) of mRNA from peripheral white blood cells of healthy and chronically or acutely infected horses detected transcription from predicted open reading frames in several of the duplicated blocks. This duplication is not present in the sequenced MHCs of most other mammals, although a similar feature at the same relative position is present in the feline MHC (FLA). Striking sequence conservation throughout Perissodactyl evolution is consistent with a functional role for at least some of the genes included within this segmental duplication. © 2010 The Authors, Journal compilation © 2010 Stichting International Foundation for Animal Genetics.

Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary.

PubMed

Krause, Johannes; Unger, Tina; Noçon, Aline; Malaspinas, Anna-Sapfo; Kolokotronis, Sergios-Orestis; Stiller, Mathias; Soibelzon, Leopoldo; Spriggs, Helen; Dear, Paul H; Briggs, Adrian W; Bray, Sarah C E; O'Brien, Stephen J; Rabeder, Gernot; Matheus, Paul; Cooper, Alan; Slatkin, Montgomery; Pääbo, Svante; Hofreiter, Michael

2008-07-28

Despite being one of the most studied families within the Carnivora, the phylogenetic relationships among the members of the bear family (Ursidae) have long remained unclear. Widely divergent topologies have been suggested based on various data sets and methods. We present a fully resolved phylogeny for ursids based on ten complete mitochondrial genome sequences from all eight living and two recently extinct bear species, the European cave bear (Ursus spelaeus) and the American giant short-faced bear (Arctodus simus). The mitogenomic data yield a well-resolved topology for ursids, with the sloth bear at the basal position within the genus Ursus. The sun bear is the sister taxon to both the American and Asian black bears, and this clade is the sister clade of cave bear, brown bear and polar bear confirming a recent study on bear mitochondrial genomes. Sequences from extinct bears represent the third and fourth Pleistocene species for which complete mitochondrial genomes have been sequenced. Moreover, the cave bear specimen demonstrates that mitogenomic studies can be applied to Pleistocene fossils that have not been preserved in permafrost, and therefore have a broad application within ancient DNA research. Molecular dating of the mtDNA divergence times suggests a rapid radiation of bears in both the Old and New Worlds around 5 million years ago, at the Miocene-Pliocene boundary. This coincides with major global changes, such as the Messinian crisis and the first opening of the Bering Strait, and suggests a global influence of such events on species radiations.

Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary

PubMed Central

2008-01-01

Background Despite being one of the most studied families within the Carnivora, the phylogenetic relationships among the members of the bear family (Ursidae) have long remained unclear. Widely divergent topologies have been suggested based on various data sets and methods. Results We present a fully resolved phylogeny for ursids based on ten complete mitochondrial genome sequences from all eight living and two recently extinct bear species, the European cave bear (Ursus spelaeus) and the American giant short-faced bear (Arctodus simus). The mitogenomic data yield a well-resolved topology for ursids, with the sloth bear at the basal position within the genus Ursus. The sun bear is the sister taxon to both the American and Asian black bears, and this clade is the sister clade of cave bear, brown bear and polar bear confirming a recent study on bear mitochondrial genomes. Conclusion Sequences from extinct bears represent the third and fourth Pleistocene species for which complete mitochondrial genomes have been sequenced. Moreover, the cave bear specimen demonstrates that mitogenomic studies can be applied to Pleistocene fossils that have not been preserved in permafrost, and therefore have a broad application within ancient DNA research. Molecular dating of the mtDNA divergence times suggests a rapid radiation of bears in both the Old and New Worlds around 5 million years ago, at the Miocene-Pliocene boundary. This coincides with major global changes, such as the Messinian crisis and the first opening of the Bering Strait, and suggests a global influence of such events on species radiations. PMID:18662376

Anatomy of major coal successions: Facies analysis and sequence architecture of a brown coal-bearing valley fill to lacustrine tract (Upper Valdarno Basin, Northern Apennines, Italy)

NASA Astrophysics Data System (ADS)

Ielpi, Alessandro

2012-07-01

A late Pliocene incised valley fill to lacustrine succession, which contains an interbedded brown coal seam (< 20 m thick), is examined in terms of facies analysis, physical stratigraphy and sequence architecture. The succession (< 50 m thick) constitutes the first depositional event of the Castelnuovo Synthem, which is the oldest unconformity bounded stratigraphic unit of the nonmarine Upper Valdarno Basin, Northern Apennines (Italy). The integration of field surveys and borehole logs identified the following event sequence: first valley filling stages by coarse alluvial fan and channelised streams; the progressive setting of low gradient floodbasins with shallow floodplain lakes; subsequent major waterlogging and extensive peat mire development; and system drowning and establishment of permanent lacustrine conditions. The deposits are grouped in a set of nested valley fills and are arranged as high-frequency depositional sequences. The sequences are bounded by minor erosive truncations and have distinctive upward trends: lowstand system tract thinning; transgressive system tract thickening; highstand system tract thinning and eventual non-deposition; and the smoothing of along-sequence boundary sub-aerial incisions. Such features fit in with the notion of an idealised model where second-order (high-frequency) fluctuations, modulated by first-order (low-frequency) base-level rising, have short-lived standing + falling phases and prolonged transgressions, respectively. Furthermore, the general sequence architecture reveals how a mixed palustrine-siliciclastic system differs substantially from a purely siliciclastic one. In the transgressive phases, terrigenous starvation induces prevailing peat accumulation, generating abnormally thick transgressive system tracts that eventually come to occupy much of the same transgression-generated accommodation space. In the highstand phases, the development of thick highstand system tracts is then prevented by sediment upstream trapping due to retrogressive fluvial aggradations, probably coupled with low-accommodation settings inherited from the transgressive phases.

Palaeogeography of late Cambrian to early Ordovician sediments in the Amadeus Basin, central Australia

NASA Astrophysics Data System (ADS)

Gorter, John D.

The depositional history of 6 sequences encompassing 18 parasequence of the Late Cambrian to Early Ordovician age in the Amadeus Basin is presented in a seried of generalized paleogeographic maps. As some of the parasequence sets are known to host large deposits of oil and gas, a thorough understanding of the potential reservoir-source rock combinations in the Amadeus Basin is essential for the discovery of further oil and gas reserves in this vast, under-explored basin. The best reservoir rocks in the Pacoota Sandstone are concentrated above the major sequence boundary between the Wallaby and Tempe Vale sequences on the Central Ridge. Poorer reservoirs occur within other sequences (e.g., parasequence set 3 and 13). Parasequence set 3 reservoirs, localized on the Central Ridge, are generally poor but owe their reservoir character to weathering at the pre-Tempe Vale sequence unconformity. Parasequence set 13 reservoirs are also concenterated along the Central Ridge, where small-scale shoaling clastic cycles are better developed. Basal Stairway Sandstone reservoirs in the Mereenie area on the Central Ridge are generally very poor, due to the cementation of the clean sandstone, but should improve to the southwest due to lesser burial-induced silicification. The source potential of the major Arenig organic-rich sediments is concentrated in the transitional zone between parasequence sets 15 and 16. East of West Waterhouse 1 well, these parasequence sets have been eroded and there is no remaining source potential. The transitional source-rich zone is better developed on the Central Ridge than in the Missionary Plain Trough. The Central Ridge is therefore of prime importance in the localization of both reservoir and source rocks in the Late Cambrian and Early Ordovician section of the Amadeus Basin.

Boundaries for algebras of holomorphic functions on Marcinkiewicz sequence spaces

NASA Astrophysics Data System (ADS)

Choi, Yun Sung; Han, Kwang Hee

2006-11-01

Let be the Banach algebra of all complex-valued bounded continuous functions on the closed unit ball BE of a complex Banach space E and holomorphic in the interior of BE and let be the closed subalgebra of those functions which are uniformly continuous on BE. For the case whose bidual is a Marcinkiewicz sequence space Mw, we describe some sufficient conditions for a set to be a boundary of either or . Moreover, we consider some analogous problems on to those which were studied on the Gowers space Gp of characteristic p by Grados and Moraes [L.R. Grados, L.A. Moraes, Boundaries for algebras of holomorphic functions, J. Math. Anal. Appl. 281 (2003) 575-586; L.R. Grados, L.A. Moraes, Boundaries for an algebra of bounded holomorphic functions, J. Korean Math. Soc. 41 (1) (2004) 231-242].

Identification of a major continuous epitope of human alpha crystallin

NASA Technical Reports Server (NTRS)

Takemoto, L.; Emmons, T.; Spooner, B. S. (Principal Investigator)

1992-01-01

Human lens proteins were digested with trypsin or V8 protease, and the resulting peptides resolved on a C18 reverse phase column. Fractions from this column were probed with polyclonal antiserum made against the whole alpha crystallin molecule. Peptides in the seropositive fraction were purified to homogeneity, then characterized by mass spectral analysis and partial Edman degradation. The tryptic and V8 digests contained only one seropositive peptide that was derived from the C-terminal region of the alpha-A molecule. To determine the exact boundaries of the epitope, various size analogues of this region were synthesized and probed with anti-alpha serum. Together, these studies demonstrate that the major continuous epitope of the alpha-A chain includes the sequence KPTSAPS, corresponding to residues 166-172 of the human alpha-A crystallin chain.

Timing is everything - implications of a new correlation of Triassic-Jurassic boundary successions and the Central Atlantic Magmatic Province

NASA Astrophysics Data System (ADS)

Lindström, Sofie; van de Schootbrugge, Bas; Pedersen, Gunver K.; Alsen, Peter; Thibault, Nicolas; Hansen, Katrine H.; Dybkjær, Karen; Bjerrum, Christian J.; Nielsen, Lars Henrik

2017-04-01

Understanding mass extinctions requires a clear insight into the stratigraphy of boundary sections, which allows for long-distance correlations and correct distinction of the sequence of events. However, even after the ratification of a Global Stratotype Section and Point, global correlations of Triassic-Jurassic boundary (TJB) successions are hampered by the fact that many of the traditionally used fossil groups were severely affected by the end-Triassic mass extinction (ETE). Recently, a new correlation of key TJB successions in Europe, U.S.A. and Peru, based on a combination of biotic (palynology and ammonites), geochemical (δ13Corg) and radiometric (U/Pb ages) constraints, was presented. This new correlation has an impact on the causality and temporal development during the end-Triassic event, as it indicates that the bulk of the hitherto dated, high-titanium, quartz normalized volcanism of the Central Atlantic Magmatic Province (CAMP) preceded or was contemporaneous to the onset of the mass extinction. It further shows that the maximum phase of the mass extinction, which affected both the terrestrial and marine ecosystems, was associated with a major regression and repeated, enhanced earthquake activity in Europe. A subsequent transgression resulted in the formation of hiati or condensed successions in many areas in Europe. Later phases of volcanic activity of the CAMP, producing low titanium, quartz normalized and high-iron, quartz normalized basaltic rocks, continued close to the first occurrence of Jurassic ammonites and the defined TJB. This new correlations enables a reconstruction of the sequence of events; including records of e.g. pCO2 from soil carbonates and plant fossils, rare earth elements, biomarkers, charcoal, which allows an insight into the causality of this biotic crises.

An Examination of Seismicity Linking the Solomon Islands and Vanuatu Subduction Zones

NASA Astrophysics Data System (ADS)

Neely, J. S.; Furlong, K. P.

2015-12-01

The Solomon Islands-Vanuatu composite subduction zone represents a tectonically complex region along the Pacific-Australia plate boundary in the southwest Pacific Ocean. Here the Australia plate subducts under the Pacific plate in two segments: the South Solomon Trench and the Vanuatu Trench. The two subducting sections are offset by a 200 km long, transform fault - the San Cristobal Trough (SCT) - which acts as a Subduction-Transform Edge Propagator (STEP) fault. The subducting segments have experienced much more frequent and larger seismic events than the STEP fault. The northern Vanuatu trench hosted a M8.0 earthquake in 2013. In 2014, at the juncture of the western terminus of the SCT and the southern South Solomon Trench, two earthquakes (M7.4 and M7.6) occurred with disparate mechanisms (dominantly thrust and strike-slip respectively), which we interpret to indicate the tearing of the Australia plate as its northern section subducts and southern section translates along the SCT. During the 2013-2014 timeframe, little seismic activity occurred along the STEP fault. However, in May 2015, three M6.8-6.9 strike-slip events occurred in rapid succession as the STEP fault ruptured east to west. These recent events share similarities with a 1993 strike-slip STEP sequence on the SCT. Analysis of the 1993 and 2015 STEP earthquake sequences provides constraints on the plate boundary geometry of this major transform fault. Preliminary research suggests that plate motion along the STEP fault is partitioned between larger east-west oriented strike-slip events and smaller north-south thrust earthquakes. Additionally, the differences in seismic activity between the subducting slabs and the STEP fault can provide insights into how stress is transferred along the plate boundary and the mechanisms by which that stress is released.

Facies and log signatures of sequence boundaries in Sembakung area, Tarakan Basin, East Kalimantan, Indonesia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bambang, P.; Hardjono, M.; Silalahi, L.

1996-08-01

Tarakan basin is one of the basins in East Kalimantan having a complicated geological condition. Tectonic repetition developed in this area constructed various stratigraphic traps. Sedimentary development in log data shows continuous regression in Meliat and Tabul Formations (Middle Meocene), Santul Formation (Late Miocene), Tarakan Formation (Pliocene) and Bunyu Formation (Pleistocene), Supported by seismic data, stratigraphic sequence in the basin is obvious, especially in Sembakung-Bangkudulis area. The sequence boundaries, mainly {open_quotes}lowstand{close_quotes} distribution as good prospective trap, can be mapped by applying tract systems and studying wavelet extract as seismic expression character of a reservoir. Subtle changes in pattern of stratigraphicmore » sequences can become a hint of sedimentary environment and its lithology content, supporting both exploration and exploitation planning.« less

The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms

PubMed Central

Bausher, Michael G; Singh, Nameirakpam D; Lee, Seung-Bum; Jansen, Robert K; Daniell, Henry

2006-01-01

Background The production of Citrus, the largest fruit crop of international economic value, has recently been imperiled due to the introduction of the bacterial disease Citrus canker. No significant improvements have been made to combat this disease by plant breeding and nuclear transgenic approaches. Chloroplast genetic engineering has a number of advantages over nuclear transformation; it not only increases transgene expression but also facilitates transgene containment, which is one of the major impediments for development of transgenic trees. We have sequenced the Citrus chloroplast genome to facilitate genetic improvement of this crop and to assess phylogenetic relationships among major lineages of angiosperms. Results The complete chloroplast genome sequence of Citrus sinensis is 160,129 bp in length, and contains 133 genes (89 protein-coding, 4 rRNAs and 30 distinct tRNAs). Genome organization is very similar to the inferred ancestral angiosperm chloroplast genome. However, in Citrus the infA gene is absent. The inverted repeat region has expanded to duplicate rps19 and the first 84 amino acids of rpl22. The rpl22 gene in the IRb region has a nonsense mutation resulting in 9 stop codons. This was confirmed by PCR amplification and sequencing using primers that flank the IR/LSC boundaries. Repeat analysis identified 29 direct and inverted repeats 30 bp or longer with a sequence identity ≥ 90%. Comparison of protein-coding sequences with expressed sequence tags revealed six putative RNA edits, five of which resulted in non-synonymous modifications in petL, psbH, ycf2 and ndhA. Phylogenetic analyses using maximum parsimony (MP) and maximum likelihood (ML) methods of a dataset composed of 61 protein-coding genes for 30 taxa provide strong support for the monophyly of several major clades of angiosperms, including monocots, eudicots, rosids and asterids. The MP and ML trees are incongruent in three areas: the position of Amborella and Nymphaeales, relationship of the magnoliid genus Calycanthus, and the monophyly of the eurosid I clade. Both MP and ML trees provide strong support for the monophyly of eurosids II and for the placement of Citrus (Sapindales) sister to a clade including the Malvales/Brassicales. Conclusion This is the first complete chloroplast genome sequence for a member of the Rutaceae and Sapindales. Expansion of the inverted repeat region to include rps19 and part of rpl22 and presence of two truncated copies of rpl22 is unusual among sequenced chloroplast genomes. Availability of a complete Citrus chloroplast genome sequence provides valuable information on intergenic spacer regions and endogenous regulatory sequences for chloroplast genetic engineering. Phylogenetic analyses resolve relationships among several major clades of angiosperms and provide strong support for the monophyly of the eurosid II clade and the position of the Sapindales sister to the Brassicales/Malvales. PMID:17010212

Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing

PubMed Central

Eastman, Alexander W.; Yuan, Ze-Chun

2015-01-01

Advances in sequencing technology have drastically increased the depth and feasibility of bacterial genome sequencing. However, little information is available that details the specific techniques and procedures employed during genome sequencing despite the large numbers of published genomes. Shotgun approaches employed by second-generation sequencing platforms has necessitated the development of robust bioinformatics tools for in silico assembly, and complete assembly is limited by the presence of repetitive DNA sequences and multi-copy operons. Typically, re-sequencing with multiple platforms and laborious, targeted Sanger sequencing are employed to finish a draft bacterial genome. Here we describe a novel strategy based on the identification and targeted sequencing of repetitive rDNA operons to expedite bacterial genome assembly and finishing. Our strategy was validated by finishing the genome of Paenibacillus polymyxa strain CR1, a bacterium with potential in sustainable agriculture and bio-based processes. An analysis of the 38 contigs contained in the P. polymyxa strain CR1 draft genome revealed 12 repetitive rDNA operons with varied intragenic and flanking regions of variable length, unanimously located at contig boundaries and within contig gaps. These highly similar but not identical rDNA operons were experimentally verified and sequenced simultaneously with multiple, specially designed primer sets. This approach also identified and corrected significant sequence rearrangement generated during the initial in silico assembly of sequencing reads. Our approach reduces the required effort associated with blind primer walking for contig assembly, increasing both the speed and feasibility of genome finishing. Our study further reinforces the notion that repetitive DNA elements are major limiting factors for genome finishing. Moreover, we provided a step-by-step workflow for genome finishing, which may guide future bacterial genome finishing projects. PMID:25653642

Step-wise extinctions at the Cretaceous-Tertiary boundary and their climatic implications

NASA Technical Reports Server (NTRS)

Maurrasse, Florentin J-M. R.

1988-01-01

A comparative study of planktonic foraminifera and radiolarian assemblages from the Cretaceous-Tertiary (K-T) boundary section of the Beloc Formation in the southern Peninsula of Haiti, and the lowermost Danian sequence of the Micara Formation in southern Cuba reveals a remarkable pattern of step-wise extinctions. This pattern is consistent in both places despite the widely different lithologies of the two formations. Because of a step-wise extinction and the delayed disappearance of taxa known to be more representative of cooler water realms, it is inferred that a cooling trend which characterized the close of the Maastrichtian and the onset of the Tertiary had the major adverse effect on the existing biota. Although repetitive lithologic and faunal fluctuations throughout the Maastrichtian sediments found at Deep Sea Drilling Project (DSDP) site 146/149 in the Caribbean Sea indicate variations reminiscent of known climatically induced cycles in the Cenozoic, rapid biotic succession appears to have taken place during a crisis period of a duration greater than 2 mission years. Widespread and abundant volcanic activities recorded in the Caribbean area during the crisis period gives further credence to earlier contention that intense volcanism may have played a major role in exhacerbating pre-existing climatic conditions during that time.

Event Boundaries Trigger Rapid Memory Reinstatement of the Prior Events to Promote Their Representation in Long-Term Memory.

PubMed

Sols, Ignasi; DuBrow, Sarah; Davachi, Lila; Fuentemilla, Lluís

2017-11-20

Although everyday experiences unfold continuously over time, shifts in context, or event boundaries, can influence how those events come to be represented in memory [1-4]. Specifically, mnemonic binding across sequential representations is more challenging at context shifts, such that successful temporal associations are more likely to be formed within than across contexts [1, 2, 5-9]. However, in order to preserve a subjective sense of continuity, it is important that the memory system bridge temporally adjacent events, even if they occur in seemingly distinct contexts. Here, we used pattern similarity analysis to scalp electroencephalographic (EEG) recordings during a sequential learning task [2, 3] in humans and showed that the detection of event boundaries triggered a rapid memory reinstatement of the just-encoded sequence episode. Memory reactivation was detected rapidly (∼200-800 ms from the onset of the event boundary) and was specific to context shifts that were preceded by an event sequence with episodic content. Memory reinstatement was not observed during the sequential encoding of events within an episode, indicating that memory reactivation was induced specifically upon context shifts. Finally, the degree of neural similarity between neural responses elicited during sequence encoding and at event boundaries correlated positively with participants' ability to later link across sequences of events, suggesting a critical role in binding temporally adjacent events in long-term memory. Current results shed light onto the neural mechanisms that promote episodic encoding not only for information within the event, but also, importantly, in the ability to link across events to create a memory representation of continuous experience. Copyright © 2017 Elsevier Ltd. All rights reserved.

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

PubMed Central

Vanneste, Kevin; Baele, Guy; Maere, Steven; Van de Peer, Yves

2014-01-01

Ancient whole-genome duplications (WGDs), also referred to as paleopolyploidizations, have been reported in most evolutionary lineages. Their attributed role remains a major topic of discussion, ranging from an evolutionary dead end to a road toward evolutionary success, with evidence supporting both fates. Previously, based on dating WGDs in a limited number of plant species, we found a clustering of angiosperm paleopolyploidizations around the Cretaceous–Paleogene (K–Pg) extinction event about 66 million years ago. Here we revisit this finding, which has proven controversial, by combining genome sequence information for many more plant lineages and using more sophisticated analyses. We include 38 full genome sequences and three transcriptome assemblies in a Bayesian evolutionary analysis framework that incorporates uncorrelated relaxed clock methods and fossil uncertainty. In accordance with earlier findings, we demonstrate a strongly nonrandom pattern of genome duplications over time with many WGDs clustering around the K–Pg boundary. We interpret these results in the context of recent studies on invasive polyploid plant species, and suggest that polyploid establishment is promoted during times of environmental stress. We argue that considering the evolutionary potential of polyploids in light of the environmental and ecological conditions present around the time of polyploidization could mitigate the stark contrast in the proposed evolutionary fates of polyploids. PMID:24835588

The production and phonetic representation of fake geminates in English

PubMed Central

Oh, Grace E.; Redford, Melissa A.

2011-01-01

The current study focused on the production of non-contrastive geminates across different boundary types in English to investigate the hypothesis that word-internal heteromorphemic geminates may differ from those that arise across a word boundary. In this study, word-internal geminates arising from affixation, and described as either assimilated or concatenated, were matched to heteromorphemic geminates arising from sequences of identical consonants that spanned a word boundary and to word-internal singletons. Word-internal geminates were found to be longer than matched singletons in absolute and relative terms. By contrast, heteromorphemic geminates that occurred at word boundaries were only longer than matched singletons in absolute terms. In addition, heteromorphemic geminates in two word phrases were typically “pulled apart” in careful speech; that is, speakers marked the boundaries between free morphemes with pitch changes and pauses. Morpheme boundaries in words with bound affixes were very rarely highlighted in this way. These results are taken to indicate that most word-internal heteromorphemic geminates are represented as a single long consonant in the speech plan rather than as a consonant sequence. Only those geminates that arise in two word phrases exhibit phonetic characteristics that are fully consistent with the representation of two identical consonants crossing a morpheme boundary. PMID:22611293

Finding the Onset of Convection in Main Sequence Stars

NASA Technical Reports Server (NTRS)

Simon, Theodore

2003-01-01

The primary goal of the work performed under this grant was to locate, if possible, the onset of subphotospheric convection zones in normal main sequence stars by using the presence of emission in high temperature lines in far ultraviolet spectra from the FUSE spacecraft as a proxy for convection. The change in stellar structure represented by this boundary between radiative and convective stars has always been difficult to find by other empirical means. A search was conducted through observations of a sample of A-type stars, which were somewhat hotter and more massive than the Sun, and which were carefully chosen to bridge the theoretically expected radiative/convective boundary line along the main sequence.

Miocene History of the East Antarctic Ice-sheet Inferred from the Eustatic and Paleoceanographic Record of The Marion Plateau, Northeastern Australia (ODP Leg 194)

NASA Astrophysics Data System (ADS)

John, C. M.; Browning, E.; Lowery, C.; Leckie, R. M.; Karner, G. D.; Schouten, S.

2012-12-01

The East Antarctic Ice Sheet (EAIS) had a major influence on Cenozoic eustasy and paleoceanography. Reconstructing changes in ice volume and climate associated with the EAIS is thus critical to a better understanding of climate dynamics, but this has proven difficult to do using only sedimentary records from Antarctica because ice sheets tend to erase evidences of their own history. It is possible, however, to gain information about the dynamics of the EAIS by reconstructing glacio-eustasy and regional paleoceanographic changes away from Antarctica. We present a record of carbonate deposition spanning the uppermost Oligocene to upper Miocene on the Marion Plateau of Northeastern Australia (ODP Leg 194). The Marion Plateau is ideally located for our study on a tectonically quiescent margin, and it is a sensitive recorder of Antarctic paleoenvironmental changes due to its geographical position in the southern hemisphere. We conducted a multi-disciplinary study involving sedimentology, sequence stratigraphy, calcareous nannofossil and foraminifer micropaleontology, and organic geochemistry. Eleven lower and middle Miocene sequence boundaries can be recognized on the Marion Plateau based on facies and seismic reflection lines, and each sequence boundary (sea-level fall) is associated with a phase of growth of the EAIS (as evidenced by positive shifts in δ18O, termed "Mi Events"). The oldest boundary recovered is 23.16 Ma old. By combining backstripping and δ18O estimates, the amplitude of four of the Miocene eustatic falls are constrained to 27±1 m at 16.5 Ma (Mi2), 27±1 m at 15.6 Ma (Mi2a), 33±3 m at 14.8 Ma (Mi3a), and 59±6 m at 13.6 Ma (Mi3). The amplitude of the eustatic drop associated with event Mi3 suggests a major growth phase of the EAIS in the middle Miocene, which is supported by other deep-sea records and several recent studies from continental Antarctica. Furthermore, nannofossil assemblages show four main clusters corresponding to changes in temperature and productivity on the Marion Plateau; for much of the Miocene, surface waters of the Marion Plateau are characterized by warm, subtropical temperatures, but at 14.8 Ma (coeval with event Mi3a) assemblages suddenly become dominated by the cold-water species Dictyococcites productus and Dictyococcites antarcticus. TEX86 data support the observation based on nannofossil assemblages, suggesting incursions of colder waters on the Marion Plateau from 14.8 Ma to 13.6 Ma, with a progressive return to sub-tropical temperatures afterwards. The combined glacio-eustatic and paleoceanographic records of the Marion Plateau suggest the onset of significant cooling on Antarctica by 14.8 Ma, followed by a major growth phase of the EAIS by 13.6 Ma.

The Structure Difference in the Southern Margin of the Dangerous Grounds: Implications for the Final Evolution of the South China Sea

NASA Astrophysics Data System (ADS)

Xi, P.; Shen, C.; Zhao, Z.; Xie, X.; Mei, L.; Gong, J.; Huang, X.

2015-12-01

We interpret two multi-channel seismic reflection profiles, more than 900 km across the entire Dangerous Grounds, locating in east and west of the southern margin of the South China Sea respectively. Eight Cenozoic sequence boundaries are determined as well as three tectono-stratigraphic units. Detailed analysis of extensional features and unconformities revealed the tectonic in the east and west. Early extension (syn-rifting sequence) occurred in the two profiles during continental rifting, which lasted from Palaeocene to Early Oligocene, and resulted in formation of half-grabens and rotated fault-blocks. Late extension (drift-rifting sequence) has the significant difference in the both profiles. The eastern Dangerous Grounds entered rifting-depression stage and some compressional deformation occurred in the Reed Bank basin at about the beginning of Early Miocene, probably resulting from the collision of the Dangerous Grounds and the Sabah-Cagayan Arc. The western Dangerous Grounds was still in rifting until the end of Early Miocene, forming the MMU or DRU which is strongly erosional and represents a major break in sedimentation and/or erosion in partial area. Denudation fold and inverted fault can be distinguished blow the MMU, indicating the cessation of the South China Sea accompanied the NW compression, while the boundary corresponding the MMU is nearly a plano-conformity in the east. The thermal sag (post-rifting sequence) is characterized by non-faulted draping strata in the whole area. The different structure in east and west may be related to the final evolution of the SCS. When the proto-SCS closed in a scissor fashion plus the clockwise rotation of Borneo, the initial collision (c.20Ma) appeared in east part building the NW foreland basin system from Palawan Trough to Reed Bank in a short-live process, while the west part was drifting southwards until c.15Ma to form the even more remarkable foreland system from Borneo Trough to deep-water Sarawak.

Joint deep shape and appearance learning: application to optic pathway glioma segmentation

NASA Astrophysics Data System (ADS)

Mansoor, Awais; Li, Ien; Packer, Roger J.; Avery, Robert A.; Linguraru, Marius George

2017-03-01

Automated tissue characterization is one of the major applications of computer-aided diagnosis systems. Deep learning techniques have recently demonstrated impressive performance for the image patch-based tissue characterization. However, existing patch-based tissue classification techniques struggle to exploit the useful shape information. Local and global shape knowledge such as the regional boundary changes, diameter, and volumetrics can be useful in classifying the tissues especially in scenarios where the appearance signature does not provide significant classification information. In this work, we present a deep neural network-based method for the automated segmentation of the tumors referred to as optic pathway gliomas (OPG) located within the anterior visual pathway (AVP; optic nerve, chiasm or tracts) using joint shape and appearance learning. Voxel intensity values of commonly used MRI sequences are generally not indicative of OPG. To be considered an OPG, current clinical practice dictates that some portion of AVP must demonstrate shape enlargement. The method proposed in this work integrates multiple sequence magnetic resonance image (T1, T2, and FLAIR) along with local boundary changes to train a deep neural network. For training and evaluation purposes, we used a dataset of multiple sequence MRI obtained from 20 subjects (10 controls, 10 NF1+OPG). To our best knowledge, this is the first deep representation learning-based approach designed to merge shape and multi-channel appearance data for the glioma detection. In our experiments, mean misclassification errors of 2:39% and 0:48% were observed respectively for glioma and control patches extracted from the AVP. Moreover, an overall dice similarity coefficient of 0:87+/-0:13 (0:93+/-0:06 for healthy tissue, 0:78+/-0:18 for glioma tissue) demonstrates the potential of the proposed method in the accurate localization and early detection of OPG.

The Eocene-Oligocene sedimentary record in the Chesapeake Bay impact structure: Implications for climate and sea-level changes on the western Atlantic margin

USGS Publications Warehouse

Schulte, P.; Wade, B.S.; Kontny, A.; ,

2009-01-01

A multidisciplinary investigation of the Eocene-Oligocene transition in the International Continental Scientific Drilling Program (ICDP)-U.S. Geological Survey (USGS) Eyreville core from the Chesapeake Bay impact basin was conducted in order to document environmental changes and sequence stratigraphic setting. Planktonic foraminifera and calcareous nannofossil biostratigraphy indicate that the Eyreville core includes an expanded upper Eocene (Biozones E15 to E16 and NP19/20 to NP21, respectively) and a condensed Oligocene-Miocene (NP24-NN1) sedimentary sequence. The Eocene-Oligocene contact corresponds to a =3-Ma-long hiatus. Eocene- Oligocene sedimentation is dominated by great diversity and varying amounts of detrital and authigenic minerals. Four sedimentary intervals are identified by lithology and mineral content: (1) A 30-m-thick, smectite- and illite-rich interval directly overlies the Exmore Formation, suggesting long-term reworking of impact debris within the Chesapeake Bay impact structure. (2) Subsequently, an increase in kaolinite content suggests erosion from soils developed during late Eocene warm and humid climate in agreement with data derived from other Atlantic sites. However, the kaolinite increase may also be explained by change to a predominant sediment input from outside the Chesapeake Bay impact structure caused by progradation of more proximal facies belts during the highstand systems tract of the late Eocene sequence E10.Spectral analysis based on gamma-ray and magnetic susceptibility logs suggests infl uence of 1.2 Ma low-amplitude oscillation of the obliquity period during the late Eocene. (3) During the latest Eocene (Biozones NP21 and E16), several lithological contacts (clay to clayey silt) occur concomitant with a prominent change in the mineralogical composition with illite as a major component: This lithological change starts close to the Biozone NP19/20-NP21 boundary and may correspond to sequence boundary E10-E11 as observed in other northwest Atlantic margin sections. It could result from a shift to more distal depositional environments and condensed sedimentation during maximum fl ooding, rather than refl ecting a climatic change in the hinterland. The distinct 1% increase of the oxygen isotopes may correspond to the short-term latest Eocene "precursor isotope event." (4) The abrupt increase of sediment grainsize, carbonate content, and abundance of authigenic minerals (glauconite) across the major unconformity that separates Eocene from Oligocene sediments in the Eyreville core refl ects deposition in shallower settings associated with erosion, winnowing, and reworking. Sediments within the central crater were affected by the rapid eustatic sea-level changes associated with the greenhouse-icehouse transition, as well as by an abrupt major uplift event and possibly enhanced current activity on the northwestern Atlantic margin. ?? 2009 The Geological Society of America.

Geochemical and petrographic studies of melt-rich breccias from the Chicxulub crater

NASA Astrophysics Data System (ADS)

Vera-Sanchez, P.; Urrutia-Fucugauchi, J.; Morton-Bermea, O.; Soler-Arechalde, A.; Reyes-Salas, M.; Lozano-Santamaria, R.; Linares-Lopez, C.; Rebolledo-Vieyra, M.

2003-04-01

The proposal by Alvarez et al. (1980) for an extraterrestrial bolide impact marking the Cretaceous/Tertiary boundary was based on the anomalous Ir content in Italian and Danish K/T clay layers. The clay layer with a worldwide distribution and enriched in platinum group elements, shocked quartz and other impact-generated features has come to be interpreted as the global ejecta layer produced by a large impact that formed the Chicxulub crater. The ~200 km diameter crater is located in the carbonate platform of northwestern Yucatan peninsula, Mexico. The crater is covered by a thick sequence of Tertiary sediments, with no surface exposures. The National University of Mexico conducted a drilling program with continuous core recovery, in which three boreholes (UNAM wells 5, 6 and 7) sampled the impact breccia sequences. Deeper drilling inside the carter has been carried out as part of the ICDP program with drilling of the Yaxcopoil-1 borehole, which also cored a section of the impact breccias. The Yaxcopoil-1 borehole has been completed as part of the Chicxulub Scientific Drilling Project. In this work, we report on the geochemical and petrographic studies of selected samples from the impact breccia sequence recovered in the Yaxcopoil-1 borehole inside the Chicxulub crater. One of the major questions emerging after the interpretation of Chicxulub as the K/T boundary impact site and its link to the global ejecta layer has been the nature of the impacting body. Studies have addressed this question from distinct fields, including investigation of the ejecta deposits near and far from the crater, from the crater itself, from impact records on the Moon and other bodies, searching for surviving fragments in K/T boundary sections, etc. The search for material with a possible small component associated to the impactor could open unique research opportunities to further understand the impact event. The melt breccia samples examined exhibit different textures and chemical composition, suggesting a complex composition. Rare earth element plots for the various fragments are on the other hand similar. We report the initial results of the petrographic, microprobe, ICP-MS, X-ray fluorescence and X-ray diffraction studies.

Major controls on architecture, sequence stratigraphy and paleosols of middle Pleistocene continental sediments ("Qc Unit"), eastern central Italy

NASA Astrophysics Data System (ADS)

Di Celma, Claudio; Pieruccini, Pierluigi; Farabollini, Piero

2015-05-01

Middle Pleistocene continental sediments in central Italy ("Qc Unit") record the oldest fluvial accumulation along the uplifting margin of the Peri-Adriatic basin. The architecture of the sediment body can be divided into two unconformity-bounded, fining-upward cycles interpreted as genetically related depositional sequences. These sequences highlight the systematic adjustment of the fluvial system to changes in the ratio between accommodation space and sediment supply (A/S ratio) and, from base to top, comprise the following surfaces and stratal components: (i) a regionally correlative sequence boundary resulting from an A/S ratio ≤ 0; (ii) a low-accommodation systems tract characterized by conglomerate-rich, amalgamated channel fills and recording an A/S ratio < 1; (iii) an expansion surface marking the turnaround point from low-accommodation systems tract to high-accommodation systems tract deposits; (iv) a high-accommodation systems tract dominated by floodplain fines encasing lens-like, fluvial channel deposits and denoting an A/S ratio > 1; and (v) a mature red argillic paleosol. To constrain the climatic signal for paleosols formation, the two sequence-capping mature paleosols have been investigated. The results of these studies suggest that they were developed under humid and warm climatic conditions associated with interglacial phases, which have been correlatively attributed to Marine Oxygen Isotope Stages 11 and 9.

Phylogenetic and Genome-Wide Deep-Sequencing Analyses of Canine Parvovirus Reveal Co-Infection with Field Variants and Emergence of a Recent Recombinant Strain

PubMed Central

Pérez, Ruben; Calleros, Lucía; Marandino, Ana; Sarute, Nicolás; Iraola, Gregorio; Grecco, Sofia; Blanc, Hervé; Vignuzzi, Marco; Isakov, Ofer; Shomron, Noam; Carrau, Lucía; Hernández, Martín; Francia, Lourdes; Sosa, Katia; Tomás, Gonzalo; Panzera, Yanina

2014-01-01

Canine parvovirus (CPV), a fast-evolving single-stranded DNA virus, comprises three antigenic variants (2a, 2b, and 2c) with different frequencies and genetic variability among countries. The contribution of co-infection and recombination to the genetic variability of CPV is far from being fully elucidated. Here we took advantage of a natural CPV population, recently formed by the convergence of divergent CPV-2c and CPV-2a strains, to study co-infection and recombination. Complete sequences of the viral coding region of CPV-2a and CPV-2c strains from 40 samples were generated and analyzed using phylogenetic tools. Two samples showed co-infection and were further analyzed by deep sequencing. The sequence profile of one of the samples revealed the presence of CPV-2c and CPV-2a strains that differed at 29 nucleotides. The other sample included a minor CPV-2a strain (13.3% of the viral population) and a major recombinant strain (86.7%). The recombinant strain arose from inter-genotypic recombination between CPV-2c and CPV-2a strains within the VP1/VP2 gene boundary. Our findings highlight the importance of deep-sequencing analysis to provide a better understanding of CPV molecular diversity. PMID:25365348

Double absorbing boundaries for finite-difference time-domain electromagnetics

DOE Office of Scientific and Technical Information (OSTI.GOV)

LaGrone, John, E-mail: jlagrone@smu.edu; Hagstrom, Thomas, E-mail: thagstrom@smu.edu

We describe the implementation of optimal local radiation boundary condition sequences for second order finite difference approximations to Maxwell's equations and the scalar wave equation using the double absorbing boundary formulation. Numerical experiments are presented which demonstrate that the design accuracy of the boundary conditions is achieved and, for comparable effort, exceeds that of a convolution perfectly matched layer with reasonably chosen parameters. An advantage of the proposed approach is that parameters can be chosen using an accurate a priori error bound.

Optic disc boundary segmentation from diffeomorphic demons registration of monocular fundus image sequences versus 3D visualization of stereo fundus image pairs for automated early stage glaucoma assessment

NASA Astrophysics Data System (ADS)

Gatti, Vijay; Hill, Jason; Mitra, Sunanda; Nutter, Brian

2014-03-01

Despite the current availability in resource-rich regions of advanced technologies in scanning and 3-D imaging in current ophthalmology practice, world-wide screening tests for early detection and progression of glaucoma still consist of a variety of simple tools, including fundus image-based parameters such as CDR (cup to disc diameter ratio) and CAR (cup to disc area ratio), especially in resource -poor regions. Reliable automated computation of the relevant parameters from fundus image sequences requires robust non-rigid registration and segmentation techniques. Recent research work demonstrated that proper non-rigid registration of multi-view monocular fundus image sequences could result in acceptable segmentation of cup boundaries for automated computation of CAR and CDR. This research work introduces a composite diffeomorphic demons registration algorithm for segmentation of cup boundaries from a sequence of monocular images and compares the resulting CAR and CDR values with those computed manually by experts and from 3-D visualization of stereo pairs. Our preliminary results show that the automated computation of CDR and CAR from composite diffeomorphic segmentation of monocular image sequences yield values comparable with those from the other two techniques and thus may provide global healthcare with a cost-effective yet accurate tool for management of glaucoma in its early stage.

Exclusion of known gene for enamel development in two Brazilian families with amelogenesis imperfecta

PubMed Central

Santos, Maria CLG; Hart, P Suzanne; Ramaswami, Mukundhan; Kanno, Cláudia M; Hart, Thomas C; Line, Sergio RP

2007-01-01

Amelogenesis imperfecta (AI) is a genetically heterogeneous group of diseases that result in defective development of tooth enamel. Mutations in several enamel proteins and proteinases have been associated with AI. The object of this study was to evaluate evidence of etiology for the six major candidate gene loci in two Brazilian families with AI. Genomic DNA was obtained from family members and all exons and exon-intron boundaries of the ENAM, AMBN, AMELX, MMP20, KLK4 and Amelotin gene were amplified and sequenced. Each family was also evaluated for linkage to chromosome regions known to contain genes important in enamel development. The present study indicates that the AI in these two families is not caused by any of the known loci for AI or any of the major candidate genes proposed in the literature. These findings indicate extensive genetic heterogeneity for non-syndromic AI. PMID:17266769

Exclusion of known gene for enamel development in two Brazilian families with amelogenesis imperfecta.

PubMed

Santos, Maria C L G; Hart, P Suzanne; Ramaswami, Mukundhan; Kanno, Cláudia M; Hart, Thomas C; Line, Sergio R P

2007-01-31

Amelogenesis imperfecta (AI) is a genetically heterogeneous group of diseases that result in defective development of tooth enamel. Mutations in several enamel proteins and proteinases have been associated with AI. The object of this study was to evaluate evidence of etiology for the six major candidate gene loci in two Brazilian families with AI. Genomic DNA was obtained from family members and all exons and exon-intron boundaries of the ENAM, AMBN, AMELX, MMP20, KLK4 and Amelotin gene were amplified and sequenced. Each family was also evaluated for linkage to chromosome regions known to contain genes important in enamel development. The present study indicates that the AI in these two families is not caused by any of the known loci for AI or any of the major candidate genes proposed in the literature. These findings indicate extensive genetic heterogeneity for non-syndromic AI.

Evolutionary history of the enolase gene family.

PubMed

Tracy, M R; Hedges, S B

2000-12-23

The enzyme enolase [EC 4.2.1.11] is found in all organisms, with vertebrates exhibiting tissue-specific isozymes encoded by three genes: alpha (alpha), beta (beta), and gamma (gamma) enolase. Limited taxonomic sampling of enolase has obscured the timing of gene duplication events. To help clarify the evolutionary history of the gene family, cDNAs were sequenced from six taxa representing major lineages of vertebrates: Chiloscyllium punctatum (shark), Amia calva (bowfin), Salmo trutta (trout), Latimeria chalumnae (coelacanth), Lepidosiren paradoxa (South American lungfish), and Neoceratodus forsteri (Australian lungfish). Phylogenetic analysis of all enolase and related gene sequences revealed an early gene duplication event prior to the last common ancestor of living organisms. Several distantly related archaebacterial sequences were designated as 'enolase-2', whereas all other enolase sequences were designated 'enolase-1'. Two of the three isozymes of enolase-1, alpha- and beta-enolase, were discovered in actinopterygian, sarcopterygian, and chondrichthian fishes. Phylogenetic analysis of vertebrate enolases revealed that the two gene duplications leading to the three isozymes of enolase-1 occurred subsequent to the divergence of living agnathans, near the Proterozoic/Phanerozoic boundary (approximately 550Mya). Two copies of enolase, designated alpha(1) and alpha(2), were found in the trout and are presumed to be the result of a genome duplication event.

An Ancient Transkingdom Horizontal Transfer of Penelope-Like Retroelements from Arthropods to Conifers

PubMed Central

Lin, Xuan; Faridi, Nurul; Casola, Claudio

2016-01-01

Comparative genomics analyses empowered by the wealth of sequenced genomes have revealed numerous instances of horizontal DNA transfers between distantly related species. In eukaryotes, repetitive DNA sequences known as transposable elements (TEs) are especially prone to move across species boundaries. Such horizontal transposon transfers, or HTTs, are relatively common within major eukaryotic kingdoms, including animals, plants, and fungi, while rarely occurring across these kingdoms. Here, we describe the first case of HTT from animals to plants, involving TEs known as Penelope-like elements, or PLEs, a group of retrotransposons closely related to eukaryotic telomerases. Using a combination of in situ hybridization on chromosomes, polymerase chain reaction experiments, and computational analyses we show that the predominant PLE lineage, EN(+)PLEs, is highly diversified in loblolly pine and other conifers, but appears to be absent in other gymnosperms. Phylogenetic analyses of both protein and DNA sequences reveal that conifers EN(+)PLEs, or Dryads, form a monophyletic group clustering within a clade of primarily arthropod elements. Additionally, no EN(+)PLEs were detected in 1,928 genome assemblies from 1,029 nonmetazoan and nonconifer genomes from 14 major eukaryotic lineages. These findings indicate that Dryads emerged following an ancient horizontal transfer of EN(+)PLEs from arthropods to a common ancestor of conifers approximately 340 Ma. This represents one of the oldest known interspecific transmissions of TEs, and the most conspicuous case of DNA transfer between animals and plants. PMID:27190138

Conodont biostratigraphy of the Permian-Triassic boundary sequence at Lung Cam, Vietnam

USGS Publications Warehouse

Wardlaw, Bruce R.; Nestell, Merlynd K.; Nestell, Galina P.; Ellwood, Brooks B.; Lan, Luu Thi Phuong

2015-01-01

The occurrences of a few specimens of Clarkina and many specimens of Hindeodus at the Permian-Triassic boundary section at Lung Cam, Vietnam allow accurate graphic correlation to the P-T boundary stratotype at Meishan, China. One species of Clarkina, ten species and two subspecies of Hindeodus, and the apparatuses of Hindeodus latidentatus and Merrillina ultima are described and illustrated.

Ammonites and magnetostratigraphy of the Berriasian-Valanginian boundary deposits from eastern Crimea

NASA Astrophysics Data System (ADS)

Arkadiev, Vladimir V.; Grishchenko, Vladimir A.; Guzhikov, Andrei Yu.; Manikin, Aleksey G.; Savelieva, Yuliya N.; Feodorova, Anna A.; Shurekova, Olga V.

2017-08-01

Euthymi, Crassicostatum and Callisto ammonite subzones, correlable with Paramimounum, Picteti, and Alpillensis subzones and probably with the Late Berriasian Otopeta Subzone of the Boissieri Standard Zone have been recognized in calcareous clays of the Berriasian-Valanginian boundary sequence in the Feodosiya district (eastern Crimea). The ammonite Leptoceras studeri (Ooster) suggests Late Berriasian to Early Valanginian age. Geomagnetic polarity indicates M16-M14r magnetozones. Therefore, the base of the Valanginian sequence in eastern Crimea should be placed within the M14r magnetozone.

Community and functional shifts in ammonia oxidizers across terrestrial and marine (soil/sediment) boundaries in two coastal Bay ecosystems.

PubMed

Zhang, Li-Mei; Duff, Aoife M; Smith, Cindy J

2018-04-24

Terrestrial-marine boundaries are significant sites of biogeochemical activity with delineated gradients from land to sea. While niche differentiation of ammonia-oxidizing archaea (AOA) and bacteria (AOB) driven by pH and nitrogen is well known, the patterns and environmental drivers of AOA and AOB community structure and activity across soil-sediment boundaries have not yet been determined. In this study, nitrification potential rate, community composition and transcriptional activity of AOA and AOB in soil, soil/sediment interface and sediments of two coastal Bays were characterized using a combination of field investigations and microcosm incubations. At DNA level, amoA gene abundances of AOA were significantly greater than AOB in soil, while in sediments AOB were significantly more abundant than AOA, but at the soil/sediment interface there were equal numbers of AOA and AOB amoA genes. Microcosm incubations provided further evidence, through qPCR and DGGE-sequencing analysis of amoA transcripts, that AOA were active in soil, AOB in sediment and both AOA and AOB were active at the soil/sediment interface. The AOA and AOB community composition shifted across the coastal soil-interface-sediment gradient with salinity and pH identified as major environmental drivers. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Supplement to the ICRPG turbulent boundary layer nozzle analysis computer program

NASA Technical Reports Server (NTRS)

Omori, S.; Gross, K. W.

1972-01-01

A supplement is presented for a turbulent boundary layer nozzle analysis computer program. It describes the program calculation sequence and presents a detailed documentation of each subroutine. Important equations are derived explicitly, and improvements to the program are discussed.

A composite lithology log while drilling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tannenbaum, E.; Sutcliffe, B.; Franks, A.

A new method for producing a computerized composite lithology log (CLL) while drilling by integrating MWD (measurement while drilling) and surface data is described. At present, lithology logs are produced at the well site by mud loggers. They provide basic description and relative amounts of lithologies. Major difficulties are encountered in relating the cuttings to their original formations due to mixing in the drilling mud while transporting to the surface, sloughing shales, flawed sampling, etc. This results in a poor control on the stratigraphic sequence and on the depth of formation boundaries. A composite log can be produced after drillingmore » this additional inputs such as wireline, petrography, and paleontology. This process is labor intensive and expensive. The CLL integrates three types of data (MWD mechanical, MWD geophysical, and surface cuttings) acquired during drilling, in three time stages: (1) Real Time. MWD drilling mechanical data including the rate of penetration and the downhole torque. This stage would provide bed boundaries and some inferred lithology. This would assist the driller with immediate drilling decisions and determine formation tops for coring, casing point, and correlation. (2) MWD Time. Recomputation of the above by adding MWD geophysical data (gamma-ray, resistivity, neutron-density). This stage would upgrade the lithology inference, and give higher resolution to bed boundaries, (3) Lag Time. Detailed analysis of surface cuttings to confirm the inferred lithologies. This last input results in a high-quality CLL with accurate lithologies and bed boundaries.« less

Early animal evolution: emerging views from comparative biology and geology

NASA Technical Reports Server (NTRS)

Knoll, A. H.; Carroll, S. B.

1999-01-01

The Cambrian appearance of fossils representing diverse phyla has long inspired hypotheses about possible genetic or environmental catalysts of early animal evolution. Only recently, however, have data begun to emerge that can resolve the sequence of genetic and morphological innovations, environmental events, and ecological interactions that collectively shaped Cambrian evolution. Assembly of the modern genetic tool kit for development and the initial divergence of major animal clades occurred during the Proterozoic Eon. Crown group morphologies diversified in the Cambrian through changes in the genetic regulatory networks that organize animal ontogeny. Cambrian radiation may have been triggered by environmental perturbation near the Proterozoic-Cambrian boundary and subsequently amplified by ecological interactions within reorganized ecosystems.

Thermal control of low-pressure fractionation processes. [in basaltic magma solidification

NASA Technical Reports Server (NTRS)

Usselman, T. M.; Hodge, D. S.

1978-01-01

Thermal models detailing the solidification paths for shallow basaltic magma chambers (both open and closed systems) were calculated using finite-difference techniques. The total solidification time for closed chambers are comparable to previously published calculations; however, the temperature-time paths are not. These paths are dependent on the phase relations and the crystallinity of the system, because both affect the manner in which the latent heat of crystallization is distributed. In open systems, where a chamber would be periodically replenished with additional parental liquid, calculations indicate that the possibility is strong that a steady-state temperature interval is achieved near a major phase boundary. In these cases it is straightforward to analyze fractionation models of the basaltic liquid evolution and their corresponding cumulate sequences. This steady thermal fractionating state can be invoked to explain large amounts of erupted basalts of similar composition over long time periods from the same volcanic center and some rhythmically layered basic cumulate sequences.

Signatures of natural selection and ecological differentiation in microbial genomes.

PubMed

Shapiro, B Jesse

2014-01-01

We live in a microbial world. Most of the genetic and metabolic diversity that exists on earth - and has existed for billions of years - is microbial. Making sense of this vast diversity is a daunting task, but one that can be approached systematically by analyzing microbial genome sequences. This chapter explores how the evolutionary forces of recombination and selection act to shape microbial genome sequences, leaving signatures that can be detected using comparative genomics and population-genetic tests for selection. I describe the major classes of tests, paying special attention to their relative strengths and weaknesses when applied to microbes. Specifically, I apply a suite of tests for selection to a set of closely-related bacterial genomes with different microhabitat preferences within the marine water column, shedding light on the genomic mechanisms of ecological differentiation in the wild. I will focus on the joint problem of simultaneously inferring the boundaries between microbial populations, and the selective forces operating within and between populations.

The Chicxulub Multiring Impact Crater and the Cretaceous/Paleogene Boundary: Results From Geophysical Surveys and Drilling

NASA Astrophysics Data System (ADS)

Urrutia-Fucugauchi, J.; Perez-Cruz, Ligia

2010-03-01

The Chicxulub crater has attracted considerable attention as one of the three largest terrestrial impact structures and its association with the Cretaceous/Paleogene boundary (K/Pg). Chicxulub is a 200 km-diameter multi-ring structure formed 65.5 Ma ago in the Yucatan carbonate platform in the southern Gulf of Mexico and which has since been buried by Paleogene and Neogene carbonates. Chicxulub is one of few large craters with preserved ejecta deposits, which include the world-wide K/Pg boundary clay layer. The impact has been related to the global major environmental and climatic effects and the organism mass extinction that mark the K/Pg boundary, which affected more than 70 % of organisms, including the dinosaurs, marine and flying reptiles, ammonites and a large part of the marine microorganisms. The impact and crater formation occur instantaneously, with excavation of the crust down to 25 km depths in fractions of second and lower crust uplift and crater formation in a few hundreds of seconds. Energy released by impact and crustal deformation generates seismic waves traveling the whole Earth, and resulting in intense fracturing and deformation at the target site. Understanding of the physics of impacts on planetary surfaces and modeling of processes of crustal deformation, rheological behavior of materials at high temperatures and pressures remain a major challenge in geosciences. Study of the Chicxulub crater and the global effects and mass extinction requires inter- and multidisciplinary approaches, with researchers from many diverse fields beyond the geosciences. With no surface exposures, geophysical surveys and drilling are required to study the crater. Differential compaction between the impact breccias and the surrounding carbonate rocks has produced a ring-fracture structure that at the surface reflects in a small topographic depression and the karstic cenote ring. The crater structure, located half offshore and half on-land, has been imaged by different geophysical aerial, land and marine methods including gravity, magnetics, electromagnetics and seismic refraction and reflection. The impact lithologies and carbonate sequence have been cored as part of several drilling projects. Here we analyze the stratigraphy of Chicxulub from borehole logging data and core analyses, with particular reference to studies on CSDP Yaxcopoil-1 and UNAM Santa Elena boreholes. Analyses of core samples have examined the stratigraphy of the cover carbonate sequence, impact breccia contact and implications for impact age, K/Pg global correlations and paleoenvironmental conditions following impact. The K/Pg age for Chicxulub has been supported from different studies, including Ar/Ar dating, magnetic polarity stratigraphy, geochemistry and biostratigraphy. A Late Maastrichtian age has also been proposed for Chicxulub from studies in Yaxcopoil-1 basal Paleocene carbonates, with impact occurring 300 ka earlier predating the K/Pg boundary. This proposal calls attention to the temporal resolution of stratigraphic and chronological methods, and the need for further detailed analyses of the basal carbonate sections in existing boreholes and new drilling/coring projects. Stratigraphy of impact ejecta and basal sediments in Yaxcopoil-1 and UNAM boreholes indicates a hiatus in the basal sequence. Modeling of post- impact processes suggest erosion effects due to seawater back surge, block slumping and partial rim collapse of post-impact crater modification. Analyses of stable isotopes and magnetostratigraphic data for the Paleocene carbonate sequences in Yaxcopoil-1 and Santa Elena boreholes permit to investigate the post- impact processes, depositional conditions and age of basal sediments. Correlation of stable isotopes with the global pattern for marine carbonate sediments provides a stratigraphic framework for the basal Paleocene carbonates. The analyses confirm a K/Pg boundary age for the Chicxulub impact. References: Collins et al, 2008. Earth Planetary Science Letters 270, 221-230; Gulick et al, 2008. Nature Geoscience 1, 131-135; Hildebrand et al, 1991. Geology 19: 867-871; Hildebrand, A.R. et al, 1998. Geological Society Sp. Publ 140, 153-173; Kring et al., 2004. Meteoritics Planetary Science 39, 879-897; Sharpton et al, 1992. Nature 359: 819-821; Urrutia Fucugauchi et al, 2004. Meteoritics Planetary Science 39: 787-790; Urrutia Fucugauchi et al, 2008. Comptes Rendus Geosciences 341, 801-810; Urrutia Fucugauchi & Perez Cruz, 2009. International Geology Review 51, doi: 10.1080/00206810902867161.

A robust interpolation procedure for producing tidal current ellipse inputs for regional and coastal ocean numerical models

NASA Astrophysics Data System (ADS)

Byun, Do-Seong; Hart, Deirdre E.

2017-04-01

Regional and/or coastal ocean models can use tidal current harmonic forcing, together with tidal harmonic forcing along open boundaries in order to successfully simulate tides and tidal currents. These inputs can be freely generated using online open-access data, but the data produced are not always at the resolution required for regional or coastal models. Subsequent interpolation procedures can produce tidal current forcing data errors for parts of the world's coastal ocean where tidal ellipse inclinations and phases move across the invisible mathematical "boundaries" between 359° and 0° degrees (or 179° and 0°). In nature, such "boundaries" are in fact smooth transitions, but if these mathematical "boundaries" are not treated correctly during interpolation, they can produce inaccurate input data and hamper the accurate simulation of tidal currents in regional and coastal ocean models. These avoidable errors arise due to procedural shortcomings involving vector embodiment problems (i.e., how a vector is represented mathematically, for example as velocities or as coordinates). Automated solutions for producing correct tidal ellipse parameter input data are possible if a series of steps are followed correctly, including the use of Cartesian coordinates during interpolation. This note comprises the first published description of scenarios where tidal ellipse parameter interpolation errors can arise, and of a procedure to successfully avoid these errors when generating tidal inputs for regional and/or coastal ocean numerical models. We explain how a straightforward sequence of data production, format conversion, interpolation, and format reconversion steps may be used to check for the potential occurrence and avoidance of tidal ellipse interpolation and phase errors. This sequence is demonstrated via a case study of the M2 tidal constituent in the seas around Korea but is designed to be universally applicable. We also recommend employing tidal ellipse parameter calculation methods that avoid the use of Foreman's (1978) "northern semi-major axis convention" since, as revealed in our analysis, this commonly used conversion can result in inclination interpolation errors even when Cartesian coordinate-based "vector embodiment" solutions are employed.

Magnetotelluric evidence for a deep-crustal mineralizing system beneath the Olympic Dam iron oxide copper-gold deposit, southern Australia

NASA Astrophysics Data System (ADS)

Heinson, Graham S.; Direen, Nicholas G.; Gill, Rob M.

2006-07-01

The iron oxide copper-gold Olympic Dam deposit, situated along the margin of the Proterozoic Gawler craton, South Australia, is the world's largest uranium deposit and sixth-largest copper deposit; it also contains significant reserves of gold, silver, and rare earth elements. Gaining a better understanding of the mechanisms for genesis of the economic liberalization is fundamental for defining exploration models in similar crustal settings. To delineate crustal structures that may constrain mineral system fluid pathways, coincident deep crustal seismic and magnetotelluric (MT) transects were obtained along a 220 km section that crosses Olympic Dam and the major crustal boundaries. In this paper we present results from 58 long-period (10 104 s) MT sites, with site spacing of 5 10 km. A two-dimensional inversion of MT data from 33 sites to a depth of 100 km shows four notable features: (1) sedimentary cover sequences with low resistivity (<20 Ω·m) thicken to 10 km toward the northern cover sequences of the Adelaide Rift Complex; (2) a northeast-dipping crustal boundary separates a highly resistive (>1000 Ω·m) Archean crustal core from a more conductive crust and mantle to the north (typically <500 Ω·m); (3) to the north of Olympic Dam, the upper-middle crust to ˜20 km is quite resistive (˜1000 Ω·m), but the lower crust is much more conductive (<100 Ω·m); and (4) beneath Olympic Dam, we image a low-resistivity region (<100 Ω·m) throughout the crust, coincident with a seismically transparent region. We argue that the cause of the low-resistivity and low-reflectivity region beneath Olympic Dam may be due to the upward movement of CO2-bearing volatiles near the time of deposit formation that precipitated conductive graphite liberalization along grain boundaries, simultaneously annihilating acoustic impedance boundaries. The source of the volatiles may be from the mantle degassing or retrograde metamorphism of the lower crust associated with Proterozoic crustal deformation.

Apical Coarticulation at Juncture Boundaries

ERIC Educational Resources Information Center

Lewis, J.; And Others

1975-01-01

Sentences were read by six informants to determine the presence or absence of /n/ in /nth/ sequences. The sentences contained seven different levels of juncture with /nth/ occurring in word final position, intervocalically, and across word boundaries, among other places. Dental coarticulation was not hindered by most junctures. (SC)

Use of Proper Orthogonal Decomposition Towards Time-resolved Image Analysis of Sprays

DTIC Science & Technology

2011-03-15

High-speed movies of optically dense sprays exiting a Gas-Centered Swirl Coaxial (GCSC) injector are subjected to image analysis to determine spray...sequence prior to image analysis . Results of spray morphology including spray boundary, widths, angles and boundary oscillation frequencies, are

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

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

Elucidating the 16S rRNA 3' boundaries and defining optimal SD/aSD pairing in Escherichia coli and Bacillus subtilis using RNA-Seq data.

PubMed

Wei, Yulong; Silke, Jordan R; Xia, Xuhua

2017-12-15

Bacterial translation initiation is influenced by base pairing between the Shine-Dalgarno (SD) sequence in the 5' UTR of mRNA and the anti-SD (aSD) sequence at the free 3' end of the 16S rRNA (3' TAIL) due to: 1) the SD/aSD sequence binding location and 2) SD/aSD binding affinity. In order to understand what makes an SD/aSD interaction optimal, we must define: 1) terminus of the 3' TAIL and 2) extent of the core aSD sequence within the 3' TAIL. Our approach to characterize these components in Escherichia coli and Bacillus subtilis involves 1) mapping the 3' boundary of the mature 16S rRNA using high-throughput RNA sequencing (RNA-Seq), and 2) identifying the segment within the 3' TAIL that is strongly preferred in SD/aSD pairing. Using RNA-Seq data, we resolve previous discrepancies in the reported 3' TAIL in B. subtilis and recovered the established 3' TAIL in E. coli. Furthermore, we extend previous studies to suggest that both highly and lowly expressed genes favor SD sequences with intermediate binding affinity, but this trend is exclusive to SD sequences that complement the core aSD sequences defined herein.

Inter-plate aseismic slip on the subducting plate boundaries estimated from repeating earthquakes

NASA Astrophysics Data System (ADS)

Igarashi, T.

2015-12-01

Sequences of repeating earthquakes are caused by repeating slips of small patches surrounded by aseismic slip areas at plate boundary zones. Recently, they have been detected in many regions. In this study, I detected repeating earthquakes which occurred in Japan and the world by using seismograms observed in the Japanese seismic network, and investigated the space-time characteristics of inter-plate aseismic slip on the subducting plate boundaries. To extract repeating earthquakes, I calculate cross-correlation coefficients of band-pass filtering seismograms at each station following Igarashi [2010]. I used two data-set based on USGS catalog for about 25 years from May 1990 and JMA catalog for about 13 years from January 2002. As a result, I found many sequences of repeating earthquakes in the subducting plate boundaries of the Andaman-Sumatra-Java and Japan-Kuril-Kamchatka-Aleutian subduction zones. By applying the scaling relations among a seismic moment, recurrence interval and slip proposed by Nadeau and Johnson [1998], they indicate the space-time changes of inter-plate aseismic slips. Pairs of repeating earthquakes with the longest time interval occurred in the Solomon Islands area and the recurrence interval was about 18.5 years. The estimated slip-rate is about 46 mm/year, which correspond to about half of the relative plate motion in this area. Several sequences with fast slip-rates correspond to the post-seismic slips after the 2004 Sumatra-Andaman earthquake (M9.0), the 2006 Kuril earthquake (M8.3), the 2007 southern Sumatra earthquake (M8.5), and the 2011 Tohoku-oki earthquake (M9.0). The database of global repeating earthquakes enables the comparison of the inter-plate aseismic slips of various plate boundary zones of the world. I believe that I am likely to detect more sequences by extending analysis periods in the area where they were not found in this analysis.

Geographic patterns of genetic differentiation among killer whales in the northern North Pacific.

PubMed

Parsons, Kim M; Durban, John W; Burdin, Alexander M; Burkanov, Vladimir N; Pitman, Robert L; Barlow, Jay; Barrett-Lennard, Lance G; LeDuc, Richard G; Robertson, Kelly M; Matkin, Craig O; Wade, Paul R

2013-01-01

The difficulties associated with detecting population boundaries have long constrained the conservation and management of highly mobile, wide-ranging marine species, such as killer whales (Orcinus orca). In this study, we use data from 26 nuclear microsatellite loci and mitochondrial DNA sequences (988bp) to test a priori hypotheses about population subdivisions generated from a decade of killer whale surveys across the northern North Pacific. A total of 462 remote skin biopsies were collected from wild killer whales primarily between 2001 and 2010 from the northern Gulf of Alaska to the Sea of Okhotsk, representing both the piscivorous "resident" and the mammal-eating "transient" (or Bigg's) killer whales. Divergence of the 2 ecotypes was supported by both mtDNA and microsatellites. Geographic patterns of genetic differentiation were supported by significant regions of genetic discontinuity, providing evidence of population structuring within both ecotypes and corroborating direct observations of restricted movements of individual whales. In the Aleutian Islands (Alaska), subpopulations, or groups with significantly different mtDNA and microsatellite allele frequencies, were largely delimited by major oceanographic boundaries for resident killer whales. Although Amchitka Pass represented a major subdivision for transient killer whales between the central and western Aleutian Islands, several smaller subpopulations were evident throughout the eastern Aleutians and Bering Sea. Support for seasonally sympatric transient subpopulations around Unimak Island suggests isolating mechanisms other than geographic distance within this highly mobile top predator.

A species boundary within the Chinese Kurixalus odontotarsus species group (Anura: Rhacophoridae): New insights from molecular evidence.

PubMed

Yu, Guohua; Zhang, Mingwang; Yang, Junxing

2010-09-01

We construct the phylogeny of the Kurixalus odontotarsus species group using two mitochondrial (12S rRNA and 16S rRNA) genes in an attempt to delimit species boundaries within the Chinese K. odontotarsus group. With strong support values, three major clades are obtained, and all phylogenetic analyses reject monophyly of K. odontotarsus. The Tibetan lineage of K. odontotarsus was clustered with Kurixalus verrucosus from Myanmar (labeled Clade I); K. odontotarsus haplotypes from the type locality and nearby regions formed a distinct clade (labeled Clade II), and K. odontotarsus haplotypes from other places, together with those from Kurixalus bisacculus, K. verrucosus from Vietnam, and Kurixalus hainanus, formed a distinct clade (labeled Clade III). Clade II is the sister taxon to Clade III. The average uncorrected p-distance of 16S rRNA sequences between these three major clades range from 3.11% to 7.88%, which is obviously higher than that within these three major clades (0.03-1.89%). We propose that K. odontotarsus, K. bisacculus, and K. verrucosus should be treated as three independent species. The Tibetan lineage of K. odontotarsus does not belong to K. odontotarsus, and we tentatively place it in K. verrucosus. Kurixalus hainanus is considered a synonym of K. bisacculus. The distribution range of K. bisacculus should be expanded widely to include most regions of South China, and in China the distribution of K. odontotarsus should be limited to its type locality and nearby regions. Copyright 2010 Elsevier Inc. All rights reserved.

Salix transect of Europe: structured genetic variation and isolation-by-distance in the nettle psyllid, Trioza urticae (Psylloidea, Hemiptera), from Greece to Arctic Norway

PubMed Central

Wonglersak, Rungtip; Cronk, Quentin; Percy, Diana

2017-01-01

Abstract Background The common nettle (Urtica dioica L.) is co-associated with willows (Salix spp.) in riparian habitats across Europe. We sampled the widespread nettle psyllid, Trioza urticae (Linné, 1758), from Urtica in willow habitats on a megatransect of Europe from the Aegean to the Arctic Ocean. The aim of this study was to use an unusually widespread insect to assess the influence of geographic distances and natural geographic barriers on patterns of genetic variation and haplotype distribution. New information Phylogeographic analysis using DNA sequences of two mtDNA regions, COI and cytB, shows that T. urticae specimens are organized into four regional groups (southern, central, northern and arctic). These groups are supported by both phylogenetic analysis (four geographically-based clades) and network analysis (four major haplotype groups). The boundary between southern and central groups corresponds to the Carpathian Mountains and the boundary between the central and northern groups corresponds to the Gulf of Finland. Overall these groups form a latitudinal cline in genetic diversity, which decreases with increasing latitude. PMID:28325977

Seismic images of a Grenvillian terrane boundary

USGS Publications Warehouse

Milkereit, B.; Forsyth, D. A.; Green, A.G.; Davidson, A.; Hanmer, S.; Hutchinson, Deborah R.; Hinze, W. J.; Mereu, R.F.

1992-01-01

A series of gently dipping reflection zones extending to mid-crustal depths is recorded by seismic data from Lakes Ontario and Erie. These prominent reflection zones define a broad complex of southeast-dipping ductile thrust faults in the interior of the Grenville orogen. One major reflection zone provides the first image of a proposed Grenvillian suture—the listric boundary zone between allochthonous terranes of the Central Gneiss and Central Metasedimentary belts. Curvilinear bands of reflections that may represent "ramp folds" and "ramp anticlines" that originally formed in a deep crustal-scale duplex abut several faults. Vertical stacking of some curvilinear features suggests coeval or later out-of-sequence faulting of imbricated and folded thrust sheets. Grenvillian structure reflections are overlain by a thin, wedge-shaped package of shallow-dipping reflections that probably originates from sediments deposited in a local half graben developed during a period of post-Grenville extension. This is the first seismic evidence for such extension in this region, which could have occurred during terminal collapse of the Grenville orogen, or could have marked the beginning of pre-Appalachian continental rifting.

Sequence stratigraphy of the ANDRILL Southern McMurdo Sound (SMS) project drillcore, Antarctica: an expanded, near-field record of Antarctic Early to Middle Miocene climate and relative sea-level change

NASA Astrophysics Data System (ADS)

Fielding, C. R.; Browne, G. H.; Field, B.; Florindo, F.; Harwood, D. M.; Krissek, L. A.; Levy, R. H.; Panter, K.; Passchier, S.; Pekar, S. F.; SMS Science Team

2008-12-01

Present understanding of Antarctic climate change during the Early to Middle Miocene, including definition of major cycles of glacial expansion and contraction, relies in large part on stable isotope proxy records from Ocean Drilling Program cores. Here, we present a sequence stratigraphic analysis of the Southern McMurdo Sound drillcore (AND-2A), which was acquired during the Austral Spring of 2007. This core offers a hitherto unavailable ice-proximal stratigraphic archive of the Early to Middle Miocene from a high-accommodation Antarctic continental margin setting, and provides clear evidence of repeated fluctuations in climate, ice expansion/contraction and attendant sea-level change over the period 20-14 Ma, with a more fragmentary record of the post-14 Ma period. A succession of seventy sequences is recognized, each bounded by a significant facies dislocation (sequence boundary), composed internally of deposits of glacimarine to open shallow marine environments, and each typically dominated by the transgressive systems tract. From changes in facies abundances and sequence character, a series of long-term (m.y.) changes in climate and relative sea-level is identified. The lithostratigraphy can be correlated confidently to glacial events Mi1b and Mi2, to the Miocene Climatic Optimum, and to the global eustatic sea-level curve. SMS provides a detailed, direct, ice-proximal reference point from which to evaluate stable isotope proxy records for Neogene Antarctic paleoclimate.

The mitochondrial intermembrane loop region of rat carnitine palmitoyltransferase 1A is a major determinant of its malonyl-CoA sensitivity.

PubMed

Borthwick, Karen; Jackson, Vicky N; Price, Nigel T; Zammit, Victor A

2006-11-03

Carnitine palmitoyltransferase (CPT) 1A adopts a polytopic conformation within the mitochondrial outer membrane, having both the N- and C-terminal segments on the cytosolic aspect of the membrane and a loop region connecting the two transmembrane (TM) segments protruding into the inter membrane space. In this study we demonstrate that the loop exerts major effects on the sensitivity of the enzyme to its inhibitor, malonyl-CoA. Insertion of a 16-residue spacer between the C-terminal part of the loop sequence (i.e. between residues 100 and 101) and TM2 (which is predicted to start at residue 102) increased the sensitivity to malonyl-CoA inhibition of the resultant mutant protein by more than 10-fold. By contrast, the same insertion made between TM1 and the loop had no effects on the kinetic properties of the enzyme, indicating that effects on the catalytic C-terminal segment were specifically induced by loop-TM2 interactions. Enhanced sensitivity was also observed in all mutants in which the native TM2-loop pairing was disrupted either by making chimeras in which the loops and TM2 segments of CPT 1A and CPT 1B were exchanged or by deleting successive 9-residue segments from the loop sequence. The data suggest that the sequence spanning the loop-TM2 boundary determines the disposition of this TM in the membrane so as to alter the conformation of the C-terminal segment and thus affect its interaction with malonyl-CoA.

30 CFR 779.24 - Maps: General requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

..., included in or contiguous to the permit area; (b) The boundaries of land within the proposed permit area... boundaries of all areas proposed to be affected over the estimated total life of the proposed surface mining activities, with a description of size, sequence, and timing of the mining of sub-areas for which it is...

30 CFR 783.24 - Maps: General requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

..., included in or contiguous to the permit area; (b) The boundaries of land within the proposed permit area... boundaries of all areas proposed to be affected over the estimated total life of the underground mining activities, with a description of size, sequence and timing of the mining of sub-areas for which it is...

30 CFR 779.24 - Maps: General requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

..., included in or contiguous to the permit area; (b) The boundaries of land within the proposed permit area... boundaries of all areas proposed to be affected over the estimated total life of the proposed surface mining activities, with a description of size, sequence, and timing of the mining of sub-areas for which it is...

30 CFR 783.24 - Maps: General requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

..., included in or contiguous to the permit area; (b) The boundaries of land within the proposed permit area... boundaries of all areas proposed to be affected over the estimated total life of the underground mining activities, with a description of size, sequence and timing of the mining of sub-areas for which it is...

Divisions of Geologic Time - Major Chronostratigraphic and Geochronologic Units

USGS Publications Warehouse

,

2007-01-01

Introduction Effective communication in the geosciences requires consistent uses of stratigraphic nomenclature, especially divisions of geologic time. A geologic time scale is composed of standard stratigraphic divisions based on rock sequences and calibrated in years (Harland and others, 1982). Over the years, the development of new dating methods and refinement of previous ones have stimulated revisions to geologic time scales. Since the mid-1990s, geologists from the U.S. Geological Survey (USGS), State geological surveys, academia, and other organizations have sought a consistent time scale to be used in communicating ages of geologic units in the United States. Many international debates have occurred over names and boundaries of units, and various time scales have been used by the geoscience community.

Using deep RNA sequencing for the structural annotation of the laccaria bicolor mycorrhizal transcriptome.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larsen, P. E.; Trivedi, G.; Sreedasyam, A.

2010-07-06

Accurate structural annotation is important for prediction of function and required for in vitro approaches to characterize or validate the gene expression products. Despite significant efforts in the field, determination of the gene structure from genomic data alone is a challenging and inaccurate process. The ease of acquisition of transcriptomic sequence provides a direct route to identify expressed sequences and determine the correct gene structure. We developed methods to utilize RNA-seq data to correct errors in the structural annotation and extend the boundaries of current gene models using assembly approaches. The methods were validated with a transcriptomic data set derivedmore » from the fungus Laccaria bicolor, which develops a mycorrhizal symbiotic association with the roots of many tree species. Our analysis focused on the subset of 1501 gene models that are differentially expressed in the free living vs. mycorrhizal transcriptome and are expected to be important elements related to carbon metabolism, membrane permeability and transport, and intracellular signaling. Of the set of 1501 gene models, 1439 (96%) successfully generated modified gene models in which all error flags were successfully resolved and the sequences aligned to the genomic sequence. The remaining 4% (62 gene models) either had deviations from transcriptomic data that could not be spanned or generated sequence that did not align to genomic sequence. The outcome of this process is a set of high confidence gene models that can be reliably used for experimental characterization of protein function. 69% of expressed mycorrhizal JGI 'best' gene models deviated from the transcript sequence derived by this method. The transcriptomic sequence enabled correction of a majority of the structural inconsistencies and resulted in a set of validated models for 96% of the mycorrhizal genes. The method described here can be applied to improve gene structural annotation in other species, provided that there is a sequenced genome and a set of gene models.« less

Diffusion modelling of metamorphic layered coronas with stability criterion and consideration of affinity

NASA Astrophysics Data System (ADS)

Ashworth, J. R.; Sheplev, V. S.

1997-09-01

Layered coronas between two reactant minerals can, in many cases, be attributed to diffusion-controlled growth with local equilibrium. This paper clarifies and unifies the previous approaches of various authors to the simplest form of modelling, which uses no assumed values for thermochemical quantities. A realistic overall reaction must be estimated from measured overall proportions of minerals and their major element compositions. Modelling is not restricted to a particular number of components S, relative to the number of phases Φ. IfΦ > S + 1, the overall reaction is a combination of simultaneous reactions. The stepwise method, solving for the local reaction at each boundary in turn, is extended to allow for recurrence of a mineral (its presence in two parts of the layer structure separated by a gap). The equations are also given in matrix form. A thermodynamic stability criterion is derived, determining which layer sequence is truly stable if several are computable from the same inputs. A layer structure satisfying the stability criterion has greater growth rate (and greater rate of entropy production) than the other computable layer sequences. This criterion of greatest entropy production is distinct from Prigogine's theorem of minimum entropy production, which distinguishes the stationary or quasi-stationary state from other states of the same layer sequence. The criterion leads to modification of previous results for coronas comprising hornblende, spinel, and orthopyroxene between olivine (Ol) and plagioclase (Pl). The outcome supports the previous inference that Si, and particularly Al, commonly behave as immobile relative to other cation-forming major elements. The affinity (-ΔG) of a corona-forming reaction is estimated, using previous estimates of diffusion coefficient and the duration t of reaction, together with a new model quantity (-ΔG) *. For an example of the Ol + Pl reaction, a rough calculation gives (-ΔG) > 1.7RT (per mole of P1 consumed, based on a 24-oxygen formula for Pl). At 600-700°C, this represents (-ΔG) > 10kJ mol -1 and departure from equilibrium temperature by at least ˜ 100°C. The lower end of this range is petrologically reasonable and, for t < 100Ma, corresponds to a Fick's-law diffusion coefficient for Al, DAl > 10 -25m 2s -1, larger than expected for lattice diffusion but consistent with fluid-absent grain-boundary diffusion and small concentration gradients.

Dynamic modeling of normal faults of the 2016 Central Italy earthquake sequence

NASA Astrophysics Data System (ADS)

Aochi, Hideo

2017-04-01

The earthquake sequence of the Central Italy in 2016 are characterized mainly by the Mw6.0 24th August, Mw5.9 26th October and Mw6.4 30th October as well as two Mw5.4 earthquakes (24th August, 26th October) (catalogue INGV). They all show normal faulting mechanisms corresponding to the Apennines's tectonics. They are aligned briefly along NNW-SSE axis, and they may not be on a single continuous fault plane. Therefore, dynamic rupture modeling of sequences should be carried out supposing co-planar normal multiple segments. We apply a Boundary Domain Method (BDM, Goto and Bielak, GJI, 2008) coupling a boundary integral equation method and a domain-based method, namely a finite difference method in this study. The Mw6.0 24th August earthquake is modeled. We use the basic information of hypocenter position, focal mechanism and potential ruptured dimension from the INGV catalogue and Tinti et al., GRL, 2016), and begin with a simple condition (homogeneous boundary condition). From our preliminary simulations, it is shown that a uniformly extended rupture model does not fit the near-field ground motions and localized heterogeneity would be required.

Incised valley fill interpretation for Mississippian Black Hand Sandstone, Appalachian Basin, USA: Implications for glacial eustasy at Kinderhookian-Osagean (Tn2-Tn3) boundary

USGS Publications Warehouse

Matchen, D.L.; Kammer, T.W.

2006-01-01

Lower Mississippian strata of east-central Ohio are predominantly fine-grained marine deposits of the Cuyahoga and Logan formations. Within these sediments is the Black Hand Sandstone of the Cuyahoga Formation. The Black Hand Sandstone is a multistory, crossbedded, coarse-grained conglomeratic sandstone. The contact between the Black Hand Sandstone and the subjacent Cuyahoga Formation is sharp and scoured, with intraclasts of the Cuyahoga Formation incorporated into the basal Black Hand Sandstone. The Black Hand Sandstone was previously thought to represent a distributary channel deposit; however, the combination of lithofacies and architectural elements indicates deposition in a braided stream setting. The Cuyahoga Formation was deposited in a shallow marine setting. The erosional basal contact of the Black Hand Sandstone and the juxtaposition of fluvial and marine sediments suggests a sequence boundary. The geographic distribution of the Black Hand Sandstone combined with the evidence for a sequence boundary suggests deposition in an incised valley. The age of the Black Hand Sandstone is key to inferring the causes of valley incision. The Black Hand Sandstone is nearly devoid of body fossils, necessitating a biostratigraphic analysis of the surrounding Cuyahoga and Logan formations. Analysis indicates the Logan Formation is early Osagean age. Data from the Cuyahoga Formation suggest a Kinderhookian age with a possible transition to the Osagean in the uppermost Cuyahoga Formation. This constrains the age of the Black Hand Sandstone to the transition at the Kinderhookian-Osagean boundary. Recent reports indicate late Kinderhookian (Tournaisian, Tn2) Gondwanan glaciation based upon tillites and sharp excursions in stable-isotope curves. A glacio-eustatic fall in sea level is inferred to have caused incision of the Cuyahoga Formation, followed by deposition of the Black Hand Sandstone and Logan Formation during the subsequent sea level rise. The associated unconformity correlates to the sequence boundary at the Kinderhookian-Osagean boundary in the stratotype area of North America, and the correlative Tn2-Tn3 boundary worldwide, supporting the hypothesis of a global eustatic event at this time. ?? 2006 Elsevier B.V. All rights reserved.

New Insights into the present-day kinematics of the central and western Papua New Guinea from GPS

NASA Astrophysics Data System (ADS)

Koulali, A.; Tregoning, P.; McClusky, S.; Stanaway, R.; Wallace, L.; Lister, G.

2015-08-01

New Guinea is a region characterized by rapid oblique convergence between the Pacific and Australian tectonic plates. The detailed tectonics of the region, including the partitioning of relative block motions and fault slip rates within this complex boundary plate boundary zone are still not well understood. In this study, we quantify the distribution of the deformation throughout the central and western parts of Papua New Guinea (PNG) using 20 yr of GPS data (1993-2014). We use an elastic block model to invert the regional GPS velocities as well as earthquake slip vectors for the location and rotation rates of microplate Euler poles as well as fault slip parameters in the region. Convergence between the Pacific and the Australian plates is accommodated in northwestern PNG largely by the New Guinea Trench with rates exceeding 90 mm yr-1, indicating that this is the major active interplate boundary. However, some convergent deformation is partitioned into a shear component with ˜12 per cent accommodated by the Bewani-Torricelli fault zone and the southern Highlands Fold-and-Thrust Belt. New GPS velocities in the eastern New Guinea Highlands region have led to the identification of the New Guinea Highlands and the Papuan Peninsula being distinctly different blocks, separated by a boundary through the Aure Fold-and-Thrust Belt complex which accommodates an estimated 4-5 mm yr-1 of left-lateral and 2-3 mm yr-1 of convergent motion. This implies that the Highlands Block is rotating in a clockwise direction relative to the rigid Australian Plate, consistent with the observed transition to left-lateral strike-slip regime observed in western New Guinea Highlands. We find a better fit of our block model to the observed velocities when assigning the current active boundary between the Papuan Peninsula and the South Bismark Block to be to the north of the city of Lae on the Gain Thrust, rather than on the more southerly Ramu-Markham fault as previously thought. This may indicate a temporary shift of activity onto out of sequence thrusts like the Gain Thrust as opposed to the main frontal thrust (the Ramu-Markham fault). In addition, we show that the southern Highlands Fold-and-Thrust Belt is the major boundary between the rigid Australian Plate and the New Guinea Highlands Block, with convergence occurring at rates between ˜6 and 13 mm yr-1.

The Influence of Grain Boundary Fluids on the Recrystallization Behavior in Calcite: A Comparison of "dry" and "wet" Marble Mylonites

NASA Astrophysics Data System (ADS)

Schenk, O.; Urai, J.; Evans, B.

2003-12-01

Carbonate rocks are able to accumulate large amounts of strain and deform crystal-plastically even at low p-T conditions and thus, marble sequences are often the site of strain localization in the upper crust during late-stage deformation in mountain building processes. In this study we sought to identify the effect of fluids on grain boundary morphology and recrystallization processes in marble mylonites during shear zone evolution, as fluids play a major role in the flow behavior of many rock materials during deformation (e.g. quartz, olivine, halite, feldspar). We compared calcite marble mylonites from two geological settings: (a) Schneeberg Complex, Southern Tyrole, Italy and (b) Naxos Metamorphic Core Complex, Greece. The shear zones of the selected areas are suitable for comparison, because they consist of similar lithology and the marble mylonites resemble each other in chemical composition. In addition, calcite-dolomite solvus geothermometry and TEM observations indicate similar p-T conditions for the shear zones formation. However, the two settings are different in the availability of fluids during the shear zone evolution: In the Schneeberg mylonites, both the alteration of minerals during retrograde metamorphism of neighboring micaschists and the existence of veins suggest that fluids were present during mylonitization. The absence of these features in the Naxos samples indicates that fluids were not present during deformation of these mylonites. This difference is also supported by the signature of stable isotopes. Microstructural investigations using optical and scanning electron microscopes on broken and planar surfaces did not indicate major differences between wet and dry mylonites: Grain boundaries of both types of samples display pores with shapes controlled by crystallography, and pore morphologies that are similar to observations from crack and grain-boundary healing experiments. Grain size reduction was predominantly the result of subgrain rotation recrystallization. However, the coarse grains inside the wet protomylonites (Schneeberg) are characterized by intracrystalline shear zones. With the exception of the intracrystalline shear zones, there were no obvious microstructural signatures that were obvious indicators of the presence of fluids, at least for these two field examples.

New Tertiary stratigraphy for the Florida Keys and southern peninsula of Florida

USGS Publications Warehouse

Cunningham, K.J.; McNeill, D.F.; Guertin, L.A.; Ciesielski, P.F.; Scott, T.M.; De Verteuil, L.

1998-01-01

Seven lithologic formations, ranging in age from Oligocene to Pleistocene, were recently penetrated by core holes in southernmost Florida. From bottom to top, they are the early Oligocene Suwannee Limestone; late-early Oligocene-to-Miocene Arcadia Formation, basal Hawthorn Group; late Miocene Peace River Formation, upper Hawthorn Group; newly proposed late Miocene-to-Pliocene Long Key and Stock Island Formations; and Pleistocene Key Largo and Miami Limestones. The rocks of the Suwannee Limestone form a third-order sequence. Although the entire thickness was not penetrated, 96 m of Suwannee core from one well contains at least 50 vertically stacked, exposure-capped limestone cycles, presumably related to rapid eustatic fluctuations while experiencing tropical to subtropical conditions. The Arcadia Formation is a composite sequence containing four high-frequency sequences composed of multiple vertically stacked carbonate cycles. Most cycles do not show evidence of subaerial exposure and were deposited under more temperate conditions, relative to the Suwannee Limestone. The Arcadia Formation in southernmost Florida is bounded by regional unconformities representing third-order sequence boundaries. Post-Arcadia transgression produced a major backstepping of sediment accumulation above the upper sequence boundary of the Arcadia Formation. The Peace River Formation, composed of diatomaceous mudstones, has been identified only beneath the Florida peninsula and is not present beneath the Florida Keys. Deposition occurred during marine transgressive to high-stand conditions and a local phosphatization event (recorded in northeast Florida). The transgression is possibly related to a global rise in sea level, which resulted in upwelling of relatively cooler, relatively nutrient-rich water masses onto the Florida Platform. It is proposed that the absence of Peace River sediments beneath the Keys is due to sediment bypass of the upper surface of the Arcadia, a result of sediment sweeping by an ancestral Florida current. During late Miocene to Pliocene time in the Florida Keys, siliciclastics of the Long Key Formation and fine-grained carbonates of the Stock Island Formation prograded toward the southern edge of the Florida Platform and downlapped onto the regional unconformity at the top of the Arcadia. Shallow-marine Pleistocene limestones (Key Largo and Miami Limestones), deposited during tropical to subtropical conditions, drape over accretionary successions of the Long Key and Stock Island Formations.

Palynology of the Lost Branch Formation of Kansas - New insights on the major floral transition at the Middle-Upper Pennsylvanian boundary

USGS Publications Warehouse

Peppers, R.A.

1997-01-01

Palynological assemblages from two outcrops of the upper part of the Memorial Formation, the Lost Branch Formation, and the overlying Hepler unit in Kansas were examined to discover which stratigraphic interval marks the change from the lycopod-dominated coal swamp floras of Middle Pennsylvanian (Westphalian D) age to the fern-dominated coal swamp floras of Late Pennsylvanian (Stephanian) age. The Lost Branch Formation underlies the Pleasanton Group, whose base is recognized as the Middle-Upper Pennsylvanian boundary in the Midcontinent. The outcrops include the youngest Middle Pennsylvanian coal (Dawson), just below the Lost Branch Formation, and the oldest Upper Pennsylvanian coal ('Hepler') within the Pleasanton Group. Lycospora dominates the spore assemblage in the Middle Pennsylvanian (Desmoinesian) Dawson coal in the Memorial Shale and is abundant in shale between the coal and just below the Glenpool limestone bed at the top of the Lost Branch Formation. It is rare between the limestone and the Upper Pennsylvanian (Missourian) 'Hepler' coal. Granasporites medius and Thymospora pseudothiessenii disappear below the limestone. The 'Hepler' coal is dominated by fern and seed fern spores Cyclogranisporites and Apiculatasporites, and the sphenopsid spore Calamospora is third in abundance. Florinites, Potonieisporites and other gymnospermic monosaccate pollen are abundant between the two coals. Bisaccate conifer-like pollen, such as Protohaploxipinus, are most common between the Dawson coal and Glenpool limestone, but Wilsonites, which is thought to have been produced by seed ferns, is very abundant from the Glenpool limestone to the 'Hepler' coal. On the basis of macroinvertebrate evidence, the Glenpool limestone is Middle Pennsylvanian in age, but the palynological evidence indicates that the floral change took place slightly before deposition of the limestone. Thus, the major change in climate that occurred near the Middle-Upper Pennsylvanian boundary apparently affected the floras earlier than the faunas. The floral change cannot be explained as resulting from a major marine regression and hiatus because the change is recorded in a marine section within a single transgressive-regressive sequence.

Distortion correction for diffusion-weighted MRI tractography and fMRI in the temporal lobes.

PubMed

Embleton, Karl V; Haroon, Hamied A; Morris, David M; Ralph, Matthew A Lambon; Parker, Geoff J M

2010-10-01

Single shot echo-planar imaging (EPI) sequences are currently the most commonly used sequences for diffusion-weighted imaging (DWI) and functional magnetic resonance imaging (fMRI) as they allow relatively high signal to noise with rapid acquisition time. A major drawback of EPI is the substantial geometric distortion and signal loss that can occur due to magnetic field inhomogeneities close to air-tissue boundaries. If DWI-based tractography and fMRI are to be applied to these regions, then the distortions must be accurately corrected to achieve meaningful results. We describe robust acquisition and processing methods for correcting such distortions in spin echo (SE) EPI using a variant of the reversed direction k space traversal method with a number of novel additions. We demonstrate that dual direction k space traversal with maintained diffusion-encoding gradient strength and direction results in correction of the great majority of eddy current-associated distortions in DWI, in addition to those created by variations in magnetic susceptibility. We also provide examples to demonstrate that the presence of severe distortions cannot be ignored if meaningful tractography results are desired. The distortion correction routine was applied to SE-EPI fMRI acquisitions and allowed detection of activation in the temporal lobe that had been previously found using PET but not conventional fMRI. © 2010 Wiley-Liss, Inc.

Application of convolutional artificial neural networks to echocardiograms for differentiating congenital heart diseases in a pediatric population

NASA Astrophysics Data System (ADS)

Perrin, Douglas P.; Bueno, Alejandra; Rodriguez, Andrea; Marx, Gerald R.; del Nido, Pedro J.

2017-03-01

In this paper we describe a pilot study, where machine learning methods are used to differentiate between congenital heart diseases. Our approach was to apply convolutional neural networks (CNNs) to echocardiographic images from five different pediatric populations: normal, coarctation of the aorta (CoA), hypoplastic left heart syndrome (HLHS), transposition of the great arteries (TGA), and single ventricle (SV). We used a single network topology that was trained in a pairwise fashion in order to evaluate the potential to differentiate between patient populations. In total we used 59,151 echo frames drawn from 1,666 clinical sequences. Approximately 80% of the data was used for training, and the remainder for validation. Data was split at sequence boundaries to avoid having related images in the training and validation sets. While training was done with echo images/frames, evaluation was performed for both single frame discrimination as well as sequence discrimination (by majority voting). In total 10 networks were generated and evaluated. Unlike other domains where this network topology has been used, in ultrasound there is low visual variation between classes. This work shows the potential for CNNs to be applied to this low-variation domain of medical imaging for disease discrimination.

Molecular and functional characterization of the promoter of ETS2, the human c-ets-2 gene.

PubMed Central

Mavrothalassitis, G J; Watson, D K; Papas, T S

1990-01-01

The 5' end of the human c-ets-2 gene, ETS2, was cloned and characterized. The major transcription initiation start sites were identified, and the pertinent sequences surrounding the ETS2 promoter were determined. The promoter region of ETS2 does not possess typical "TATA" and "CAAT" elements. However, this promoter contains several repeat regions, as well as two consensus AP2 binding sites and three putative Sp1 sites. There is also a palindromic region similar to the serum response element of the c-fos gene, located 1400 base pairs (bp) upstream from the first major transcription initiation site. A G + C-rich sequence (GC element) with dyad symmetry can be seen in the ETS2 promoter, immediately following an unusually long (approximately 250-bp) polypurine-polypyrimidine tract. A series of deletion fragments from the putative promoter region were ligated in front of the bacterial chloramphenicol acetyltransferase gene and tested for activity following transfection into HeLa cells. The 5' boundary of the region needed for maximum promoter activity was found to be 159 bp upstream of the major initiation site. This region of 159 bp contains putative binding sites for transcription factors Sp1 and AP2 (one for each), the GC element, one small forward repeat, one inverted repeat, and half of the polypurine-pyrimidine tract. The promoter of ETS2 (within the polypyrimidine tract) serves to illustrate an alternative structure that may be present in genes with "TATA-less" promoters. Images PMID:2405393

Research in Stochastic Processes.

DTIC Science & Technology

1982-12-01

constant high level boundary. References 1. Jurg Husler , Extremie values of non-stationary sequ-ences ard the extr-rmal index, Center for Stochastic...A. Weron, Oct. 82. 20. "Extreme values of non-stationary sequences and the extremal index." Jurg Husler , Oct. 82. 21. "A finitely additive white noise...string model, Y. Miyahara, Carleton University and Nagoya University. Sept. 22 On extremfe values of non-stationary sequences, J. Husler , University of

Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics.

PubMed

James, Katherine; Cockell, Simon J; Zenkin, Nikolay

2017-05-01

The identification of the protein-coding regions of a genome is straightforward due to the universality of start and stop codons. However, the boundaries of the transcribed regions, conditional operon structures, non-coding RNAs and the dynamics of transcription, such as pausing of elongation, are non-trivial to identify, even in the comparatively simple genomes of prokaryotes. Traditional methods for the study of these areas, such as tiling arrays, are noisy, labour-intensive and lack the resolution required for densely-packed bacterial genomes. Recently, deep sequencing has become increasingly popular for the study of the transcriptome due to its lower costs, higher accuracy and single nucleotide resolution. These methods have revolutionised our understanding of prokaryotic transcriptional dynamics. Here, we review the deep sequencing and data analysis techniques that are available for the study of transcription in prokaryotes, and discuss the bioinformatic considerations of these analyses. Copyright © 2017 Elsevier Inc. All rights reserved.

Robust boundary detection of left ventricles on ultrasound images using ASM-level set method.

PubMed

Zhang, Yaonan; Gao, Yuan; Li, Hong; Teng, Yueyang; Kang, Yan

2015-01-01

Level set method has been widely used in medical image analysis, but it has difficulties when being used in the segmentation of left ventricular (LV) boundaries on echocardiography images because the boundaries are not very distinguish, and the signal-to-noise ratio of echocardiography images is not very high. In this paper, we introduce the Active Shape Model (ASM) into the traditional level set method to enforce shape constraints. It improves the accuracy of boundary detection and makes the evolution more efficient. The experiments conducted on the real cardiac ultrasound image sequences show a positive and promising result.

Young children pause on phrase boundaries in self-paced music listening: The role of harmonic cues.

PubMed

Kragness, Haley E; Trainor, Laurel J

2018-05-01

Proper segmentation of auditory streams is essential for understanding music. Many cues, including meter, melodic contour, and harmony, influence adults' perception of musical phrase boundaries. To date, no studies have examined young children's musical grouping in a production task. We used a musical self-pacing method to investigate (1) whether dwell times index young children's musical phrase grouping and, if so, (2) whether children dwell longer on phrase boundaries defined by harmonic cues specifically. In Experiment 1, we asked 3-year-old children to self-pace through chord progressions from Bach chorales (sequences in which metrical, harmonic, and melodic contour grouping cues aligned) by pressing a computer key to present each chord in the sequence. Participants dwelled longer on chords in the 8th position, which corresponded to phrase endings. In Experiment 2, we tested 3-, 4-, and 7-year-old children's sensitivity to harmonic cues to phrase grouping when metrical regularity cues and melodic contour cues were misaligned with the harmonic phrase boundaries. In this case, 7 and 4 year olds but not 3 year olds dwelled longer on harmonic phrase boundaries, suggesting that the influence of harmonic cues on phrase boundary perception develops substantially between 3 and 4 years of age in Western children. Overall, we show that the musical dwell time method is child-friendly and can be used to investigate various aspects of young children's musical understanding, including phrase grouping and harmonic knowledge. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

On the edge of language acquisition: inherent constraints on encoding multisyllabic sequences in the neonate brain.

PubMed

Ferry, Alissa L; Fló, Ana; Brusini, Perrine; Cattarossi, Luigi; Macagno, Francesco; Nespor, Marina; Mehler, Jacques

2016-05-01

To understand language, humans must encode information from rapid, sequential streams of syllables - tracking their order and organizing them into words, phrases, and sentences. We used Near-Infrared Spectroscopy (NIRS) to determine whether human neonates are born with the capacity to track the positions of syllables in multisyllabic sequences. After familiarization with a six-syllable sequence, the neonate brain responded to the change (as shown by an increase in oxy-hemoglobin) when the two edge syllables switched positions but not when two middle syllables switched positions (Experiment 1), indicating that they encoded the syllables at the edges of sequences better than those in the middle. Moreover, when a 25 ms pause was inserted between the middle syllables as a segmentation cue, neonates' brains were sensitive to the change (Experiment 2), indicating that subtle cues in speech can signal a boundary, with enhanced encoding of the syllables located at the edges of that boundary. These findings suggest that neonates' brains can encode information from multisyllabic sequences and that this encoding is constrained. Moreover, subtle segmentation cues in a sequence of syllables provide a mechanism with which to accurately encode positional information from longer sequences. Tracking the order of syllables is necessary to understand language and our results suggest that the foundations for this encoding are present at birth. © 2015 John Wiley & Sons Ltd.

A new Lower Pleistocene archeological site in Europe (Vallparadís, Barcelona, Spain)

PubMed Central

Martínez, Kenneth; Garcia, Joan; Carbonell, Eudald; Agustí, Jordi; Bahain, Jean-Jaques; Blain, Hugues-Alexandre; Burjachs, Francesc; Cáceres, Isabel; Duval, Mathieu; Falguères, Christophe; Gómez, Manuel; Huguet, Rosa

2010-01-01

Here we report the discovery of a new late Lower Pleistocene site named Vallparadís (Barcelona, Spain) that produced a rich archeological and paleontological sequence dated from the upper boundary of the Jaramillo subchron to the early Middle Pleistocene. This deposit contained a main archeological layer with numerous artifacts and a rich macromammalian assemblage, some of which bore cut marks, that could indicate that hominins had access to carcasses. Paleomagnetic analysis, electron spin resonance-uranium series (ESR-US), and the biostratigraphic chronological position of the macro- and micromammal and lithic assemblages of this layer reinforce the proposal that hominins inhabited Europe during the Lower Pleistocene. The archeological sequence provides key information on the successful adaptation of European hominins that preceded the well-known fossil population from Atapuerca and succeeded the finds from Orce basin. Hence, this discovery enables us to close a major chronological gap in the early prehistory of Iberia. According to the information in this paper and the available data from these other sites, we propose that Mediterranean Western Europe was repeatedly and perhaps continuously occupied during the late Matuyama chron. PMID:20231433

Sedimentology, conodonts and ostracods of the Devonian - Carboniferous strata of the Anseremme railway bridge section, Dinant Basin, Belgium

USGS Publications Warehouse

Casier, J.-G.; Mamet, B.; Preat, A.; Sandberg, C.A.

2004-01-01

Seven major carbonate microfacies are defined in the Devonian - Carboniferous (D/C) strata (50 m) of the Anseremme railway bridge section, south of Dinant. They permit recognition of several levels encompassing the Etroeungt and Hastie??re formations. "Bathymetric" sequences range from open marine, below the storm wave base, to semi-restricted lagoon. This sequence records a shallowing-upward trend of the relative sea level, from environments below the storm wave base to strongly eroded supraticial pre-evaporitic environments. Faunal components (echinoderms, brachiopods...) indicate open-marine domain for the first six microfacies located within the dysphoticeuphotic zone in relatively shallow waters. The textures of the rocks (mudstones to rudstones) associated with lamination characteristics indicate the position of the storm (SWB) and the fair-weather (FWWB) wave bases. Microfacies seven suggests a semi-restricted platform with salinity fluctuations from hypersaline brines to brackish waters. Thus, the boundary of the Etroeungt/Hastie??re formations is marked by an abrupt drop in sea level. Carbonate micro-conglomerates recording an important erosive phase and a sedimentary hiatus. The environment is again open marine in the upper part of the Hastie??re Formation. Our conclusion is that the Anseremme section is not a reliable continuous succession for the study of the D/C boundary. This confirms the VAN STEENWINKEL (1988, 1993 hypothesis based on other arguments. Conodont faunas demonstrate that the Devonian sequence spans the five youngest conodont zones, but that two of these zones are not represented. The Epinette Formation is dated as the youngest part of the Middle expansa Zone. Thus, the boundary with the Late praesulcata Zone probably coincides with the sharp sedimentological change at the base of the Etroeungt Formation, which is interpreted to belong entirely to this zone. The disconformably overlying basal bed 159 of the Hastie??re Formation is dated as Late praesulcata Zone, with the Early and Middle praesulcata Zones unrepresented because of an hiatus or unconformity. Sparse conodont faunas suggest that only the two next-to-oldest Carboniferous duplicata and sandbergi Zones are represented in the higher part of the Hastie??re Formation. The oldest Carboniferous sulcata Zone and possibly part ofthe duplicata Zone are unrepresented because of an hiatus or unconformity above bed 159. Ostracods are abundant and diversified at most levels in the Anseremme railway bridge section and sixty taxa, the majority in open nomenclature, have been identified and nearly all of them are figured. The ostracod fauna is indicative of shallow-marine environments between fair-weather and storm wave bases in the Etroeungt Formation, and to shallower water conditions periodically subjected to minor salinity variations in the base of the Hastie??re Formation. The upper part of the Hastie??re Formation is marked by a sea-level rise associated with a moderate decrease of the oxygenation of bottom waters. The intra-Devonian hiatus at the Etroeungt-Hastie??re boundary shows no abnormal extinctions and no appearance of new taxa. Thus, the Hangenberg Event is not recognizable in the studied section. Neither the sedimentological analysis nor the palaeontological study of the Bocahut quarry in the Avesnois and of the Anseremme railway bridge section confirm the hypothesis of a highstand for the Hastie??re Formation.

Sequence stratigraphy of the Monterey Formation, Santa Barbara County: Integration of physical, chemical, and biofacies data from outcrop and subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bohacs, K.M.

1990-05-01

Deep basinal rocks of the Monterey Formation can be allocated to different depositional environments based on an integration of bedding, facies stacking patterns, lithology, biofacies, and inorganic and organic chemistry. These rocks show evidence of systematic changes in depositional environments that can be related to eustatic sea level change and basin evolution. Even deep-basinal environments are affected by changing sea level through changes in circulation patterns and intensities nutrient budgets and dispersal patterns, and location and intensity of the oceanic oxygen minimum. The sequence-stratigraphic framework was constructed based on the physical expression of the outcrop strata and confirmed by typingmore » the outcrop sections to an integrated well-log/seismic grid through outcrop gamma-ray-spectral profiles. Interpretation of a sequence boundary was based on increased proportions of hemipelagic facies, evidence of increased bottom-energy levels above the boundary, and local erosion and relief on the surface. The proportion of shallower water and reworked dinoflagellates increased to a local maximum above the boundary, Downlap surfaces exhibited increased proportions of pelagic facies around the surface, evidence of decreased bottom-energy levels and terrigenous sedimentation rates, and little or no significant erosion on the surface. The proportion of deeper water dinoflagellates increased to a local maximum at or near the downlap surface; there was no evidence of reworked individuals. The detailed sequence-stratigraphic framework makes it possible to the rock properties to genetic processes for construction of predictive models.« less

The First Complete Chloroplast Genome Sequences in Actinidiaceae: Genome Structure and Comparative Analysis.

PubMed

Yao, Xiaohong; Tang, Ping; Li, Zuozhou; Li, Dawei; Liu, Yifei; Huang, Hongwen

2015-01-01

Actinidia chinensis is an important economic plant belonging to the basal lineage of the asterids. Availability of a complete Actinidia chloroplast genome sequence is crucial to understanding phylogenetic relationships among major lineages of angiosperms and facilitates kiwifruit genetic improvement. We report here the complete nucleotide sequences of the chloroplast genomes for Actinidia chinensis and A. chinensis var deliciosa obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. The total genome size ranges from 155,446 to 157,557 bp, with an inverted repeat (IR) of 24,013 to 24,391 bp, a large single copy region (LSC) of 87,984 to 88,337 bp and a small single copy region (SSC) of 20,332 to 20,336 bp. The genome encodes 113 different genes, including 79 unique protein-coding genes, 30 tRNA genes and 4 ribosomal RNA genes, with 16 duplicated in the inverted repeats, and a tRNA gene (trnfM-CAU) duplicated once in the LSC region. Comparisons of IR boundaries among four asterid species showed that IR/LSC borders were extended into the 5' portion of the psbA gene and IR contraction occurred in Actinidia. The clap gene has been lost from the chloroplast genome in Actinidia, and may have been transferred to the nucleus during chloroplast evolution. Twenty-seven polymorphic simple sequence repeat (SSR) loci were identified in the Actinidia chloroplast genome. Maximum parsimony analyses of a 72-gene, 16 taxa angiosperm dataset strongly support the placement of Actinidiaceae in Ericales within the basal asterids.

Aircraft Noise Prediction Program theoretical manual: Propeller aerodynamics and noise

NASA Technical Reports Server (NTRS)

Zorumski, W. E. (Editor); Weir, D. S. (Editor)

1986-01-01

The prediction sequence used in the aircraft noise prediction program (ANOPP) is described. The elements of the sequence are called program modules. The first group of modules analyzes the propeller geometry, the aerodynamics, including both potential and boundary-layer flow, the propeller performance, and the surface loading distribution. This group of modules is based entirely on aerodynamic strip theory. The next group of modules deals with the first group. Predictions of periodic thickness and loading noise are determined with time-domain methods. Broadband noise is predicted by a semiempirical method. Near-field predictions of fuselage surface pressrues include the effects of boundary layer refraction and scattering. Far-field predictions include atmospheric and ground effects.

Loess 10Be evidence for an asynchronous Brunhes-Matuyama magnetic polarity reversal

NASA Astrophysics Data System (ADS)

Zhou, Weijian; Beck, J. Warren; Kong, Xianghui; An, Zhisheng; Qiang, Xiaoke; Wu, Zhenkun; Xian, Feng; Ao, Hong

2015-04-01

In Chinese loess the Brunhes-Matuyama (B-M) geomagnetic reversal appears to occur about 25 ka prior to the established axial dipole reversal age found in many marine sediments, i.e., in Chinese loess this magnetic reversal boundary is found in glacial loess unit L8 which is thought to be correlated with Marine Isotope Stage 20 (MIS 20), in marine sediment records, however, this boundary is commonly found in interglacial period of MIS 19 (Tauxe et al., 1996; Zhou and Shackleton, 1999), leading to the debate on uncertainties of paleoclimatic correlation between the Chinese loess-paleosol sequences and marine sediments (Wang et al., 2006; Liu et al., 2008; Jin and Liu, 2011). Based on this issue, here we propose to use the cosmogenic 10Be to address this conundrum. 10Be is a long-lived radionuclide produced in the atmosphere by cosmic ray spallation reactions and carried to the ground attached to aerosols. Its atmospheric production rate is inversely proportional to the geomagnetic field intensity (Masarik and Beer, 1999). This allows us to reconstruct past geomagnetic field intensity variations using 10Be concentrations recorded in different sedimentary archives. We carried out both the 10Be studies and paleogeomagnetic measurements in Luochuan and Xifeng sections in Chinese Loess Plateau. Both loess profiles show that 10Be production rate was at a maximum-an indication of the dipole field reversal-at ca. 780 ± 3 ka BP., in paleosol unit S7 corresponding to MIS 19, proving that the timing of B-M reversal recorded in Chinese loess is synchronous with that seen in marine records (Tauxe et al., 1996). These results reaffirmed the conventional paleoclimatic correlation of loess-paleosol sequences with marine isotope stages and the standard loess timescale as correct. However, it is ~25 ka younger than the age (depth) of the paleogeomagnetic measurements which show that the B-M boundary is in L8 in these two Chinese loess-paleosol sequences, demonstrating that loess magnetic overprinting has occurred. References: 1. Jin, C.S., and Liu, Q.S., 2011, Revisiting the stratigraphic position of the Matuyama-Brunhes geomagnetic polarity boundary in Chinese loess: Palaeogeography, Palaeoclimatology, Palaeoecology, v. 299, p. 309-317. 2. Liu, Q.S., Roberts, A.P., Rohling, E.J., Zhu, R.X., and Sun, Y.B., 2008, Post-depositional remanent magnetization lock-in and the location of the Matuyama-Brunhes geomagnetic reversal boundary in marine and Chinese loess sequences: Earth and Planetary Science Letters, v. 275, no. 1-2, p. 102-110. 3. Masarik, J., and Beer, J., 1999, Simulation of particle fluxes and cosmogenic nuclide production in the Earth's atmosphere: Jounal of Geophysical Research, v. 104, p. 12099-12111. 4. Tauxe, L., Herbert, T., Shackleton, N.J., and Kok, Y.S., 1996, Astronomical calibration of the Matuyama-Brunhes boundary: Consequences for magnetic remanence acquisition in marine carbonates and the Asian loess sequences: Earth and Planetary Science Letters, v. 140, p. 133-146. 5. Wang, X.S., Yang, Z.Y., Løvlie, R., Sun, Z.M., and Pei, J.L., 2006, A magnetostratigraphic reassessment of correlation between Chinese loess and marine oxygen isotope records over the last 1.1Ma: Physics of the Earth and Planetary Interiors, v. 159, p. 109-117. 6. Zhou, L.P., and Shackleton, N.J., 1999, Misleading positions of geomagnetic reversal boundaries in Eurasian loess and implications for correlation between continental and marine sedimentary sequences: Earth and Planetary Science Letters, v. 168, p. 117-130.

Genome-Wide Identification of Chromatin Transitional Regions Reveals Diverse Mechanisms Defining the Boundary of Facultative Heterochromatin

PubMed Central

Li, Guangyao; Zhou, Lei

2013-01-01

Due to the self-propagating nature of the heterochromatic modification H3K27me3, chromatin barrier activities are required to demarcate the boundary and prevent it from encroaching into euchromatic regions. Studies in Drosophila and vertebrate systems have revealed several important chromatin barrier elements and their respective binding factors. However, epigenomic data indicate that the binding of these factors are not exclusive to chromatin boundaries. To gain a comprehensive understanding of facultative heterochromatin boundaries, we developed a two-tiered method to identify the Chromatin Transitional Region (CTR), i.e. the nucleosomal region that shows the greatest transition rate of the H3K27me3 modification as revealed by ChIP-Seq. This approach was applied to identify CTRs in Drosophila S2 cells and human HeLa cells. Although many insulator proteins have been characterized in Drosophila, less than half of the CTRs in S2 cells are associated with known insulator proteins, indicating unknown mechanisms remain to be characterized. Our analysis also revealed that the peak binding of insulator proteins are usually 1–2 nucleosomes away from the CTR. Comparison of CTR-associated insulator protein binding sites vs. those in heterochromatic region revealed that boundary-associated binding sites are distinctively flanked by nucleosome destabilizing sequences, which correlates with significant decreased nucleosome density and increased binding intensities of co-factors. Interestingly, several subgroups of boundaries have enhanced H3.3 incorporation but reduced nucleosome turnover rate. Our genome-wide study reveals that diverse mechanisms are employed to define the boundaries of facultative heterochromatin. In both Drosophila and mammalian systems, only a small fraction of insulator protein binding sites co-localize with H3K27me3 boundaries. However, boundary-associated insulator binding sites are distinctively flanked by nucleosome destabilizing sequences, which correlates with significantly decreased nucleosome density and increased binding of co-factors. PMID:23840609

Sequence stratigraphic principles applied to the Miocene Hawthorn Group, west-central Florida

DOE Office of Scientific and Technical Information (OSTI.GOV)

Norton, V.L.; Randazzo, A.F.

1993-03-01

Sequence boundaries for the Miocene Hawthorn Group in the ROMP 20 drill core from Osprey, Sarasota County, FL were generally delineated by lithologic variations recognized from core slabs, thin section analysis, and geophysical logs. At least six depositional sequences representing third order sea level fluctuations were identified. Depositional environments were determined on the basis of the characteristic lithologic constituents including rip-up clasts, pellets, fossils, laminations, burrow, degree of induration, and grain sorting. The sequence boundaries appear to have formed when the rate of the eustatic fall exceeded basin subsidence rates producing a relative sea level fall at a depositional shorelinemore » break. As a result of the basinward facies shift associated with this sequence type, peritidal facies may directly overlie deeper water facies. Subaerial exposure and erosion can be expected. The sequence of facies representing progressively deeper water depositional environments, followed by a progressive shallowing, were present between bounding surfaces. Among the six sequences recognized, four were clearly delineated as representative of regression, subaerial exposure, and subsequent transgression. Two sequences were less clearly defined and probably represent transitional facies which had exposure surfaces developed. Comparison of the petrologically established sequence stratigraphy with published sea level curves resulted in a strong correlation between the number of sequences recognized and the number of coastal on-lap/off-lap cycles depicted for the early to middle Miocene. This correlation suggests that petrologic examination of core slabs, with supplemental thin section data, can provide useful information regarding the recognition of stratigraphic sequences and relative sea level fluctuations, particularly, in situations where seismic data may not be available.« less

Iridium profile for 10 million years across the Cretaceous-Tertiary boundary at Gubbio (Italy)

NASA Technical Reports Server (NTRS)

Alvarez, Walter; Asaro, Frank; Montanari, Alessandro

1990-01-01

The iridium anomaly at the Cretaceous-Tertiary (KT) boundary was discovered in the pelagic limestone sequence at Gubbio on the basis of 12 samples analyzed by neutron activation analysis (NAA) and was interpreted as indicating impact of a large extraterrestrial object at exactly the time of the KT mass extinction. Continuing controversy over the shape of the Ir profile at the Gubbio KT boundary and its interpretation called for a more detailed follow-up study. Analysis of a 57-meter-thick, 10-million-year-old part of the Gubbio sequence using improved NAA techniques revealed that there is only one Ir anomaly at the KT boundary, but this anomaly shows an intricate fine structure, the origin of which cannot yet be entirely explained. The KT Ir anomaly peaks in a 1-centimeter-thick clay layer, where the average Ir concentration is 3000 parts per trillion (ppt); this peak is flanked by tails with Ir concentrations of 20 to 80 ppt that rise above a background of 12 to 13 ppt. The fine structure of the tails is probably due in part to lateral reworking, diffusion, burrowing, and perhaps Milankovitch cyclicity.

An Ancient Transkingdom Horizontal Transfer of Penelope-Like Retroelements from Arthropods to Conifers.

PubMed

Lin, Xuan; Faridi, Nurul; Casola, Claudio

2016-05-02

Comparative genomics analyses empowered by the wealth of sequenced genomes have revealed numerous instances of horizontal DNA transfers between distantly related species. In eukaryotes, repetitive DNA sequences known as transposable elements (TEs) are especially prone to move across species boundaries. Such horizontal transposon transfers, or HTTs, are relatively common within major eukaryotic kingdoms, including animals, plants, and fungi, while rarely occurring across these kingdoms. Here, we describe the first case of HTT from animals to plants, involving TEs known as Penelope-like elements, or PLEs, a group of retrotransposons closely related to eukaryotic telomerases. Using a combination of in situ hybridization on chromosomes, polymerase chain reaction experiments, and computational analyses we show that the predominant PLE lineage, EN(+)PLEs, is highly diversified in loblolly pine and other conifers, but appears to be absent in other gymnosperms. Phylogenetic analyses of both protein and DNA sequences reveal that conifers EN(+)PLEs, or Dryads, form a monophyletic group clustering within a clade of primarily arthropod elements. Additionally, no EN(+)PLEs were detected in 1,928 genome assemblies from 1,029 nonmetazoan and nonconifer genomes from 14 major eukaryotic lineages. These findings indicate that Dryads emerged following an ancient horizontal transfer of EN(+)PLEs from arthropods to a common ancestor of conifers approximately 340 Ma. This represents one of the oldest known interspecific transmissions of TEs, and the most conspicuous case of DNA transfer between animals and plants. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2016. This work is written by US Government employees and is in the public domain in the US.

The Interaction of FABP with Kapα

PubMed Central

Amber-Vitos, Ortal; Kucherenko, Nataly; Nachliel, Esther; Gutman, Menachem; Tsfadia, Yossi

2015-01-01

Gene-activating lipophilic compounds are carried into the nucleus when loaded on fatty-acid-binding proteins (FABP). Some of these proteins are recognized by the α-Karyopherin (Kapα) through its nuclear localization signal (NLS) consisting of three positive residues that are not in a continuous sequence. The Importin system can distinguish between FABP loaded with activating and non-activating compounds. In the present study, we introduced molecular dynamics as a tool for clarifying the mechanism by which FABP4, loaded with activating ligand (linoleate) is recognized by Kapα. In the first phase, we simulated the complex between KapαΔIBB (termed “Armadillo”) that was crystallized with two NLS hepta-peptides. The trajectory revealed that the crystal-structure orientation of the peptides is rapidly lost and new interactions dominate. Though, the NLS sequence of FABP4 is cryptic, since the functional residues are not in direct sequence, implicating more than one possible conformation. Therefore, four possible docked conformations were generated, in which the NLS of FABP4 is interacting with either the major or the minor sites of Kapα, and the N → C vectors are parallel or anti-parallel. Out of these four basic starting positions, only the FABP4-minor site complex exhibited a large number of contact points. In this complex, the FABP interacts with the minor and the major sites, suppressing the self-inhibitory interaction of the Kapα, rendering it free to react with Kapβ. Finally, we propose that the transportable conformation generated an extended hydrophobic domain which expanded out of the boundary of the FABP4, allowing the loaded linoleate to partially migrate out of the FABP into a joint complex in which the Kapα contributes part of a combined binding pocket. PMID:26284534

Geometry and structure of the pull-apart basins developed along the western South American-Scotia plate boundary (SW Atlantic Ocean)

NASA Astrophysics Data System (ADS)

Esteban, F. D.; Tassone, A.; Isola, J. I.; Lodolo, E.; Menichetti, M.

2018-04-01

The South American-Scotia plate boundary is a left-lateral fault system which runs roughly E-W for more than 3000 km across the SW Atlantic Ocean and the Tierra del Fuego Island, reaching to the west the southern Chile Trench. Analyses of a large dataset of single- and multi-channel seismic reflection profiles acquired offshore has allowed to map the trace of the plate boundary from Tierra del Fuego to the Malvinas Trough, a tectonic depression located in the eastern part of the fault system, and to reconstruct the shape and geometry of the basins formed along the principal displacement zone of the fault system. Three main Neogene pull-apart basins that range from 70 to 100 km in length, and from 12 to 22 km in width, have been identified along this segment of the plate boundary. These basins have elongated shapes with their major axes parallel to the ENE-WSW direction of the fault zone. The sedimentary architecture and the infill geometry of the basins suggest that they represent mostly strike-slip dominated transtension basins which propagated from E to W. The basins imaged by seismic data show in some cases geometrical and structural features linked to the possible reactivation of previous wedge-top basins and inherited structures pertaining to the external front of the Magallanes fold-and-thrust compression belt, along which the South American-Scotia fault system has been superimposed. It is suggested that the sequence of the elongated basins occur symmetrically to a thorough going strike-slip fault, in a left-stepping geometrical arrangement, in a manner similar to those basins seen in other transcurrent environments.

Reprint of: A numerical investigation of fine sediment resuspension in the wave boundary layer-Uncertainties in particle inertia and hindered settling

NASA Astrophysics Data System (ADS)

Cheng, Zhen; Yu, Xiao; Hsu, Tian-Jian; Balachandar, S.

2016-05-01

The wave bottom boundary layer is a major conduit delivering fine terrestrial sediments to continental margins. Hence, studying fine sediment resuspensions in the wave boundary layer is crucial to the understanding of various components of the earth system, such as carbon cycles. By assuming the settling velocity to be a constant in each simulation, previous turbulence-resolving numerical simulations reveal the existence of three transport modes in the wave boundary layer associated with sediment availabilities. As the sediment availability and hence the sediment-induced stable stratification increases, a sequence of transport modes, namely, (I) well-mixed transport, (II) formulation of lutocline resembling a two-layer system, and (III) completely laminarized transport are observed. In general, the settling velocity is a flow variable due to hindered settling and particle inertia effects. Present numerical simulations including the particle inertia suggest that for a typical wave condition in continental shelves, the effect of particle inertia is negligible. Through additional numerical experiments, we also confirm that the particle inertia tends (up to the Stokes number St = 0.2) to attenuate flow turbulence. On the other hand, for flocs with lower gelling concentrations, the hindered settling can play a key role in sustaining a large amount of suspended sediments and results in the laminarized transport (III). For the simulation with a very significant hindered settling effect due to a low gelling concentration, results also indicate the occurrence of gelling ignition, a state in which the erosion rate is always higher than the deposition rate. A sufficient condition for the occurrence of gelling ignition is hypothesized for a range of wave intensities as a function of sediment/floc properties and erodibility parameters.

Gradual unlocking of plate boundary controlled initiation of the 2014 Iquique earthquake.

PubMed

Schurr, Bernd; Asch, Günter; Hainzl, Sebastian; Bedford, Jonathan; Hoechner, Andreas; Palo, Mauro; Wang, Rongjiang; Moreno, Marcos; Bartsch, Mitja; Zhang, Yong; Oncken, Onno; Tilmann, Frederik; Dahm, Torsten; Victor, Pia; Barrientos, Sergio; Vilotte, Jean-Pierre

2014-08-21

On 1 April 2014, Northern Chile was struck by a magnitude 8.1 earthquake following a protracted series of foreshocks. The Integrated Plate Boundary Observatory Chile monitored the entire sequence of events, providing unprecedented resolution of the build-up to the main event and its rupture evolution. Here we show that the Iquique earthquake broke a central fraction of the so-called northern Chile seismic gap, the last major segment of the South American plate boundary that had not ruptured in the past century. Since July 2013 three seismic clusters, each lasting a few weeks, hit this part of the plate boundary with earthquakes of increasing peak magnitudes. Starting with the second cluster, geodetic observations show surface displacements that can be associated with slip on the plate interface. These seismic clusters and their slip transients occupied a part of the plate interface that was transitional between a fully locked and a creeping portion. Leading up to this earthquake, the b value of the foreshocks gradually decreased during the years before the earthquake, reversing its trend a few days before the Iquique earthquake. The mainshock finally nucleated at the northern end of the foreshock area, which skirted a locked patch, and ruptured mainly downdip towards higher locking. Peak slip was attained immediately downdip of the foreshock region and at the margin of the locked patch. We conclude that gradual weakening of the central part of the seismic gap accentuated by the foreshock activity in a zone of intermediate seismic coupling was instrumental in causing final failure, distinguishing the Iquique earthquake from most great earthquakes. Finally, only one-third of the gap was broken and the remaining locked segments now pose a significant, increased seismic hazard with the potential to host an earthquake with a magnitude of >8.5.

On High-Order Radiation Boundary Conditions

NASA Technical Reports Server (NTRS)

Hagstrom, Thomas

1995-01-01

In this paper we develop the theory of high-order radiation boundary conditions for wave propagation problems. In particular, we study the convergence of sequences of time-local approximate conditions to the exact boundary condition, and subsequently estimate the error in the solutions obtained using these approximations. We show that for finite times the Pade approximants proposed by Engquist and Majda lead to exponential convergence if the solution is smooth, but that good long-time error estimates cannot hold for spatially local conditions. Applications in fluid dynamics are also discussed.

Apollo 17 Index: 70 mm, 35 mm, and 16 mm Photographs

NASA Technical Reports Server (NTRS)

Wells, Ronald A. (Compiler)

1974-01-01

This index lists and provides supplemental data for all Apollo 17 70 mm, 35 mm, and 16 mm photographs. The 70 mm and 35 mm photographs are indexed in three ways: (1) all photographs are listed in numerical sequence according to NASA photograph number, (2) photographs exposed in lunar orbit are listed according to longitude in 10deg increments, and (3) all photographs exposed on the lunar surface are listed in chronological order. In indexing the 70 mm and 35 mm orbital photographs, individual frames were matched to imagery on the 1:2,750,000 scale Lunar Planning Charts (LOC). Each frame was outlined on the LOC base map, and the principal point determined. The latitude and longitude of each principal point, to the nearest 0.1 degree, is recorded in this index, If the principal point of a photograph is in space or its location obscured by shadow, an approximate longitude was recorded so that the photograph would not be excluded from the computer-generated listing by longitude. Each frame is described in terms of a named lunar surface feature within the boundaries of the frame or, if no named features are within the frame boundaries, a major nearby feature.

Synthetic signal sequences that enable efficient secretory protein production in the yeast Kluyveromyces marxianus.

PubMed

Yarimizu, Tohru; Nakamura, Mikiko; Hoshida, Hisashi; Akada, Rinji

2015-02-14

Targeting of cellular proteins to the extracellular environment is directed by a secretory signal sequence located at the N-terminus of a secretory protein. These signal sequences usually contain an N-terminal basic amino acid followed by a stretch containing hydrophobic residues, although no consensus signal sequence has been identified. In this study, simple modeling of signal sequences was attempted using Gaussia princeps secretory luciferase (GLuc) in the yeast Kluyveromyces marxianus, which allowed comprehensive recombinant gene construction to substitute synthetic signal sequences. Mutational analysis of the GLuc signal sequence revealed that the GLuc hydrophobic peptide length was lower limit for effective secretion and that the N-terminal basic residue was indispensable. Deletion of the 16th Glu caused enhanced levels of secreted protein, suggesting that this hydrophilic residue defined the boundary of a hydrophobic peptide stretch. Consequently, we redesigned this domain as a repeat of a single hydrophobic amino acid between the N-terminal Lys and C-terminal Glu. Stretches consisting of Phe, Leu, Ile, or Met were effective for secretion but the number of residues affected secretory activity. A stretch containing sixteen consecutive methionine residues (M16) showed the highest activity; the M16 sequence was therefore utilized for the secretory production of human leukemia inhibitory factor protein in yeast, resulting in enhanced secreted protein yield. We present a new concept for the provision of secretory signal sequence ability in the yeast K. marxianus, determined by the number of residues of a single hydrophobic residue located between N-terminal basic and C-terminal acidic amino acid boundaries.

Cretaceous-Tertiary boundary in the Antarctic: Climatic cooling precedes biotic crisis

NASA Technical Reports Server (NTRS)

Stott, Lowell D.; Kennett, James P.

1988-01-01

Stable isotopic investigations were conducted on calcareous microfossils across two deep sea Cretaceous-Tertiary boundary sequences on Maud Rise, Weddell Sea, Antarctica. The boundary is taken at the level of massive extinctions in calcareous planktonic microfossils, and coincides with a sharp lithologic change from pure calcareous ooze to calcareous ooze with a large volcanic clay component. The uppermost Maestrichtian is marked by a long-term decrease in delta value of 0 to 18 which spans most of the lower and middle A. mayaroensis Zone and represents a warming trend which culminated in surface water temperatures of about 16 C. At approximately 3 meters below the K-T boundary this warming trend terminates abruptly and benthic and planktonic isotopic records exhibit a rapid increase in delta value of 0 to 18 that continues up to the K-T boundary. The trend towards cooler surface water temperatures stops abruptly at the K-T boundary and delta value of 0 to 18 values remain relatively stable through the Paleocene. Comparison of the Antarctic sequence with the previously documented deep sea records in the South Atlantic reveal shifts of similar magnitude in the latest Maestrichtian. It is indicated that the Southern Ocean underwent the most significant, and apparently permanent, climatic change. The latest Cretaceous oxygen isotopic shift recorded at Maud Rise and other deep sea sites is similar in magnitude to large positive delta valve of 0 to 18 shifts in the middle Eocene, at the Eocene/Oligocene boundary and in the middle Miocene that marked large scale climatic transitions which ultimately lead to cryospheric development of the Antarctic. The climatic shift at the end of the Cretaceous represents one of the most significant climatic transitions recorded in the latest Phanerozoic and had a profound effect on global climate as well as oceanic circulation.

Optimizing expression of the pregnancy malaria vaccine candidate, VAR2CSA in Pichia pastoris.

PubMed

Avril, Marion; Hathaway, Marianne J; Cartwright, Megan M; Gose, Severin O; Narum, David L; Smith, Joseph D

2009-06-29

VAR2CSA is the main candidate for a vaccine against pregnancy-associated malaria, but vaccine development is complicated by the large size and complex disulfide bonding pattern of the protein. Recent X-ray crystallographic information suggests that domain boundaries of VAR2CSA Duffy binding-like (DBL) domains may be larger than previously predicted and include two additional cysteine residues. This study investigated whether longer constructs would improve VAR2CSA recombinant protein secretion from Pichia pastoris and if domain boundaries were applicable across different VAR2CSA alleles. VAR2CSA sequences were bioinformatically analysed to identify the predicted C11 and C12 cysteine residues at the C-termini of DBL domains and revised N- and C-termimal domain boundaries were predicted in VAR2CSA. Multiple construct boundaries were systematically evaluated for protein secretion in P. pastoris and secreted proteins were tested as immunogens. From a total of 42 different VAR2CSA constructs, 15 proteins (36%) were secreted. Longer construct boundaries, including the predicted C11 and C12 cysteine residues, generally improved expression of poorly or non-secreted domains and permitted expression of all six VAR2CSA DBL domains. However, protein secretion was still highly empiric and affected by subtle differences in domain boundaries and allelic variation between VAR2CSA sequences. Eleven of the secreted proteins were used to immunize rabbits. Antibodies reacted with CSA-binding infected erythrocytes, indicating that P. pastoris recombinant proteins possessed native protein epitopes. These findings strengthen emerging data for a revision of DBL domain boundaries in var-encoded proteins and may facilitate pregnancy malaria vaccine development.

Optimizing expression of the pregnancy malaria vaccine candidate, VAR2CSA in Pichia pastoris

PubMed Central

Avril, Marion; Hathaway, Marianne J; Cartwright, Megan M; Gose, Severin O; Narum, David L; Smith, Joseph D

2009-01-01

Background VAR2CSA is the main candidate for a vaccine against pregnancy-associated malaria, but vaccine development is complicated by the large size and complex disulfide bonding pattern of the protein. Recent X-ray crystallographic information suggests that domain boundaries of VAR2CSA Duffy binding-like (DBL) domains may be larger than previously predicted and include two additional cysteine residues. This study investigated whether longer constructs would improve VAR2CSA recombinant protein secretion from Pichia pastoris and if domain boundaries were applicable across different VAR2CSA alleles. Methods VAR2CSA sequences were bioinformatically analysed to identify the predicted C11 and C12 cysteine residues at the C-termini of DBL domains and revised N- and C-termimal domain boundaries were predicted in VAR2CSA. Multiple construct boundaries were systematically evaluated for protein secretion in P. pastoris and secreted proteins were tested as immunogens. Results From a total of 42 different VAR2CSA constructs, 15 proteins (36%) were secreted. Longer construct boundaries, including the predicted C11 and C12 cysteine residues, generally improved expression of poorly or non-secreted domains and permitted expression of all six VAR2CSA DBL domains. However, protein secretion was still highly empiric and affected by subtle differences in domain boundaries and allelic variation between VAR2CSA sequences. Eleven of the secreted proteins were used to immunize rabbits. Antibodies reacted with CSA-binding infected erythrocytes, indicating that P. pastoris recombinant proteins possessed native protein epitopes. Conclusion These findings strengthen emerging data for a revision of DBL domain boundaries in var-encoded proteins and may facilitate pregnancy malaria vaccine development. PMID:19563628

Inverted temperature sequences: role of deformation partitioning

NASA Astrophysics Data System (ADS)

Grujic, D.; Ashley, K. T.; Coble, M. A.; Coutand, I.; Kellett, D.; Whynot, N.

2015-12-01

The inverted metamorphism associated with the Main Central thrust zone in the Himalaya has been historically attributed to a number of tectonic processes. Here we show that there is actually a composite peak and deformation temperature sequence that formed in succession via different tectonic processes. The deformation partitioning seems to the have played a key role, and the magnitude of each process has varied along strike of the orogen. To explain the formation of the inverted metamorphic sequence across the Lesser Himalayan Sequence (LHS) in eastern Bhutan, we used Raman spectroscopy of carbonaceous material (RSCM) to determine the peak metamorphic temperatures and Ti-in-quartz thermobarometry to determine the deformation temperatures combined with thermochronology including published apatite and zircon U-Th/He and fission-track data and new 40Ar/39Ar dating of muscovite. The dataset was inverted using 3D-thermal-kinematic modeling to constrain the ranges of geological parameters such as fault geometry and slip rates, location and rates of localized basal accretion, and thermal properties of the crust. RSCM results indicate that there are two peak temperature sequences separated by a major thrust within the LHS. The internal temperature sequence shows an inverted peak temperature gradient of 12 °C/km; in the external (southern) sequence, the peak temperatures are constant across the structural sequence. Thermo-kinematic modeling suggest that the thermochronologic and thermobarometric data are compatible with a two-stage scenario: an Early-Middle Miocene phase of fast overthrusting of a hot hanging wall over a downgoing footwall and inversion of the synkinematic isotherms, followed by the formation of the external duplex developed by dominant underthrusting and basal accretion. To reconcile our observations with the experimental data, we suggest that pervasive ductile deformation within the upper LHS and along the Main Central thrust zone at its top stopped at ~11 Ma at which time the deformation shifted and focused within the external duplex and the Main Boundary Thrust.

Stratigraphy of Atlantic coastal margin of United States north of Cape Hatteras; brief survey

USGS Publications Warehouse

Perry, W.J.; Minard, J.P.; Weed, E.G.A.; Robbins, E.I.; Rhodehamel, E.C.

1975-01-01

A synthesis of studies of sea-floor outcrops of the sedimentary wedge beneath the northeastern United States continental shelf and slope and a reassessment of coastal plain Mesozoic stratigraphy, particularly of the coastal margin, provide insight for estimating the oil and gas potential and provide geologic control for marine seismic investigations of the Atlantic continental margin. The oldest strata known to crop out on the continental slope are late Campanian in age. The Cretaceous-Tertiary contact along the slope ranges from a water depth of 0.6 to 1.5 km south of Georges Bank to 1.8 km in Hudson Canyon. Few samples are available from Tertiary and Late Cretaceous outcrops along the slope. Sediments of the Potomac Group, chiefly of Early Cretaceous age, constitute a major deltaic sequence in the emerged coastal plain. This thick sequence lies under coastal Virginia, Maryland, Delaware, southeastern New Jersey, and the adjacent continental shelf. Marine sands associated with this deltaic sequence may be present seaward under the outer continental shelf. South of the Norfolk arch, under coastal North Carolina, carbonate rocks interfinger with Lower Cretaceous clastic strata. From all available data, Mesozoic correlations in coastal wells between coastal Virginia and Long Island have been revised. The Upper-Lower Cretaceous boundary is placed at the transition between Albian and Cenomanian floras. Potential hydrocarbon source beds are present along the coast in the subsurface sediments of Cretaceous age. Potential reservoir sandstones are abundant in this sequence.

Investigation of Tectonic Boundaries in Taiwan Obtained with a Hierarchical Clustering of Dense GNSS Data

NASA Astrophysics Data System (ADS)

Takahashi, A.; Hashimoto, M.; Hu, J. C.; Fukahata, Y.

2017-12-01

Taiwan Island is composed of many geological structures. The main tectonic feature is the collision of the Luzon volcanic arc with the Eurasian continent, which propagates westward and generates complicated crustal deformation. One way to model crustal deformation is to divide Taiwan island into man rigid blocks that moves relatively each other along the boundaries (deformation zones) of the blocks. Since earthquakes tend to occur in the deformation zones, identification of such tectonic boundaries is important. So far, many tectonic boundaries have been proposed on the basis of geology, geomorphology, seismology and geodesy. However, which is the most significant boundary depends on disciplines and there is no way to objectively classify them. Here, we introduce an objective method to identify significant tectonic boundaries with a hierarchical representation proposed by Simpson et al. [2012].We apply a hierarchical agglomerative clustering algorithm to dense GNSS horizontal velocity data in Taiwan. One of the significant merits of the hierarchical representation of the clustering results is that we can consistently explore crustal structures from larger to smaller scales. This is because a higher hierarchy corresponds to a larger crustal structure, and a lower hierarchy corresponds to a smaller crustal structure. Relative motion between clusters can be obtained from this analysis.The first major boundary is identified along the eastern margin of the Longitudinal Valley, which corresponds to the separation of the Philippine Sea plate and the Eurasian continental margin. The second major boundary appears along the Chaochou fault and the Chishan fault in southwestern Taiwan. The third major boundary appears along the eastern margin of the coastal plane. The identified major clusters can be divided into several smaller blocks without losing consistency with geological boundaries. For example, the Fengshun fault, concealed beneath thick sediment layers, is identified. Furthermore, obtained relative motion between clusters demands a reverse fault or a left lateral fault in the off shore of the coastal range.Our clustering based block modeling is consistent with tectonics of Taiwan, implying that observed crustal deformation in Taiwan can be attributed to motion or deformation of shallow structures.

Building a Lego wall: Sequential action selection.

PubMed

Arnold, Amy; Wing, Alan M; Rotshtein, Pia

2017-05-01

The present study draws together two distinct lines of enquiry into the selection and control of sequential action: motor sequence production and action selection in everyday tasks. Participants were asked to build 2 different Lego walls. The walls were designed to have hierarchical structures with shared and dissociated colors and spatial components. Participants built 1 wall at a time, under low and high load cognitive states. Selection times for correctly completed trials were measured using 3-dimensional motion tracking. The paradigm enabled precise measurement of the timing of actions, while using real objects to create an end product. The experiment demonstrated that action selection was slowed at decision boundary points, relative to boundaries where no between-wall decision was required. Decision points also affected selection time prior to the actual selection window. Dual-task conditions increased selection errors. Errors mostly occurred at boundaries between chunks and especially when these required decisions. The data support hierarchical control of sequenced behavior. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

The Cretaceous/Paleogene Transition on the East Tasman Plateau, Southwestern Pacific

NASA Technical Reports Server (NTRS)

Schellenberg, Stephen A.; Brinkhuis, Henk; Stickley, Catherine E.; Fuller, Michael; Kyte, Frank T.; Williams, Graham L.

2004-01-01

Ocean Drilling Program Leg 189 recovered a potentially complete shallow marine record of the Cretaceous-Paleogene boundary (KPB) at Site 1172 on the East Tasman Plateau. Here we present high-resolution (cm-scale) data from micropaleontology, geochemistry, sedimentology, and paleomagnetism that provide no evidence for a complete KPB, but instead suggest a boundary-spanning hiatus of at least 0.8 Ma. We interpret this hiatus to represent the sequence boundary between the uppermost Maastrichtian Tal.1 and lowermost Danian Ta1.2/ Da- 1 3rd-order sequence stratigraphic cycles. Microfloral assemblages indicate generally shallow paleodepths, restricted circulation, and eutrophic conditions through the section. Paleodepths progressively shallow through the late Maastrichtian, while more oceanic and warmer conditions dominate the early Danian. The Site 1172 KPB section is broadly comparable to other southern highlatitude sections in Antarctica and New Zealand, but appears to record a shallower and more restricted environment that permitted a eustatically-driven hiatus across the KPB mass extinction event.

Stable isotope stratigraphy of Latest Miocene sequences in northwest Morocco: The Bou Regreg section

NASA Astrophysics Data System (ADS)

Hodell, David A.; Benson, Richard H.; Kennett, James P.; Rakic-El Bied, Kruna

1989-08-01

Oxygen and carbon isotopic ratios of foraminifers were measured from outcrop and drill core sequences from the Bou Regreg Section, northwest Morocco. This composite section was located at the western end of the Rifian Corridor during the late Miocene and thus potentially contains a record of water exchange between the Atlantic and Mediterranean during the late Tortonian and Messinian stages. Here we correlate isotopic and sedimentologic events in the Bou Regreg Section with Mediterranean and deep-sea sequences during the time leading up to and including the deposition of the Messinian evaporites. The late Miocene chron 6 carbon shift was identified in two Moroccan sequences, providing a valuable 6.3-Ma datum level. In both sections, the carbon shift coincides with the first occurrence of Globorotalia conomiozea and the Tortonian/Messinian boundary. Near this boundary, a major faunal turnover occurred in ostracod, planktonic foraminiferal, and nannofossil assemblages that indicates a cooling of surface and deep water in the Rifian Corridor. At 6.1 Ma, just above the Tortonian/Messinian boundary, mean ∂18O values of benthic foraminifers increased by 0.4-0.5‰ suggesting decreased temperature and/or increased continental ice volume. The faunal and isotopic changes are interpreted as reflecting a reversal in the direction of deep water flow through the Rifian Corridor that occurred between 6.3 and 6.1 Ma. At this time, cold, nutrient-rich waters filled the Mediterranean basins from intermediate depths of the Atlantic, and the production of Mediterranean Outflow Water ceased. The upwelling of nutrient-rich Atlantic intermediate water stimulated productivity in the Mediterranean, which led to the deposition of organic-rich strata such as those found in the Tripoli Formation. At ˜5.5 Ma, coincident with a coiling shift in Neogloboquadrina acostaensis, the variability of the benthic ∂18O signal increased markedly, and strong color variations appeared in the sediments (alternating between red and blue marls). These isotopic and sedimentologic changes at Bou Regreg represented markedly fluctuating oceanographic conditions in the Rifian Corridor between 5.5 and 4.8 Ma. We speculate that these cycles were related to sea level variations that controlled the periodic influx of marine water into the Mediterranean during the time of evaporite deposition. The onset of these cycles occurred at 5.5 Ma and is correlated to a eustatic fall in sea level at the base of the Caliza Tosca Formation in Carmona, Spain, and to the base of the lowermost evaporite unit in the Mediterranean (e.g., Calcare di Base in Sicily). In this proposed scenario, the duration of the Messinian salinity crisis was 700,000 years and lasted between 5.5 and 4.8 Ma.

Evaluating a robust contour tracker on echocardiographic sequences.

PubMed

Jacob, G; Noble, J A; Mulet-Parada, M; Blake, A

1999-03-01

In this paper we present an evaluation of a robust visual image tracker on echocardiographic image sequences. We show how the tracking framework can be customized to define an appropriate shape space that describes heart shape deformations that can be learnt from a training data set. We also investigate energy-based temporal boundary enhancement methods to improve image feature measurement. Results are presented demonstrating real-time tracking on real normal heart motion data sequences and abnormal synthesized and real heart motion data sequences. We conclude by discussing some of our current research efforts.

Relation of the lower Pennsylvanian unconformity to a mid-carboniferous eustatic event in the eastern United States

USGS Publications Warehouse

Englund, K.J.; Thomas, R.E.

1997-01-01

Two contrasting concepts specifying the age and duration of the hiatus resulting from a mid-Carboniferous eustatic event in the eastern United States are based on different evidence. The original model indicated that the hiatus is at an unconformity in cratonic areas that was assumed to coincide with the Mississippian-Pennsylvanian boundary at the contact between the Mississippian Bluestone Formation and the Pennsylvanian Pocahontas Formation in the Appalachian foreland basin. This concept was adhered to exclusively until 1969 and continues to reappear in reports dealing with global correlations and division of the Carboniferous into the Mississippian and Pennsylvanian Systems. This division is at a major eustatic event that supposedly occurred at about 330 Ma in scattered parts of the world, including the Appalachian basin. An alternative concept, fully supported by geologic mapping and biostratigraphic studies, indicates that the unconformity and associated hiatus are much younger because they originate in the Appalachian foreland basin in the lower part (upper Namurian) of the Lower Pennsylvanian New River Formation, about 260 m above the Mississippian-Pennsylvanian boundary. The duration of this hiatus increases in a northwesterly direction onto the cratonic shelf because the unconformity progressively truncated the underlying Lower Pennsylvanian and Upper Mississippian successions. The westward onlap of Pennsylvanian strata onto the eroded surface resulted in a hiatus from the Early Mississippian (Tournaisian) to the Middle Pennsylvanian (Westphalian B). The systemic boundary, which is in a depositional continuous sequence of strata in the Appalachian foreland basin, was correlated biostratigraphically by Pfefferkorn and Gillespie in 1982 with Gothan's "Florensprung" (floral break) described in 1913 at the Namurian A-B boundary in the Upper Silesian basin. An intra-Namurian erosive event was noted also in the Upper Silesian basin by Havlena, who reported in 1982 that an intra-Namurian erosive contact occurs well above the Florensprung. The origin of the Florensprung in depositional continuous strata has been attributed to tectonism, environment, or climate. However, spherules found in depositional continuous strata near the Mississippian-Pennsylvanian boundary in the Appalachian basin indicate that the effect of an asteroid impact may be the underlying cause for the biodiversity noted at the systemic boundary.

Deletion endpoint allele-specificity in the developmentally regulated elimination of an internal sequence (IES) in Paramecium.

PubMed Central

Dubrana, K; Le Mouël, A; Amar, L

1997-01-01

Ciliated protozoa undergo thousands of site-specific DNA deletion events during the programmed development of micronuclear genomes to macronuclear genomes. Two deletion elements, W1 and W2, were identified in the Paramecium primaurelia wild-type 156 strain. Here, we report the characterization of both elements in wild-type strain 168 and show that they display variant deletion patterns when compared with those of strain 156. The W1 ( 168 ) element is defective for deletion. The W2 ( 168 ) element is excised utilizing two alternative boundaries on one side, both are different from the boundary utilized to excise the W2156 element. By crossing the 156 and 168 strains, we demonstrate that the definition of all deletion endpoints are each controlled by cis -acting determinant(s) rather than by strain-specific trans-acting factor(s). Sequence comparison of all deleted DNA segments indicates that the 5'-TA-3'terminal sequence is strictly required at their ends. Furthermore the identity of the first eight base pairs of these ends to a previously established consensus sequence correlates with the frequency of the corresponding deletion events. Our data implies the existence of an adaptive convergent evolution of these Paramecium deleted DNA segment end sequences. PMID:9171098

Sequence stratigraphy of the Monterey Formation, Santa Barbara County: Integration of physical, chemical, and biofacies data from outcrop and subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bohacs, K.M.

1991-02-01

Deep basinal rocks of the Monterey Formation can be allocated to different depositional environments based on an integration of bedding, stacking patterns of facies, lithology, biofacies, and inorganic and organic chemistry. These rocks show evidence of systematic changes in depositional environments that can be related to eustatic sea level changes and basin evolution. Even deep-basinal environments are affected by changing sea level through changes in circulation patterns and intensities, nutrient budgets and dispersal patterns, and location and intensity of the oceanic oxygen minimum. The sequence-stratigraphic framework was constructed based on the physical expression of the outcrop strata and confirmed bymore » typing the outcrop sections to an integrated will-log/seismic grid through outcrop gamma-ray spectral profiles. Interpretation of a sequence boundary was based on increased proportions of hemipelagic facies and evidence of increased bottom-energy levels above the boundary, and local erosion and relief on the surface. The proportion of shallower water and reworked dinoflagellates increased to a local maximum above the boundary. Downlap surfaces exhibited increased proportions of pelagic facies around the surface, a secular change in the dominant lithology across the surface, evidence of decreased bottom-energy levels and terrigenous sedimentation rates, and little or not significant erosion on the surface. The proportion of deeper water dinoflagellates increased to a local maximum at or near the downlap surface; there was no evidence of reworked individuals. The detailed sequence-stratigraphic framework makes it possible to tie rock properties to genetic processes for construction of predictive models.« less

Form drag in rivers due to small-scale natural topographic features: 2. Irregular sequences

USGS Publications Warehouse

Kean, J.W.; Smith, J.D.

2006-01-01

The size, shape, and spacing of small-scale topographic features found on the boundaries of natural streams, rivers, and floodplains can be quite variable. Consequently, a procedure for determining the form drag on irregular sequences of different-sized topographic features is essential for calculating near-boundary flows and sediment transport. A method for carrying out such calculations is developed in this paper. This method builds on the work of Kean and Smith (2006), which describes the flow field for the simpler case of a regular sequence of identical topographic features. Both approaches model topographic features as two-dimensional elements with Gaussian-shaped cross sections defined in terms of three parameters. Field measurements of bank topography are used to show that (1) the magnitude of these shape parameters can vary greatly between adjacent topographic features and (2) the variability of these shape parameters follows a lognormal distribution. Simulations using an irregular set of topographic roughness elements show that the drag on an individual element is primarily controlled by the size and shape of the feature immediately upstream and that the spatial average of the boundary shear stress over a large set of randomly ordered elements is relatively insensitive to the sequence of the elements. In addition, a method to transform the topography of irregular surfaces into an equivalently rough surface of regularly spaced, identical topographic elements also is given. The methods described in this paper can be used to improve predictions of flow resistance in rivers as well as quantify bank roughness.

PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies.

PubMed

Jeon, Jouhyun; Arnold, Roland; Singh, Fateh; Teyra, Joan; Braun, Tatjana; Kim, Philip M

2016-04-01

The identification of structured units in a protein sequence is an important first step for most biochemical studies. Importantly for this study, the identification of stable structured region is a crucial first step to generate novel synthetic antibodies. While many approaches to find domains or predict structured regions exist, important limitations remain, such as the optimization of domain boundaries and the lack of identification of non-domain structured units. Moreover, no integrated tool exists to find and optimize structural domains within protein sequences. Here, we describe a new tool, PAT ( http://www.kimlab.org/software/pat ) that can efficiently identify both domains (with optimized boundaries) and non-domain putative structured units. PAT automatically analyzes various structural properties, evaluates the folding stability, and reports possible structural domains in a given protein sequence. For reliability evaluation of PAT, we applied PAT to identify antibody target molecules based on the notion that soluble and well-defined protein secondary and tertiary structures are appropriate target molecules for synthetic antibodies. PAT is an efficient and sensitive tool to identify structured units. A performance analysis shows that PAT can characterize structurally well-defined regions in a given sequence and outperforms other efforts to define reliable boundaries of domains. Specially, PAT successfully identifies experimentally confirmed target molecules for antibody generation. PAT also offers the pre-calculated results of 20,210 human proteins to accelerate common queries. PAT can therefore help to investigate large-scale structured domains and improve the success rate for synthetic antibody generation.

COMOC 2: Two-dimensional aerodynamics sequence, computer program user's guide

NASA Technical Reports Server (NTRS)

Manhardt, P. D.; Orzechowski, J. A.; Baker, A. J.

1977-01-01

The COMOC finite element fluid mechanics computer program system is applicable to diverse problem classes. The two dimensional aerodynamics sequence was established for solution of the potential and/or viscous and turbulent flowfields associated with subsonic flight of elementary two dimensional isolated airfoils. The sequence is constituted of three specific flowfield options in COMOC for two dimensional flows. These include the potential flow option, the boundary layer option, and the parabolic Navier-Stokes option. By sequencing through these options, it is possible to computationally construct a weak-interaction model of the aerodynamic flowfield. This report is the user's guide to operation of COMOC for the aerodynamics sequence.

Reappraisal of the sequence boundary in time and space: Case and considerations for an SU (subaerial unconformity) that is not a sediment bypass surface, a time barrier, or an unconformity

NASA Astrophysics Data System (ADS)

Holbrook, John M.; Bhattacharya, Janok P.

2012-07-01

The sequence-bounding unconformity bears the key defining traits of being "a surface separating younger from older strata, along which there is evidence of subaerial erosional truncation … or subaerial exposure, with a significant hiatus indicated (Van Wagoner et al., 1988)." This subaerial component of sequence boundaries (subaerial unconformity—SU) is also broadly considered to form as a topographic surface of sediment bypass, carved during relative sea level fall and buried by backfilling during relative sea level rise. Accordingly, the SU is commonly presumed to record an approximate time barrier, which separates older from younger strata along its full length. In this paper we show that regional composite scour (RCS) surfaces that are traditionally mapped as an integral component of the SU were never a single subaerial topographic surface characterized by sediment bypass, are not unconformities, do not record an effective time barrier, and form diachronously at the channel-belt scale over the entire fall to rise of a base-level cycle. These RCS surfaces, and by inference the SU surfaces they comprise, thus do not fully fit key defining characteristics embodied in the conceptual sequence boundary. Flume observations and field data show that the RCS is buried by fluvial sediment simultaneously as it is scoured. Accordingly, the RCS is perennially covered with stored sediment during formation, is only exposed as a subaerial topographic surface at the local place and time where it is undergoing active growth, and forms over the duration of local marine drainage during a relative sea-level cycle. This "cut-and-cover" model differs greatly from more established "bypass" models, which assume that the RCS was roughly sediment free and subaerially exposed for long durations of incision during regression and thus preserves a significant depositional hiatus upon later burial. Instead, the RCS may commonly and locally record a hiatus more typical of a facies-bounding diastem without a lacuna significantly greater than that of surfaces within the strata it binds. Fragments of fluvial strata may commonly and sporadically be preserved above the RCS that are older than underlying marine units overrun by this surface. Consequently, the RCS is not an effective time barrier. Lateral planation by migrating and avulsing channels as the RCS expands laterally after nucleation can place younger fluvial strata over much older units, which means that this surface is also composite and highly diachronous laterally at the scale of channel belts. The cut-and-cover model has additional implications not captured by the bypass model. First, significant sediments may be stored within fluvial strata above the RCS during regression that are not available for contemporary falling stage and lowstand marine shorelines. This can result in marine sediment starvation, particularly of the sand fraction, and in extreme cases can result in sand autodetachment and an absence of regressive marine reservoir sandstones. Second, cutting of the RCS co-generates a suprafluvial surface above the covering fluvial strata during regression that may be used as a mappable proxy for the conceptual maximum regressive surface (MRS). The MRS may be raised above this surface locally by low-accommodation aggradation during lowstand normal regression, but in either case preserves an approximate time line where not reworked during later transgression. Third, valley development across the RCS does not exclusively form by landward knickpoint growth, and may include complexly formed and potentially cross-cutting buffer valleys. SU valley incision can be divided into four modes, which include denudation, structural, buttress, and buffer valley components, which may work together locally and tend to have variable importance along the shore-to-hinterland profile. Although the RCS is not a good rock proxy for the conceptual sequence boundary it remains a very mappable surface which may separate facies of potentially very different origin and reservoir quality. The RCS is also inseparable from the SU and typically the only terrestrial erosional surface of extent in most short-duration sequences. Its nullification as a sequence boundary would mean abandonment of depositional sequence stratigraphy as a correlation and interpretive tool within these sections. An alternative to abandonment of the SU as a sequence boundary is to loosen the definition of a sequence boundary to 'a discrete surface of erosional truncation carved landward of contemporary shorelines that is traceable beyond the scale of a single valley or comparable local system, and its correlative surfaces of conformity and/or non-deposition', and continue its use as before.

Precessional forcing of lacustrine sedimentation in the late Cenozoic Chemeron Basin, Central Kenya Rift, and calibration of the Gauss/Matuyama boundary

USGS Publications Warehouse

Deino, A.L.; Kingston, J.D.; Glen, J.M.; Edgar, R.K.; Hill, A.

2006-01-01

The fluviolacustrine sedimentary sequence of the Chemeron Formation exposed in the Barsemoi River drainage, Tugen Hills, Kenya, contains a package of five successive diatomite/fluvial cycles that record the periodic development of freshwater lakes within the axial portion of the Central Kenya Rift. The overwhelming abundance in the diatomite of planktonic species of the genera Aulacoseira and Stephanodiscus, and the virtual absence of benthic littoral diatoms and detrital material indicate areally extensive, deep lake systems. A paleomagnetic reversal stratigraphy has been determined and chronostratigraphic tie points established by 40Ar/39Ar dating of intercalated tuffs. The sequence spans the interval 3.1-2.35??Ma and bears a detailed record of the Gauss/Matuyama paleomagnetic transition. The 40Ar/39Ar age for this boundary of 2.589 ?? 0.003??Ma can be adjusted to concordance with the Astronomical Polarity Time Scale (APTS) on the basis of an independent calibration to 2.610??Ma, 29??kyr older than the previous APTS age. The diatomites recur at an orbital precessional interval of 23??kyr and are centered on a 400-kyr eccentricity maximum. It is concluded that these diatomite/fluvial cycles reflect a narrow interval of orbitally forced wet/dry climatic conditions that may be expressed regionally across East Africa. The timing of the lacustrine pulses relative to predicted insolation models favors origination of moisture from the northern Africa monsoon, rather than local circulation driven by direct equatorial insolation. This moisture event at 2.7-2.55??Ma, and later East African episodes at 1.9-1.7 and 1.1-0.9??Ma, are approximately coincident with major global climatic and oceanographic events. ?? 2006 Elsevier B.V. All rights reserved.

Propeller noise prediction

NASA Technical Reports Server (NTRS)

Zorumski, W. E.

1983-01-01

Analytic propeller noise prediction involves a sequence of computations culminating in the application of acoustic equations. The prediction sequence currently used by NASA in its ANOPP (aircraft noise prediction) program is described. The elements of the sequence are called program modules. The first group of modules analyzes the propeller geometry, the aerodynamics, including both potential and boundary layer flow, the propeller performance, and the surface loading distribution. This group of modules is based entirely on aerodynamic strip theory. The next group of modules deals with the actual noise prediction, based on data from the first group. Deterministic predictions of periodic thickness and loading noise are made using Farassat's time-domain methods. Broadband noise is predicted by the semi-empirical Schlinker-Amiet method. Near-field predictions of fuselage surface pressures include the effects of boundary layer refraction and (for a cylinder) scattering. Far-field predictions include atmospheric and ground effects. Experimental data from subsonic and transonic propellers are compared and NASA's future direction is propeller noise technology development are indicated.

Program for the solution of multipoint boundary value problems of quasilinear differential equations

NASA Technical Reports Server (NTRS)

1973-01-01

Linear equations are solved by a method of superposition of solutions of a sequence of initial value problems. For nonlinear equations and/or boundary conditions, the solution is iterative and in each iteration a problem like the linear case is solved. A simple Taylor series expansion is used for the linearization of both nonlinear equations and nonlinear boundary conditions. The perturbation method of solution is used in preference to quasilinearization because of programming ease, and smaller storage requirements; and experiments indicate that the desired convergence properties exist although no proof or convergence is given.

Aptian-Albian boundary in Central Southern Atlas of Tunisia: New tectono-sedimentary facts

NASA Astrophysics Data System (ADS)

Ghanmi, Mohamed Abdelhamid; Barhoumi, Amine; Ghanmi, Mohamed; Zargouni, Fouad

2017-08-01

The Aptian-Albian boundary preserves one of the most important events in Central-Southern Atlas of Tunisia, which belongs to the Southern Tethyan margin. A major sedimentary break was recorded between Early Aptian and Albian series in Bouhedma-Boudouaou Mountains. This major hiatus probably linked to the ''Austrian phase'' and to the Aptian and Albian ''Crisis'' testify a period of major tectonic events. In this paper, field observations on the Mid-Cretaceous stratigraphy combined with seismic profile interpretation were used for the first time to characterize the Aptian-Albian boundary in Central-Southern Atlas of Tunisia. Our new results reveal that Aptian-Albian boundary marks a critical interval not only in Maknassy-Mezzouna orogenic system but also in the Tunisian Atlas. Furthermore, Aptian-Albian series outcrop is marked by the important sedimentary gaps as well as a dramatic thickness change from West to East and predominately from North to South. This is linked to the extensional tectonic features which characterize all the Central-Southern Atlas of Tunisia.

Magnetostratigraphic correlations of Permian-Triassic marine-to-terrestrial sections from China

USGS Publications Warehouse

Glen, J.M.G.; Nomade, S.; Lyons, J.J.; Metcalfe, I.; Mundil, R.; Renne, P.R.

2009-01-01

We have studied three Permian–Triassic (PT) localities from China as part of a combined magnetostratigraphic, 40Ar/39Ar and U–Pb radioisotopic, and biostratigraphic study aimed at resolving the temporal relations between terrestrial and marine records across the Permo-Triassic boundary, as well as the rate of the biotic recovery in the Early Triassic. The studied sections from Shangsi (Sichuan Province), Langdai (Guihzou Province), and the Junggar basin (Xinjiang Province), span marine, paralic, and terrestrial PT environments, respectively. Each of these sections was logged in detail in order to place geochronologic, paleomagnetic, geochemical, conodont and palynologic samples within a common stratigraphic context. Here we present rock-magnetic, paleomagnetic and magnetostratigraphic results from the three localities.At Shangsi, northern Sichuan Province, we sampled three sections spanning Permo-Triassic marine carbonates. Magnetostratigraphic results from the three sections indicate that the composite section contains at least eight polarity chrons and that the PT boundary occurs within a normal polarity chron a short distance above the mass extinction level and a reversed-to-normal (R-N) polarity reversal. Furthermore, the onset of the Illawarra mixed interval lies below the sampled section indicating that the uppermost Permian Changhsingian and at least part of the Wuchiapingian stages postdate the end of the Kiaman Permo-Carboniferous Reversed Superchron.At Langdai, Guizhou Province, we studied magnetostratigraphy of PT paralic mudstone and carbonate sediments in two sections. The composite section spans an R-N polarity sequence. Section-mean directions pass a fold test at the 95% confidence level, and the section-mean poles are close to the mean PT pole for the South China block. Based on biostratigraphic constraints, the R-N transition recorded at Langdai is consistent with that at Shangsi and demonstrates that the PT boundary occurred within a normal polarity chron a short distance above the mass extinction level.In the southern Junggar basin, Xinjiang Province, in northwest China, we determined the magnetostratigraphy of three sections of a terrestrial sequence. Normal and reversed polarity directions are roughly antipodal, and magnetostratigraphies from the three sections are highly consistent. Combined bio- and magneto-stratigraphy used to correlate this sequence to other PT sequences suggests that the previously-proposed biostratigraphic PT boundary in the Junggar sections was most likely misplaced by earlier workers suggesting that further work is necessary to confidently place the PT boundary there.

Whole-brain intracranial vessel wall imaging at 3 Tesla using cerebrospinal fluid-attenuated T1-weighted 3D turbo spin echo.

PubMed

Fan, Zhaoyang; Yang, Qi; Deng, Zixin; Li, Yuxia; Bi, Xiaoming; Song, Shlee; Li, Debiao

2017-03-01

Although three-dimensional (3D) turbo spin echo (TSE) with variable flip angles has proven to be useful for intracranial vessel wall imaging, it is associated with inadequate suppression of cerebrospinal fluid (CSF) signals and limited spatial coverage at 3 Tesla (T). This work aimed to modify the sequence and develop a protocol to achieve whole-brain, CSF-attenuated T 1 -weighted vessel wall imaging. Nonselective excitation and a flip-down radiofrequency pulse module were incorporated into a commercial 3D TSE sequence. A protocol based on the sequence was designed to achieve T 1 -weighted vessel wall imaging with whole-brain spatial coverage, enhanced CSF-signal suppression, and isotropic 0.5-mm resolution. Human volunteer and pilot patient studies were performed to qualitatively and quantitatively demonstrate the advantages of the sequence. Compared with the original sequence, the modified sequence significantly improved the T 1 -weighted image contrast score (2.07 ± 0.19 versus 3.00 ± 0.00, P = 0.011), vessel wall-to-CSF contrast ratio (0.14 ± 0.16 versus 0.52 ± 0.30, P = 0.007) and contrast-to-noise ratio (1.69 ± 2.18 versus 4.26 ± 2.30, P = 0.022). Significant improvement in vessel wall outer boundary sharpness was observed in several major arterial segments. The new 3D TSE sequence allows for high-quality T 1 -weighted intracranial vessel wall imaging at 3 T. It may potentially aid in depicting small arteries and revealing T 1 -mediated high-signal wall abnormalities. Magn Reson Med 77:1142-1150, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

The Complete Chloroplast Genome of Banana (Musa acuminata, Zingiberales): Insight into Plastid Monocotyledon Evolution

PubMed Central

Martin, Guillaume; Baurens, Franc-Christophe; Cardi, Céline; Aury, Jean-Marc; D’Hont, Angélique

2013-01-01

Background Banana (genus Musa) is a crop of major economic importance worldwide. It is a monocotyledonous member of the Zingiberales, a sister group of the widely studied Poales. Most cultivated bananas are natural Musa inter-(sub-)specific triploid hybrids. A Musa acuminata reference nuclear genome sequence was recently produced based on sequencing of genomic DNA enriched in nucleus. Methodology/Principal Findings The Musa acuminata chloroplast genome was assembled with chloroplast reads extracted from whole-genome-shotgun sequence data. The Musa chloroplast genome is a circular molecule of 169,972 bp with a quadripartite structure containing two single copy regions, a Large Single Copy region (LSC, 88,338 bp) and a Small Single Copy region (SSC, 10,768 bp) separated by Inverted Repeat regions (IRs, 35,433 bp). Two forms of the chloroplast genome relative to the orientation of SSC versus LSC were found. The Musa chloroplast genome shows an extreme IR expansion at the IR/SSC boundary relative to the most common structures found in angiosperms. This expansion consists of the integration of three additional complete genes (rps15, ndhH and ycf1) and part of the ndhA gene. No such expansion has been observed in monocots so far. Simple Sequence Repeats were identified in the Musa chloroplast genome and a new set of Musa chloroplastic markers was designed. Conclusion The complete sequence of M. acuminata ssp malaccensis chloroplast we reported here is the first one for the Zingiberales order. As such it provides new insight in the evolution of the chloroplast of monocotyledons. In particular, it reinforces that IR/SSC expansion has occurred independently several times within monocotyledons. The discovery of new polymorphic markers within Musa chloroplast opens new perspectives to better understand the origin of cultivated triploid bananas. PMID:23840670

The complete chloroplast genome of banana (Musa acuminata, Zingiberales): insight into plastid monocotyledon evolution.

PubMed

Martin, Guillaume; Baurens, Franc-Christophe; Cardi, Céline; Aury, Jean-Marc; D'Hont, Angélique

2013-01-01

Banana (genus Musa) is a crop of major economic importance worldwide. It is a monocotyledonous member of the Zingiberales, a sister group of the widely studied Poales. Most cultivated bananas are natural Musa inter-(sub-)specific triploid hybrids. A Musa acuminata reference nuclear genome sequence was recently produced based on sequencing of genomic DNA enriched in nucleus. The Musa acuminata chloroplast genome was assembled with chloroplast reads extracted from whole-genome-shotgun sequence data. The Musa chloroplast genome is a circular molecule of 169,972 bp with a quadripartite structure containing two single copy regions, a Large Single Copy region (LSC, 88,338 bp) and a Small Single Copy region (SSC, 10,768 bp) separated by Inverted Repeat regions (IRs, 35,433 bp). Two forms of the chloroplast genome relative to the orientation of SSC versus LSC were found. The Musa chloroplast genome shows an extreme IR expansion at the IR/SSC boundary relative to the most common structures found in angiosperms. This expansion consists of the integration of three additional complete genes (rps15, ndhH and ycf1) and part of the ndhA gene. No such expansion has been observed in monocots so far. Simple Sequence Repeats were identified in the Musa chloroplast genome and a new set of Musa chloroplastic markers was designed. The complete sequence of M. acuminata ssp malaccensis chloroplast we reported here is the first one for the Zingiberales order. As such it provides new insight in the evolution of the chloroplast of monocotyledons. In particular, it reinforces that IR/SSC expansion has occurred independently several times within monocotyledons. The discovery of new polymorphic markers within Musa chloroplast opens new perspectives to better understand the origin of cultivated triploid bananas.

Early rifting deposition: examples from carbonate sequences of Sardinia (Cambrian) and Tuscany (Triassic-Jurassic), Italy: an analogous tectono-sedimentary and climatic context

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cocozza, T.; Gandin, A.

Lower Cambrian Ceroide Limestone (Sardinia) and Lower Jurassic Massiccio Limestone (Tuscany) belong to sequences deposited in analogous tectono-sedimentary context: the former linked to the Caledonian Sardic Phase, the latter to the Alpine Orogeny. Both units consist of massive pure limestone characterized by marginal and lagoonal sequences repeatedly interfingering in the same geological structure. This distribution indicates a morphology of the platforms composed of banks (marginal facies) and shallow basins (lagoonal facies) comparable with a Bahamian complex. Dolomitization affects patchily the massive limestone bodies, and karstic features, breccias, and sedimentary dikes occur at their upper boundary. Both units overlie early dolomitemore » and evaporites (sabkha facies) containing siliciclastic intercalations in their lower and/or upper part and are unconformably covered by open-shelf red (hematitic), nodular limestone Ammonitico Rosso facies). The sedimentary evolution of the two sequences appears to have been controlled by synsedimentary tectonics whose major effects are the end of the terrigenous input, the bank-and-basin morphology of the platform, the irregular distribution of the dolomitization, and the nodular fabric of the overlying facies. The end of the Bahamian-type system is marked by the karstification of the emerged blocks and is followed by their differential sinking and burial under red-nodular facies. From a geodynamic viewpoint, sequences composed of Bahamian-like platform carbonates followed by Ammonitico Rosso facies imply deposition along continental margins subjected to block-faulting during an extensional regime connected with the beginning of continental rifting. Moreover, the variation from sabkha to Bahamian conditions suggests the drifting of the continent from arid to humid, tropical areas.« less

Population subdivision of hydrothermal vent polychaete Alvinella pompejana across equatorial and Easter Microplate boundaries.

PubMed

Jang, Sook-Jin; Park, Eunji; Lee, Won-Kyung; Johnson, Shannon B; Vrijenhoek, Robert C; Won, Yong-Jin

2016-10-28

The Equator and Easter Microplate regions of the eastern Pacific Ocean exhibit geomorphological and hydrological features that create barriers to dispersal for a number of animals associated with deep-sea hydrothermal vent habitats. This study examined effects of these boundaries on geographical subdivision of the vent polychaete Alvinella pompejana. DNA sequences from one mitochondrial and eleven nuclear genes were examined in samples collected from ten vent localities that comprise the species' known range from 23°N latitude on the East Pacific Rise to 38°S latitude on the Pacific Antarctic Ridge. Multi-locus genotypes inferred from these sequences clustered the individual worms into three metapopulation segments - the northern East Pacific Rise (NEPR), southern East Pacific Rise (SEPR), and northeastern Pacific Antarctic Ridge (PAR) - separated by the Equator and Easter Microplate boundaries. Genetic diversity estimators were negatively correlated with tectonic spreading rates. Application of the isolation-with-migration (IMa2) model provided information about divergence times and demographic parameters. The PAR and NEPR metapopulation segments were estimated to have split roughly 4.20 million years ago (Mya) (2.42-33.42 Mya, 95 % highest posterior density, (HPD)), followed by splitting of the SEPR and NEPR segments about 0.79 Mya (0.07-6.67 Mya, 95 % HPD). Estimates of gene flow between the neighboring regions were mostly low (2 Nm < 1). Estimates of effective population size decreased with southern latitudes: NEPR > SEPR > PAR. Highly effective dispersal capabilities allow A. pompejana to overcome the temporal instability and intermittent distribution of active hydrothermal vents in the eastern Pacific Ocean. Consequently, the species exhibits very high levels of genetic diversity compared with many co-distributed vent annelids and mollusks. Nonetheless, its levels of genetic diversity in partially isolated populations are inversely correlated with tectonic spreading rates. As for many other vent taxa, this pioneering colonizer is similarly affected by local rates of habitat turnover and by major dispersal filters associated with the Equator and the Easter Microplate region.

Structural organization of the inactive X chromosome in the mouse

PubMed Central

Giorgetti, Luca; Lajoie, Bryan R.; Carter, Ava C.; Attia, Mikael; Zhan, Ye; Xu, Jin; Chen, Chong Jian; Kaplan, Noam; Chang, Howard Y.; Heard, Edith; Dekker, Job

2017-01-01

X-chromosome inactivation (XCI) involves major reorganization of the X chromosome as it becomes silent and heterochromatic. During female mammalian development, XCI is triggered by upregulation of the non-coding Xist RNA from one of the two X chromosomes. Xist coats the chromosome in cis and induces silencing of almost all genes via its A-repeat region1,2, although some genes (constitutive escapees) avoid silencing in most cell types, and others (facultative escapees) escape XCI only in specific contexts3. A role for Xist in organizing the inactive X (Xi) chromosome has been proposed4–6. Recent chromosome conformation capture approaches have revealed global loss of local structure on the Xi chromosome and formation of large mega-domains, separated by a region containing the DXZ4 macrosatellite7–10. However, the molecular architecture of the Xi chromosome, in both the silent and expressed regions, remains unclear. Here we investigate the structure, chromatin accessibility and expression status of the mouse Xi chromosome in highly polymorphic clonal neural progenitors (NPCs) and embryonic stem cells. We demonstrate a crucial role for Xist and the DXZ4-containing boundary in shaping Xi chromosome structure using allele-specific genome-wide chromosome conformation capture (Hi-C) analysis, an assay for transposase-accessible chromatin with high throughput sequencing (ATAC–seq) and RNA sequencing. Deletion of the boundary disrupts mega-domain formation, and induction of Xist RNA initiates formation of the boundary and the loss of DNA accessibility. We also show that in NPCs, the Xi chromosome lacks active/inactive compartments and topologically associating domains (TADs), except around genes that escape XCI. Escapee gene clusters display TAD-like structures and retain DNA accessibility at promoter-proximal and CTCF-binding sites. Furthermore, altered patterns of facultative escape genes in different neural progenitor clones are associated with the presence of different TAD-like structures after XCI. These findings suggest a key role for transcription and CTCF in the formation of TADs in the context of the Xi chromosome in neural progenitors. PMID:27437574

MOLECULAR SYSTEMATICS OF THE AVIAN SCHISTOSOME GENUS TRICHOBILHARZIA (TREMATODA: SCHISTOSOMATIDAE) IN NORTH AMERICA

PubMed Central

Brant, Sara V.; Loker, Eric S.

2010-01-01

Trichobilharzia is a genus of thread-like schistosomes with a cosmopolitan distribution in birds. Species of Trichobilharzia achieve notoriety as major etiological agents of cercarial dermatitis, or swimmer’s itch. There are 40 species described in the literature, for which the majority lacks molecular sequence information. To better understand the phylogenetic relationships, diversity, species boundaries, host use, and geographic distribution of this genus, we surveyed 378 birds and over 10,000 snails from North America. The phylogenetic analysis was based on nuclear 18S, 28S rDNA, internal transcribed spacer region and mitochondrial cytochrome oxidase I sequence data. Specimens were recovered that could be related to 6 of the 14 described species of Trichobilharzia from North America (T. physellae, T. querquedulae, T. szidati, T. stagnicolae, T. franki, and T. brantae). An additional 5 lineages were found that could not be related directly to previously described species. Trichobilharzia brantae, transmitted by Gyraulus parvus, grouped outside the clade containing the recognized species of Trichobilharzia. A subgroup of the Trichobilharzia clade designated Clade Q was comprised of closely related species whose adults and eggs are similar, yet the European species use lymnaeids whereas the North American species use physids as snail hosts. This molecular phylogeny provides a useful framework to: 1) facilitate identification of worms, including those involved in dermatitis outbreaks; 2) test hypotheses about the evolution, diversification, host-parasite interactions and character evolution of Trichobilharzia; and 3) guide future taxonomic revision of Trichobilharzia. PMID:20049999

Phrase boundary effects on the temporal kinematics of sequential tongue tip consonants1

PubMed Central

Byrd, Dani; Lee, Sungbok; Campos-Astorkiza, Rebeka

2008-01-01

This study evaluates the effects of phrase boundaries on the intra- and intergestural kinematic characteristics of blended gestures, i.e., overlapping gestures produced with a single articulator. The sequences examined are the juncture geminate [d(#)d], the sequence [d(#)z], and, for comparison, the singleton tongue tip gesture in [d(#)b]. This allows the investigation of the process of gestural aggregation [Munhall, K. G., and Löfqvist, A. (1992). “Gestural aggregation in speech: laryngeal gestures,” J. Phonetics 20, 93–110] and the manner in which it is affected by prosodic structure. Juncture geminates are predicted to be affected by prosodic boundaries in the same way as other gestures; that is, they should display prosodic lengthening and lesser overlap across a boundary. Articulatory prosodic lengthening is also investigated using a signal alignment method of the functional data analysis framework [Ramsay, J. O., and Silverman, B. W. (2005). Functional Data Analysis, 2nd ed. (Springer-Verlag, New York)]. This provides the ability to examine a time warping function that characterizes relative timing difference (i.e., lagging or advancing) of a test signal with respect to a given reference, thus offering a way of illuminating local nonlinear deformations at work in prosodic lengthening. These findings are discussed in light of the π-gesture framework of Byrd and Saltzman [(2003) “The elastic phrase: Modeling the dynamics of boundary-adjacent lengthening,” J. Phonetics 31, 149–180]. PMID:18537396

Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates.

PubMed

Weng, Mao-Lun; Blazier, John C; Govindu, Madhumita; Jansen, Robert K

2014-03-01

Geraniaceae plastid genomes are highly rearranged, and each of the four genera already sequenced in the family has a distinct genome organization. This study reports plastid genome sequences of six additional species, Francoa sonchifolia, Melianthus villosus, and Viviania marifolia from Geraniales, and Pelargonium alternans, California macrophylla, and Hypseocharis bilobata from Geraniaceae. These genome sequences, combined with previously published species, provide sufficient taxon sampling to reconstruct the ancestral plastid genome organization of Geraniaceae and the rearrangements unique to each genus. The ancestral plastid genome of Geraniaceae has a 4 kb inversion and a reduced, Pelargonium-like small single copy region. Our ancestral genome reconstruction suggests that a few minor rearrangements occurred in the stem branch of Geraniaceae followed by independent rearrangements in each genus. The genomic comparison demonstrates that a series of inverted repeat boundary shifts and inversions played a major role in shaping genome organization in the family. The distribution of repeats is strongly associated with breakpoints in the rearranged genomes, and the proportion and the number of large repeats (>20 bp and >60 bp) are significantly correlated with the degree of genome rearrangements. Increases in the degree of plastid genome rearrangements are correlated with the acceleration in nonsynonymous substitution rates (dN) but not with synonymous substitution rates (dS). Possible mechanisms that might contribute to this correlation, including DNA repair system and selection, are discussed.

An ancient trans-kingdom horizontal transfer of Penelope -like retroelements from arthropods to conifers

Treesearch

Xuan Lin; Nurul Faridi; Claudio Casola

2016-01-01

Comparative genomics analyses empowered by the wealth of sequenced genomes have revealed numerous instances of horizontal DNA transfers between distantly related species. In  eukaryotes, repetitive DNA sequences known as transposable elements (TEs) are especially prone to  move across species boundaries. Such horizontal transposon transfers, or HTTs, are relatively  ...

Accounting for rate-dependent category boundary shifts in speech perception.

PubMed

Bosker, Hans Rutger

2017-01-01

The perception of temporal contrasts in speech is known to be influenced by the speech rate in the surrounding context. This rate-dependent perception is suggested to involve general auditory processes because it is also elicited by nonspeech contexts, such as pure tone sequences. Two general auditory mechanisms have been proposed to underlie rate-dependent perception: durational contrast and neural entrainment. This study compares the predictions of these two accounts of rate-dependent speech perception by means of four experiments, in which participants heard tone sequences followed by Dutch target words ambiguous between /ɑs/ "ash" and /a:s/ "bait". Tone sequences varied in the duration of tones (short vs. long) and in the presentation rate of the tones (fast vs. slow). Results show that the duration of preceding tones did not influence target perception in any of the experiments, thus challenging durational contrast as explanatory mechanism behind rate-dependent perception. Instead, the presentation rate consistently elicited a category boundary shift, with faster presentation rates inducing more /a:s/ responses, but only if the tone sequence was isochronous. Therefore, this study proposes an alternative, neurobiologically plausible account of rate-dependent perception involving neural entrainment of endogenous oscillations to the rate of a rhythmic stimulus.

Regional stratigraphic framework of the Lisburne Group of ANWR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Watts, K.F.; Carlson, R.C.; Harris, A.G.

1995-05-01

The Carboniferous Lisburne Group, a major carbonate platform succession, is widely exposed in the Brooks Range and forms an extensive hydrocarbon target in the subsurface of the North Slope of Alaska. Gradationally beneath carbonates of the Lisburne Group, terrigenous sediments of the Mississippian Endicott Group (conglomerate and sandstone of the Kekiktuk Formation overlain by the Kayak Shale) were derived from local and northern (Ellesmerian) source areas. Locally, at the Endicott-Lisburne transition, sandy limestones of the Itkilyariak Formation record another phase of siliciclastic influx that lies above and/or is a lateral equivalent of the Kayak Shale and Lisburne Group in areasmore » adjacent to paleotopographic highs. This siliciclastic to carbonate transition represents a major transgressive succession that onlaps northward over the sub-Mississippian unconformity, a regional angular unconformity and sequence boundary in northern Alaska. The age and nature of onlap depend upon the paleotopography of the underlying sub-Mississippian rocks and regional passive margin subsidence. The Lisburne Group is a thick succession of carbonate rocks subdivided into the Alapah Limestone and overlying Wahoo Limestone, both having informal members.« less

DIGITAL CARTOGRAPHY AIDS IN THE SOLUTION OF BOUNDARY DISPUTE.

USGS Publications Warehouse

Beck, Francis J.

1983-01-01

The boundary between the States of Ohio and Kentucky and Indiana and Kentucky has been in dispute for many years. A major breakthrough in this continuing dispute has been a recent agreement between the States to accept the boundary line as depicted on U. S. Geological Survey 7. 5-minute quadrangle maps. A new segment of the boundary line was established utilizing the shoreline depicted on the 1966 U. S. Army Corps of Engineers charts. Segments of the boundary were then digitized from the quadrangle maps.

Does similarity in call structure or foraging ecology explain interspecific information transfer in wild Myotis bats?

PubMed

Hügel, Theresa; van Meir, Vincent; Muñoz-Meneses, Amanda; Clarin, B-Markus; Siemers, Björn M; Goerlitz, Holger R

2017-01-01

Animals can gain important information by attending to the signals and cues of other animals in their environment, with acoustic information playing a major role in many taxa. Echolocation call sequences of bats contain information about the identity and behaviour of the sender which is perceptible to close-by receivers. Increasing evidence supports the communicative function of echolocation within species, yet data about its role for interspecific information transfer is scarce. Here, we asked which information bats extract from heterospecific echolocation calls during foraging. In three linked playback experiments, we tested in the flight room and field if foraging Myotis bats approached the foraging call sequences of conspecifics and four heterospecifics that were similar in acoustic call structure only (acoustic similarity hypothesis), in foraging ecology only (foraging similarity hypothesis), both, or none. Compared to the natural prey capture rate of 1.3 buzzes per minute of bat activity, our playbacks of foraging sequences with 23-40 buzzes/min simulated foraging patches with significantly higher profitability. In the flight room, M. capaccinii only approached call sequences of conspecifics and of the heterospecific M. daubentonii with similar acoustics and foraging ecology. In the field, M. capaccinii and M. daubentonii only showed a weak positive response to those two species. Our results confirm information transfer across species boundaries and highlight the importance of context on the studied behaviour, but cannot resolve whether information transfer in trawling Myotis is based on acoustic similarity only or on a combination of similarity in acoustics and foraging ecology. Animals transfer information, both voluntarily and inadvertently, and within and across species boundaries. In echolocating bats, acoustic call structure and foraging ecology are linked, making echolocation calls a rich source of information about species identity, ecology and activity of the sender, which receivers might exploit to find profitable foraging grounds. We tested in three lab and field experiments if information transfer occurs between bat species and if bats obtain information about ecology from echolocation calls. Myotis capaccinii/daubentonii bats approached call playbacks, but only those from con- and heterospecifics with similar call structure and foraging ecology, confirming interspecific information transfer. Reactions differed between lab and field, emphasising situation-dependent differences in animal behaviour, the importance of field research, and the need for further studies on the underlying mechanism of information transfer and the relative contributions of acoustic and ecological similarity.

Sequence stratigraphy of upper Paleogene to Neogene carbonates exposed from Guánica bay to Guayanilla, Southern Puerto Rico.

NASA Astrophysics Data System (ADS)

Flores Hots, V. E.; Santos, H.

2016-12-01

Detailed stratigraphic columns were measured and microfacies analysis was performed in southwestern Puerto Rico to conduct a sequence stratigraphic analysis of Paleogene to Neogene strata. Two of the best exposed outcrops include the Guánica Bay and outcrops along Highway PR-132 in Guayanilla. Three depositional sequences, separated by two major sequence boundaries were found. The lower sequence occurs within the Juana Díaz Formation and is an open shelf to reef facies indicative of a Transgressive System Tract (TST), that is overlain by a High Stand System Tract (HST) marked by reef progradation. The HST in both Guánica Bay and Guayanilla is characterized by coral-rhodolith cyclicity however sections in Guánica Bay show pervasive recrystallization due to diagenetic alteration as a result of a long periods of exposure. This first sequence is Oligocene in age. The middle sequence, exposed at the eastern section of the Guánica Bay is also part of the Juana Díaz Formation and includes a turbiditic Lowstand System Tract (LST) of slope-like deposits flow, a TST constituted by coral rubble and skeletal grainstones belonging to a shallow island slope environment; and a HST that consists of an island slope chalk facies intercalated with turbidite grainstones derived storm events at the Guayanilla location. During the deposition of the middle sequence the Guánica Bay west section was topographically higher and exposed. The upper depositional sequence is Miocene in age and is composed of a TST with the transgression starting distally in the Guánica area and transgressing northward toward the Guayanilla area. These was correlated using high resolution 87Sr/86Sr isotope concentrations of shallow marine mollusks Kuphus incrassatus in the Ponce Formation at the Guánica Bay and Guayanilla locations. Facies patterns like the ones in the studied outcrops of southwestern Puerto Rico provide an exemplary environmental model of variability of paleodepositional relief, tectonic setting, variability in depositional setting of reef Sediment acumulations, the influence of storm events and variability in rock porosity by diagenetic processes yielding valuable models that may apply to potential Oligocene - Miocene hydrocarbon reservoirs.

Accommodation of end-state comfort reveals subphonemic planning in speech

PubMed Central

Gick, Bryan

2015-01-01

Applying Rosenbaum’s “end-state comfort” hypothesis (Rosenbaum et al., 1992, 1996) to tongue motion provides evidence of long-distance subphonemic planning in speech. Speakers’ tongue postures may anticipate upcoming speech up to three segments, two syllables, and a morpheme or word boundary later. We used m-mode ultrasound imaging to measure the direction of tongue tip/blade movements for known variants of flap/tap allophones of North American English /t/ and /d/. Results show that speakers produce different flap variants early in words or word sequences so as to facilitate the kinematic needs of flap/tap or other /r/ variants that appear later in the word or word sequence. Similar results were also observed across word boundaries, indicating that this is not a lexical effect. PMID:25790787

The HIP1 binding site is required for growth regulation of the dihydrofolate reductase gene promoter.

PubMed

Means, A L; Slansky, J E; McMahon, S L; Knuth, M W; Farnham, P J

1992-03-01

The transcription rate of the dihydrofolate reductase (DHFR) gene increases at the G1/S boundary of the proliferative cell cycle. Through analysis of transiently and stably transfected NIH 3T3 cells, we have now demonstrated that DHFR promoter sequences extending from -270 to +20 are sufficient to confer similar regulation on a reporter gene. Mutation of a protein binding site that spans sequences from -16 to +11 in the DHFR promoter resulted in loss of the transcriptional increase at the G1/S boundary. Purification of an activity from HeLa nuclear extract that binds to this region enriched for a 180-kDa polypeptide (HIP1). Using this HIP1 preparation, we have identified specific positions within the binding site that are critical for efficient protein-DNA interactions. An analysis of association and dissociation rates suggests that bound HIP1 protein can exchange rapidly with free protein. This rapid exchange may facilitate the burst of transcriptional activity from the DHFR promoter at the G1/S boundary.

The HIP1 binding site is required for growth regulation of the dihydrofolate reductase gene promoter.

PubMed Central

Means, A L; Slansky, J E; McMahon, S L; Knuth, M W; Farnham, P J

1992-01-01

The transcription rate of the dihydrofolate reductase (DHFR) gene increases at the G1/S boundary of the proliferative cell cycle. Through analysis of transiently and stably transfected NIH 3T3 cells, we have now demonstrated that DHFR promoter sequences extending from -270 to +20 are sufficient to confer similar regulation on a reporter gene. Mutation of a protein binding site that spans sequences from -16 to +11 in the DHFR promoter resulted in loss of the transcriptional increase at the G1/S boundary. Purification of an activity from HeLa nuclear extract that binds to this region enriched for a 180-kDa polypeptide (HIP1). Using this HIP1 preparation, we have identified specific positions within the binding site that are critical for efficient protein-DNA interactions. An analysis of association and dissociation rates suggests that bound HIP1 protein can exchange rapidly with free protein. This rapid exchange may facilitate the burst of transcriptional activity from the DHFR promoter at the G1/S boundary. Images PMID:1545788

Structure and DNA-Binding Sites of the SWI1 AT-rich Interaction Domain (ARID) Suggest Determinants for Sequence-Specific DNA Recognition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Suhkmann; Zhang, Ziming; Upchurch, Sean

2004-04-16

2 ARID is a homologous family of DNA-binding domains that occur in DNA binding proteins from a wide variety of species, ranging from yeast to nematodes, insects, mammals and plants. SWI1, a member of the SWI/SNF protein complex that is involved in chromatin remodeling during transcription, contains the ARID motif. The ARID domain of human SWI1 (also known as p270) does not select for a specific DNA sequence from a random sequence pool. The lack of sequence specificity shown by the SWI1 ARID domain stands in contrast to the other characterized ARID domains, which recognize specific AT-rich sequences. We havemore » solved the three-dimensional structure of human SWI1 ARID using solution NMR methods. In addition, we have characterized non-specific DNA-binding by the SWI1 ARID domain. Results from this study indicate that a flexible long internal loop in ARID motif is likely to be important for sequence specific DNA-recognition. The structure of human SWI1 ARID domain also represents a distinct structural subfamily. Studies of ARID indicate that boundary of the DNA binding structural and functional domains can extend beyond the sequence homologous region in a homologous family of proteins. Structural studies of homologous domains such as ARID family of DNA-binding domains should provide information to better predict the boundary of structural and functional domains in structural genomic studies. Key Words: ARID, SWI1, NMR, structural genomics, protein-DNA interaction.« less

Phylogeography of Sophora davidii (Leguminosae) across the 'Tanaka-Kaiyong Line', an important phytogeographic boundary in Southwest China.

PubMed

Fan, Deng Mei; Yue, Ji Pei; Nie, Ze Long; Li, Zhi Min; Comes, Hans Peter; Sun, Hang

2013-08-01

The 'Tanaka-Kaiyong Line' (TKL) is a major phytogeographic boundary in Southwest China, separating East Asia's Sino-Himalayan and Sino-Japanese Floras. However, little is known about the importance of this boundary in promoting intraspecific phylogeographic subdivision and divergence. Using chloroplast (cpDNA) and nuclear-intron (nDNA) sequence data, we reconstructed the population history of Sophora davidii, a drought-tolerant riparian shrub widely distributed on either side of the TKL. Specifically, we aimed at testing two long-standing explanations for possible vicariant events across the TKL: (i) Late Pliocene (c. 3 Ma) geological uplift of the eastern Qinghai-Tibetan Plateau (QTP) or (ii) a sharp environmental gradient associated with the establishment of different monsoon regimes on either side of the TKL during the (Late) Pleistocene. Our genealogical analyses detected a major west-east split in cpDNA, geographically largely consistent with the TKL, and dated to c. 1.28 Ma (95% HPD: 0.21-2.96 Ma), hence postdating the latest phase of eastern QTP uplift. Furthermore, integrating cpDNA phylogeographic patterns with mismatch analyses, we found multiple refugial isolation and long-term demographic stability of populations in the west (Hengduan Mountain Range) compared with extensive range expansions in the east, possibly during the last glacial period(s) and followed by differentiation into regional sublineages (southeast: Yunnan-Guizhou Plateau vs. northeast: Qinling Mts./Loess Plateau). Although nuclear differentiation was less marked, the geographical pattern of nDNA haplotypes provided some further indication of the species' eastward expansion, possibly from source populations located just east of the TKL (lower Jinshajiang region). Overall, the present data reject the geological (tectonic) explanation for the TKL and, instead, provide supportive evidence for its role as a climatically driven barrier to present-day plant dispersal. In addition, our study highlights changing temperatures and vegetation types during the last glacial period(s), along with aspects of regional topography, to be important determinants of the glacial eastward expansion of S. davidii. In consequence, our study lends support to a 'glacial out-of-Hengduan Mts'. hypothesis for the xerophytic-riparian flora of Southwest China, which in turn is inconsistent with the traditional view of the TKL as a 'classical' vicariant-biogeographic boundary. © 2013 John Wiley & Sons Ltd.

The Complete Chloroplast Genome Sequences of Five Epimedium Species: Lights into Phylogenetic and Taxonomic Analyses

PubMed Central

Zhang, Yanjun; Du, Liuwen; Liu, Ao; Chen, Jianjun; Wu, Li; Hu, Weiming; Zhang, Wei; Kim, Kyunghee; Lee, Sang-Choon; Yang, Tae-Jin; Wang, Ying

2016-01-01

Epimedium L. is a phylogenetically and economically important genus in the family Berberidaceae. We here sequenced the complete chloroplast (cp) genomes of four Epimedium species using Illumina sequencing technology via a combination of de novo and reference-guided assembly, which was also the first comprehensive cp genome analysis on Epimedium combining the cp genome sequence of E. koreanum previously reported. The five Epimedium cp genomes exhibited typical quadripartite and circular structure that was rather conserved in genomic structure and the synteny of gene order. However, these cp genomes presented obvious variations at the boundaries of the four regions because of the expansion and contraction of the inverted repeat (IR) region and the single-copy (SC) boundary regions. The trnQ-UUG duplication occurred in the five Epimedium cp genomes, which was not found in the other basal eudicotyledons. The rapidly evolving cp genome regions were detected among the five cp genomes, as well as the difference of simple sequence repeats (SSR) and repeat sequence were identified. Phylogenetic relationships among the five Epimedium species based on their cp genomes showed accordance with the updated system of the genus on the whole, but reminded that the evolutionary relationships and the divisions of the genus need further investigation applying more evidences. The availability of these cp genomes provided valuable genetic information for accurately identifying species, taxonomy and phylogenetic resolution and evolution of Epimedium, and assist in exploration and utilization of Epimedium plants. PMID:27014326

Solid-state dewetting of Au-Ni bi-layer films mediated through individual layer thickness and stacking sequence

NASA Astrophysics Data System (ADS)

Herz, Andreas; Theska, Felix; Rossberg, Diana; Kups, Thomas; Wang, Dong; Schaaf, Peter

2018-06-01

In the present work, the solid-state dewetting of Au-Ni bi-layer thin films deposited on SiO2/Si is systematically studied with respect to individual layer thickness and stacking sequence. For this purpose, a rapid heat treatment at medium temperatures is applied in order to examine void formation at the early stages of the dewetting. Compositional variations are realized by changing the thickness ratio of the bi-layer films, while the total thickness is maintained at 20 nm throughout the study. In the event of Au/Ni films annealed at 500 °C, crystal voids exposing the substrate are missing regardless of chemical composition. In reverse order, the number of voids per unit area in two-phase Au-Ni thin films is found to be governed by the amount of Au-rich material. At higher temperatures up to 650 °C, a decreased probability of nucleation comes at the expense of a major portion of cavities, resulting in the formation of bubbles in 15 nm Ni/5 nm Au bi-layers. Film buckling predominantly occurred at phase boundaries crossing the bubbles.

Extended period of K/T boundary mass extinction in the marine realm

NASA Technical Reports Server (NTRS)

Keller, G.

1988-01-01

The Cretaceous/Tertiary (K/T) boundary mass extinction has been widely recognized as a nearly instantaneous catastrophy among marine plankton such as foraminifera. However, the suddenness of this extinction event may have been overemphasized because most pelagic K/T boundary sequences are stratigraphically incomplete and generally lack the earliest Tertiary (Zones P0 and P1a) either due to carbonate dissolution and/or non-deposition. Stratigraphically complete sections appear to be restricted to continental shelf regions with high sedimentation rates and deposition well above the CCD. Such sections have been recovered from El Kef, Tunisia (1) and Brazos River, Texas. Quantitative foraminiferal analysis of these sections indicate an extinction pattern beginning below the K/T boundary and ending above the boundary. These data imply that the mass extinction event was not geologically instantaneous, but occurred over an extended period of time. Evidence supporting this conclusion is discussed.

Influence of Alloying upon Grain-Boundary Creep

NASA Technical Reports Server (NTRS)

Rhines, F N; Bond, W E; Kissel, M A

1957-01-01

Grain-boundary displacement, occurring in bicrystals during creep at elevated temperature (350 degrees c), has been measured as a function of the copper content (0.1 to 3 percent) in a series of aluminum-rich aluminum-copper solid-solution alloys. The minimums in stress and temperature, below which grain-boundary motion does not occur, increase regularly with the copper content as would be expected if recovery is necessary for movement. Otherwise, the effects, if any, of the copper solute upon grain-boundary displacement and its rate are too small for identification by the experimental technique employed. It was shown, additionally, that grain-boundary displacement appears regular and proceeds at a constant rate if observed parallel to the stress axis, whereas the motion is seen to occur in a sequence of surges and the rate to diminish with time if the observations are made perpendicular to the stress axis.

Defining boundaries across borders: a case study extending a major land resource area into Mexico

Treesearch

Rebecca MacEwen; Roy S. Mann; Philip Heilman; Jeffry J. Stone; Alicia Melgoza Castillo; D. Phillip Guertin

2005-01-01

Geographic information science (GIS) and field work were applied to extend Major Land Resource Area (MLRA) 41, Southeastern Arizona Basin and Range, from Arizona and New Mexico into Sonora and Chihuahua, Mexico. The result of this analysis is a tentative boundary line that delineates MLRA 41 for both the United States and Mexico based on elevation, soils, temperature,...

Dispersion-relation-preserving finite difference schemes for computational acoustics

NASA Technical Reports Server (NTRS)

Tam, Christopher K. W.; Webb, Jay C.

1993-01-01

Time-marching dispersion-relation-preserving (DRP) schemes can be constructed by optimizing the finite difference approximations of the space and time derivatives in wave number and frequency space. A set of radiation and outflow boundary conditions compatible with the DRP schemes is constructed, and a sequence of numerical simulations is conducted to test the effectiveness of the DRP schemes and the radiation and outflow boundary conditions. Close agreement with the exact solutions is obtained.

Sources and Propagation of High Frequency Waves in the Solar Photosphere and Chromosphere

NASA Astrophysics Data System (ADS)

Lawrence, John K.; Cadavid, A. C.

2009-05-01

We study the spatial distribution of oscillatory power in two sequences of high-cadence, high-resolution images taken by the Solar Optical Telescope on board Hinode. The sequences consist of simultaneous, co-registered G-Band (GB) and Ca II H-Line (HL) images with pixel scale 80 km and fields of view 40 x 40 Mm and 80 x 40 Mm. The first sequence has cadence 21 s over 3 hours on 2007 April 14; the other has cadence 24 s over 2 hours on 2007 March 30. Both sequences include network and internetwork at heliocentric angle 35 degrees. Time averaging of Morlet wavelet transforms gives smoothed Fourier spectra for each spatial location in the GB and HL data. We averaged over four different frequency bands to highlight different physical regimes: "evolutionary” timescales (f < 1.2 mHz); evanescent frequencies just below the acoustic cutoff ( 2.6 mHz < f < 4.2 mHz); high frequencies just above the cutoff (5.5 mHz

Improvements in Block-Krylov Ritz Vectors and the Boundary Flexibility Method of Component Synthesis

NASA Technical Reports Server (NTRS)

Carney, Kelly Scott

1997-01-01

A method of dynamic substructuring is presented which utilizes a set of static Ritz vectors as a replacement for normal eigenvectors in component mode synthesis. This set of Ritz vectors is generated in a recurrence relationship, proposed by Wilson, which has the form of a block-Krylov subspace. The initial seed to the recurrence algorithm is based upon the boundary flexibility vectors of the component. Improvements have been made in the formulation of the initial seed to the Krylov sequence, through the use of block-filtering. A method to shift the Krylov sequence to create Ritz vectors that will represent the dynamic behavior of the component at target frequencies, the target frequency being determined by the applied forcing functions, has been developed. A method to terminate the Krylov sequence has also been developed. Various orthonormalization schemes have been developed and evaluated, including the Cholesky/QR method. Several auxiliary theorems and proofs which illustrate issues in component mode synthesis and loss of orthogonality in the Krylov sequence have also been presented. The resulting methodology is applicable to both fixed and free- interface boundary components, and results in a general component model appropriate for any type of dynamic analysis. The accuracy is found to be comparable to that of component synthesis based upon normal modes, using fewer generalized coordinates. In addition, the block-Krylov recurrence algorithm is a series of static solutions and so requires significantly less computation than solving the normal eigenspace problem. The requirement for less vectors to form the component, coupled with the lower computational expense of calculating these Ritz vectors, combine to create a method more efficient than traditional component mode synthesis.

Late Cretaceous base level lowering in Campanian and Maastrichtian depositional sequences, Kure Beach, North Carolina

USGS Publications Warehouse

Harris, W.B.; ,

2006-01-01

Campanian through Maastrichtian mixed carbonate and siliciclastic sediments in a 422 m continuous core drilled at Kure Beach, NC provide a record of sea-level change. Based on lithology and stratigraphy, depositional sequences are defined, and calcareous nannofossil zones and 87Sr/86Sr ratios and corresponding ages using the LOWESS Table determined. Campanian and Maastrichtian sediments comprise six depositional sequences. The oldest is Tar Heel 1 and contains calcareous nannofossils that indicate assignment to the upper part of Zones CC18a, CC18c and the lower part of CC19. 87Sr/86 Sr ratios indicate ages from 83.2 to 80.0 Ma or lower Campanian. Tar Heel II contains calcareous nannofossils that indicate assignment to the upper part of Zone CC 19 and CC20. 87Sr/86Sr ratios indicate ages from 78.0 to 76.3 Ma or middle Campanian. Donoho Creek I and II are thin and contain calcareous nannofossils referable to upper Zone CC21 and Zone CC22, and to CC23, respectively. The top of Donoho Creek II marks the Campanian-Maastrichtian boundary. Donoho Creek I 87Sr/86Sr ratios cluster into two groups, and provide ages from 78.0 to 76.2 Ma and 73.7 to 72.3 Ma, respectively. 87Sr/86Sr ratios in Donoho Creek II indicate ages from 71.4 to 69.6 Ma. Two Maastrichtian sequences are present; the lowermost Peedee I contains calcareous nannofossils that place it in Zones CC25a and CC25b. 87Sr/86Sr r ratios indicate an age from 69.3 to 66.9 Ma or late Maastrichtian. Peedee II is assigned to calcareous nannofossil Zone CC26a. 87Sr/86Sr ratios indicate ages from 66.4 to 65.2 Ma or late Maastrichtian. The four Campanian sequences correlate to three depositional sequences in New Jersey; the sequence boundary between upper Campanian Donoho Creek I and Donoho Creek II is not recognized in New Jersey. This boundary is interpreted to result from Gulf Stream impingement and subsequent erosion on the outer shelf. The two Maastrichtian sequences recognized in the Kure Beach core correlate to the two identified Maastrichtian sequences in New Jersey. These data support base-level lowering of sea-level during the Campanian-Maastrichtian, and suggest that the western margin of the North Atlantic may contain one of the best Late Cretaceous records of sea-level change.

Evidence from central Mexico supporting the Younger Dryas extraterrestrial impact hypothesis

USGS Publications Warehouse

Israde-Alcántara, Isabel; Bischoff, James L.; Domínguez-Vázquez, Gabriela; Li, Hong-Chun; DeCarli, Paul S.; Bunch, Ted E.; Wittke, James H.; Weaver, James C.; Firestone, Richard B.; West, Allen; Kennett, James P.; Mercer, Chris; Xie, Sujing; Richman, Eric K.; Kinzie, Charles R.; Wolbach, Wendy S.

2012-01-01

We report the discovery in Lake Cuitzeo in central Mexico of a black, carbon-rich, lacustrine layer, containing nanodiamonds, microspherules, and other unusual materials that date to the early Younger Dryas and are interpreted to result from an extraterrestrial impact. These proxies were found in a 27-m-long core as part of an interdisciplinary effort to extract a paleoclimate record back through the previous interglacial. Our attention focused early on an anomalous, 10-cm-thick, carbon-rich layer at a depth of 2.8 m that dates to 12.9 ka and coincides with a suite of anomalous coeval environmental and biotic changes independently recognized in other regional lake sequences. Collectively, these changes have produced the most distinctive boundary layer in the late Quaternary record. This layer contains a diverse, abundant assemblage of impact-related markers, including nanodiamonds, carbon spherules, and magnetic spherules with rapid melting/quenching textures, all reaching synchronous peaks immediately beneath a layer containing the largest peak of charcoal in the core. Analyses by multiple methods demonstrate the presence of three allotropes of nanodiamond: n-diamond, i-carbon, and hexagonal nanodiamond (lonsdaleite), in order of estimated relative abundance. This nanodiamond-rich layer is consistent with the Younger Dryas boundary layer found at numerous sites across North America, Greenland, and Western Europe. We have examined multiple hypotheses to account for these observations and find the evidence cannot be explained by any known terrestrial mechanism. It is, however, consistent with the Younger Dryas boundary impact hypothesis postulating a major extraterrestrial impact involving multiple airburst(s) and and/or ground impact(s) at 12.9 ka.

Evidence from Central Mexico supporting the Younger Dryas extraterrestrial impact hypothesis

USGS Publications Warehouse

Israde-Alcántaraa, Isabel; Bischoff, James L.; Domínguez-Vázquez, Gabriela; Li, Hong-Chun; DeCarli, Paul S.; Bunch, Ted E.; Wittke, James H.; Weaver, James C.; Firestone, Richard B.; West, Allen; Kennett, James P.; Mercer, Chris; Xie, Sujing; Richman, Eric K.; Kinzie, Charles R.; Wolbach, Wendy S.; Stanley, Steven M.

2012-01-01

We report the discovery in Lake Cuitzeo in central Mexico of a black, carbon-rich, lacustrine layer, containing nanodiamonds, microspherules, and other unusual materials that date to the early Younger Dryas and are interpreted to result from an extraterrestrial impact. These proxies were found in a 27-m-long core as part of an interdisciplinary effort to extract a paleoclimate record back through the previous interglacial. Our attention focused early on an anomalous, 10-cm-thick, carbon-rich layer at a depth of 2.8 m that dates to 12.9 ka and coincides with a suite of anomalous coeval environmental and biotic changes independently recognized in other regional lake sequences. Collectively, these changes have produced the most distinctive boundary layer in the late Quaternary record. This layer contains a diverse, abundant assemblage of impact-related markers, including nanodiamonds, carbon spherules, and magnetic spherules with rapid melting/quenching textures, all reaching synchronous peaks immediately beneath a layer containing the largest peak of charcoal in the core. Analyses by multiple methods demonstrate the presence of three allotropes of nanodiamond: n-diamond, i-carbon, and hexagonal nanodiamond (lonsdaleite), in order of estimated relative abundance. This nanodiamond-rich layer is consistent with the Younger Dryas boundary layer found at numerous sites across North America, Greenland, and Western Europe. We have examined multiple hypotheses to account for these observations and find the evidence cannot be explained by any known terrestrial mechanism. It is, however, consistent with the Younger Dryas boundary impact hypothesis postulating a major extraterrestrial impact involving multiple airburst(s) and and/or ground impact(s) at 12.9 ka.

Sequence stratigraphy of the subaqueous Changjiang (Yangtze River) delta since the Last Glacial Maximum

NASA Astrophysics Data System (ADS)

Xu, Taoyu; Wang, Guoqing; Shi, Xuefa; Wang, Xin; Yao, Zhengquan; Yang, Gang; Fang, Xisheng; Qiao, Shuqing; Liu, Shengfa; Wang, Xuchen; Zhao, Quanhong

2016-01-01

This study focuses on sedimentary research at the subaqueous Changjiang (Yangtze River) delta, based on five high-resolution seismic profiles and seven borehole cores with accurate AMS 14C datings. Three distinct seismic units were identified from the seismic profiles according to seismic reflection characteristics, and five sedimentary facies were recognized from borehole cores. These facies constituted a fining upward sedimentary sequence in relation to postglacial sea-level transgression. Three sequence surfaces (sequence boundary (SB), transgressive surface (TS), and maximum flooding surface (MFS)) demarcate the boundaries between early transgressive system tract (E-TST), late transgressive system tract (L-TST), early highstand system tract (E-HST) and late highstand system tract (L-HST), which constitute the sixth order sequence. These system tracts were developed coevally with postglacial sea-level rise. E-TST (~ 19-12 ka BP) corresponds to an incised-valley infilling in the early stages of postglacial transgression whereas L-TST (~ 12-7.5 ka BP) was formed during the last stage of postglacial transgression. The progradational structure of L-TST reflected in seismic profiles is possibly related to the intensification of the East Asian summer monsoon. E-HST (~ 7.5-2 ka BP) was deposited in response to the highstand after maximum postglacial transgression was reached, while L-HST (~ 2 ka BP-present) was initiated by accelerated progradation of the Changjiang delta.

Cross-sectional characterization of the dewetting of a Au/Ni bilayer film.

PubMed

Cen, Xi; Thron, Andrew M; Zhang, Xinming; van Benthem, Klaus

2017-07-01

The solid state dewetting of Au/Ni bilayer films was investigated by cross-sectional transmission electron microscopy techniques, including energy-dispersive X-ray spectroscopy, electron energy-loss spectroscopy and precession electron diffraction. After annealing under high vacuum conditions the early stage of film agglomeration revealed significant changes in film morphology and chemical distribution. Both Au and Ni showed texturing. Despite the initial deposition sequence of the as-deposited Au/Ni/SiO 2 /Si interface structure, the majority of the metal/SiO 2 interface was Au/SiO 2 after annealing at 675°C for 1h. Void nucleation was predominantly observed at Au/Ni/SiO 2 triple junctions, rather than grain boundary grooving at free surface of the metal film. Detailed cross-sectional characterization reveals that the Au/Ni interface in addition to small amounts of metal alloying strongly affects film break-up and agglomeration kinetics. The formation of Au/SiO 2 interface sections is found to be energetically preferred over Ni/SiO 2 due to compressive stress in the as-deposited Ni layer. Void nucleation is observed at the film/substrate interface, while the formation of voids at Ni/Au phase boundaries inside the metal film is caused by the Kirkendall effect. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparing the November 2002 Denali and November 2001 Kunlun earthquakes

USGS Publications Warehouse

Bufe, C.G.

2004-01-01

Major strike-slip earthquakes recently occurred in Alaska on the central Denali fault (M 7.9) on 3 November 2002, and in Tibet on the central Kunlun fault (M 7.8) on 14 November 2001. Both earthquakes generated large surface waves with Ms [U.S. Geological Survey (USGS)] of 8.5 (Denali) and 8.0 (Kunlun). Each event occurred on an east-west-trending strike-slip fault situated near the northern boundary of an intense deformation zone that is characterized by lateral extrusion and rotation of crustal blocks. Each earthquake produced east-directed nearly unilateral ruptures that propagated 300 to 400 km. Maximum lateral surface offsets and maximum moment release occurred well beyond 100 km from the rupture initiation, with the events exhibiting by far the largest separations of USGS hypocenter and Harvard Moment Tensor Centroid (CMT) for strike-slip earthquakes in the 27-year CMT catalog. In each sequence, the largest aftershock was more than two orders of magnitude smaller than the mainshock. Regional moment release had been accelerating prior to the main shocks. The close proximity in space and time of the 1964 Prince William Sound and 2002 Denali earthquakes, relative to their rupture lengths and estimated return times, suggests that these events may be part of a recurrent cluster in the vicinity of a complex plate boundary.

New approach to the boundary-parallel plastic / viscous diapiric flow patterns in the curvilinear boundary zones: an implication for structural geology studies

NASA Astrophysics Data System (ADS)

Sarkarinejad, Khalil

2010-05-01

New approach to the boundary-parallel plastic / viscous diapiric flow patterns in the curvilinear boundary zones: an implication for structural geology studies Khalil Sarkarinejad and Abdolreza Partabian Department of Earth Sciences, College of Sciences, Shiraz University, Shiraz, Iran (Sarkarinejad@geology.susc.ac.ir). In the oceanic diverging away plates, the asthenospheric flow at solidus high-temperature conditions typically produces mineral foliations and lineations in peridotites. Foliation and lineation of mantle are defined by preferred flattening and alignment of olivine, pyroxene and spinel. In the areas with steep foliations trajectories which are associated with the steeply plunging stretching lineation trajectories, reflecting localized vertical flow and has been related to mantle diapir. The mantle flow patterns are well documented through detail structural mapping of the Neyriz ophiolite along the Zagros inclined dextral transpression and Oman ophiolite. Such models of the diverging asthenaspheric mantle flow and formation of mantle diapir are rarely discussed and paid any attention in the mathematical models of transpressional deformation in converging continental crusts. Systematic measurements of the mineral preferred orientations and construction of the foliation and lineation trajectories of the Zagros high-strain zone reveal two diapers with the shape of the inclined NW-SE boundary-parallel semi-ellipses shape and one rotated asymmetric diapir. These diapers made of quartzo-feldspathic gneiss and garnet amphibolite core with phyllite, phyllonite, muscovite schist and deformed conglomerate as a cover sequences. These boundary-parallel and rotated diapirs are formed by the interaction of Afro-Arabian lower to middle continental detachment and hot subdacting Tethyan oceanic crust, due to increasing effective pressure and temperature. The plastic/viscous gneissic diapers were squeezed between in Zagros transpression curvilinear boundary zones in an angle alpha=25°. Constructed finite strain ellipsoid based on the X-axes of the elliptical shaped deformed markers of the diapir cover sequences show trend X-axis of the strain ellipsoid making an angle phai=2° with the boundary zones. The steep plunging stretching lineation primarily controlled by the plastic/viscous flow. This also show that during inclined upwelling boundary-parallel diapers, X-, Y-axes of the strain ellipsoid rotated clockwise and Z-axis experienced counter clockwise rotation with triclinic symmetries relative to the Zagros curvilinear transpression boundary zones with an orientation of N42°plus/minus 24°W.

Interactive web-based identification and visualization of transcript shared sequences.

PubMed

Azhir, Alaleh; Merino, Louis-Henri; Nauen, David W

2018-05-12

We have developed TraC (Transcript Consensus), a web-based tool for detecting and visualizing shared sequences among two or more mRNA transcripts such as splice variants. Results including exon-exon boundaries are returned in a highly intuitive, data-rich, interactive plot that permits users to explore the similarities and differences of multiple transcript sequences. The online tool (http://labs.pathology.jhu.edu/nauen/trac/) is free to use. The source code is freely available for download (https://github.com/nauenlab/TraC). Copyright © 2018 Elsevier Inc. All rights reserved.

Major wildfires at the Cretaceous-Tertiary boundary

NASA Technical Reports Server (NTRS)

Anders, Edward; Wolbach, Wendy S.; Gilmour, Iain

1991-01-01

The current status of the reconstruction of major biomass fire events at the Cretaceous-Tertiary boundary is discussed. Attention is given to the sources of charcoal and soot, the identification of biomass and fossil carbon, and such ignition-related problems as delated fires, high atmospheric O2 content, ignition mechanisms, and the greenhouse-effect consequences of fire on the scale envisioned. Consequences of these factors for species extinction patterns are noted.

Multi-contrast MRI registration of carotid arteries based on cross-sectional images and lumen boundaries

NASA Astrophysics Data System (ADS)

Wu, Yu-Xia; Zhang, Xi; Xu, Xiao-Pan; Liu, Yang; Zhang, Guo-Peng; Li, Bao-Juan; Chen, Hui-Jun; Lu, Hong-Bing

2017-02-01

Ischemic stroke has great correlation with carotid atherosclerosis and is mostly caused by vulnerable plaques. It's particularly important to analysis the components of plaques for the detection of vulnerable plaques. Recently plaque analysis based on multi-contrast magnetic resonance imaging has attracted great attention. Though multi-contrast MR imaging has potentials in enhanced demonstration of carotid wall, its performance is hampered by the misalignment of different imaging sequences. In this study, a coarse-to-fine registration strategy based on cross-sectional images and wall boundaries is proposed to solve the problem. It includes two steps: a rigid step using the iterative closest points to register the centerlines of carotid artery extracted from multi-contrast MR images, and a non-rigid step using the thin plate spline to register the lumen boundaries of carotid artery. In the rigid step, the centerline was extracted by tracking the crosssectional images along the vessel direction calculated by Hessian matrix. In the non-rigid step, a shape context descriptor is introduced to find corresponding points of two similar boundaries. In addition, the deterministic annealing technique is used to find a globally optimized solution. The proposed strategy was evaluated by newly developed three-dimensional, fast and high resolution multi-contrast black blood MR imaging. Quantitative validation indicated that after registration, the overlap of two boundaries from different sequences is 95%, and their mean surface distance is 0.12 mm. In conclusion, the proposed algorithm has improved the accuracy of registration effectively for further component analysis of carotid plaques.

Maps showing petroleum exploration intensity and production in major Cambrian to Ordovician reservoir rocks in the Anadarko Basin

USGS Publications Warehouse

Henry, Mitch; Hester, Tim

1996-01-01

The Anadarko basin is a large, deep, two-stage Paleozoic basin (Feinstein, 1981) that is petroleum rich and generally well explored. The Anadarko basin province, a geogrphic area used here mostly for the convenience of mapping and data management, is defined by political boundaries that include the Anadarko basin proper. The boundaries of the province are identical to those used by the U.S. Geological Survey (USGS) in the 1995 National Assessment of United Stated Oil and Gas Resources. The data in this report, also identical to those used in the national assessment, are from several computerized data bases including Nehring Research Group (NRG) Associates Inc., Significant Oil and Gas Fields of the United States (1992); Petroleum Information (PI), Inc., Well History Control System (1991); and Petroleum Information (PI), Inc., Petro-ROM: Production data on CD-ROM (1993). Although generated mostly in response to the national assessment, the data presented here arc grouped differently and arc displayed and described in greater detail. In addition, the stratigraphic sequences discussed may not necessarily correlate with the "plays" of the 1995 national assessment. This report uses computer-generated maps to show drilling intensity, producing wells, major fields, and other geologic information relevant to petroleum exploration and production in the lower Paleozoic part of the Anadarko basin province as defined for the U.S. Geological Survey's 1995 national petroleum assessment. Hydrocarbon accumulations must meet a minimum standard of 1 million barrels of oil (MMBO) or 6 billion cubic feet of gas (BCFG) estimated ultimate recovery to be included in this report as a major field or revoir. Mapped strata in this report include the Upper Cambrian to Lower Ordovician Arbuckle and Low Ordovician Ellenburger Groups, the Middle Ordovician Simpson Group, and the Middle to Upper Ordovician Viola Group.

The origin of Karaj dam basement sill marginal reversal by Soret fractionation

NASA Astrophysics Data System (ADS)

Maghdour-Mashhour, Reza; Esmaeily, Dariush

2010-05-01

The Karaj dam basement sill (KDBS), located North West of Tehran, northern Iran, is one of the several E-W-trending plutons in the Albourz Mountains. The KDBS consists of a layered series between upper and lower chilled margins. The rocks of the chilled margins are gabbroic in composition and porphyritic, with euhedral to subhedral plagioclase and clinopyroxene megacrysts up to 5 mm long. The rocks become coarse-grained toward the center of the sill and show a gradual transition from porphyritic to equigranular texture. Field and petrographic observations reveal a reverse trend in marginal units crystallization from the eutectic point to the main magma composition; i.e., the olivine-bearing gabbro (porphyritic chilled margin), which has a eutectic composition, crystallized prior to the marginal gabbros, which have a cotectic or near-cotectic composition, as plagioclase laths in the gabbroic unit are embedded in large crystals of clinopyroxene and this phenomenon is believed to result from the cotectic crystallization of plagioclase and clinopyroxene. Four major mechanisms are proposed and discussed in order to find the exact mechanism responsible for marginal reversal formation as following: 1) Crystal settling is a gravity-dependent mechanism and phenocrysts must have settled to form a layer at the bottom of the sill, showing sharp upper boundary which is not observable in KDBS. Besides, the reverse fractionation of inwardly-dipping sequence of mentioned sill occurs in layers with primary dips up to 55°. Consequently capability of marginal reversals to develop along steeply inclined chamber margins, by this mechanism is implausible. 2) Multiple injections of successive magma pulses fails to explain the origin of marginal reversal since the transition along the entire length of marginal reversal is gradual also there is no compositional break or chilled contact between two mentioned units of KDBS margin (Olivine-gabbro and marginal gabbro). 3) The idea of supercooling could not be applied to the marginal series as well. Because the high degree of supercooling would make the marginal series with a fine-grained chilled margins which is far from being observed in KDBS. 4) Soret fractionation is the most probable mechanism among the others which has recently taken into account by researchers (e.g. Latypov, 2003). As shown by Worster et al. (1990), vigorous convection can be logically assumed to be a major process responsible for the generation of smooth trends in the distribution of cumulate minerals in the accumulation zone and the gradual transition between different layers, which are characteristic features of the KDBS confirm the occurrence of vigorous convection in the main magma reservoir. Vigorous magma convection in the KDBS chamber leads to the formation of a thin thermal boundary layer along the chamber margins, thereby maintaining the temperature contrast from fading and ensuring the continuous exchange of HMPCs (e.g., MgO) across the liquid boundary layer from the margins toward the main magma chamber and for LMPCs in opposite direction, by Soret diffusion. Consequently further decrease in the magnitude of the thermal gradient within the boundary layer would have caused a gradual change in the composition of the liquids in the boundary layer, becoming progressively depleted in LMPCs, shifting away from the eutectic point Ol + Pl + Cpx + L along the cotectic line Cpx + Pl + L. In this way, crystallization of the developing cumulus front in the liquid boundary layer produced the compositional sequence in reverse order, from the eutectic point to the initial parental magma, resulting in the occurrence of olivine-bearing gabbro in the chilled margins and gabbros toward the center of chamber.

Myocardial strain estimation from CT: towards computer-aided diagnosis on infarction identification

NASA Astrophysics Data System (ADS)

Wong, Ken C. L.; Tee, Michael; Chen, Marcus; Bluemke, David A.; Summers, Ronald M.; Yao, Jianhua

2015-03-01

Regional myocardial strains have the potential for early quantification and detection of cardiac dysfunctions. Although image modalities such as tagged and strain-encoded MRI can provide motion information of the myocardium, they are uncommon in clinical routine. In contrary, cardiac CT images are usually available, but they only provide motion information at salient features such as the cardiac boundaries. To estimate myocardial strains from a CT image sequence, we adopted a cardiac biomechanical model with hyperelastic material properties to relate the motion on the cardiac boundaries to the myocardial deformation. The frame-to-frame displacements of the cardiac boundaries are obtained using B-spline deformable image registration based on mutual information, which are enforced as boundary conditions to the biomechanical model. The system equation is solved by the finite element method to provide the dense displacement field of the myocardium, and the regional values of the three principal strains and the six strains in cylindrical coordinates are computed in terms of the American Heart Association nomenclature. To study the potential of the estimated regional strains on identifying myocardial infarction, experiments were performed on cardiac CT image sequences of ten canines with artificially induced myocardial infarctions. The leave-one-subject-out cross validations show that, by using the optimal strain magnitude thresholds computed from ROC curves, the radial strain and the first principal strain have the best performance.

Perceptual recovery from consonant-cluster simplification in Korean using language-specific phonological knowledge.

PubMed

Cho, Taehong; McQueen, James M

2011-08-01

Two experiments examined whether perceptual recovery from Korean consonant-cluster simplification is based on language-specific phonological knowledge. In tri-consonantal C1C2C3 sequences such as /lkt/ and /lpt/ in Seoul Korean, either C1 or C2 can be completely deleted. Seoul Koreans monitored for C2 targets (/p/ or / k/, deleted or preserved) in the second word of a two-word phrase with an underlying /l/-C2-/t/ sequence. In Experiment 1 the target-bearing words had contextual lexical-semantic support. Listeners recovered deleted targets as fast and as accurately as preserved targets with both Word and Intonational Phrase (IP) boundaries between the two words. In Experiment 2, contexts were low-pass filtered. Listeners were still able to recover deleted targets as well as preserved targets in IP-boundary contexts, but better with physically-present targets than with deleted targets in Word-boundary contexts. This suggests that the benefit of having target acoustic-phonetic information emerges only when higher-order (contextual and phrase-boundary) information is not available. The strikingly efficient recovery of deleted phonemes with neither acoustic-phonetic cues nor contextual support demonstrates that language-specific phonological knowledge, rather than language-universal perceptual processes which rely on fine-grained phonetic details, is employed when the listener perceives the results of a continuous-speech process in which reduction is phonetically complete.

Contrasting morphological and DNA barcode-suggested species boundaries among shallow-water amphipod fauna from the southern European Atlantic coast.

PubMed

Lobo, Jorge; Ferreira, Maria S; Antunes, Ilisa C; Teixeira, Marcos A L; Borges, Luisa M S; Sousa, Ronaldo; Gomes, Pedro A; Costa, Maria Helena; Cunha, Marina R; Costa, Filipe O

2017-02-01

In this study we compared DNA barcode-suggested species boundaries with morphology-based species identifications in the amphipod fauna of the southern European Atlantic coast. DNA sequences of the cytochrome c oxidase subunit I barcode region (COI-5P) were generated for 43 morphospecies (178 specimens) collected along the Portuguese coast which, together with publicly available COI-5P sequences, produced a final dataset comprising 68 morphospecies and 295 sequences. Seventy-five BINs (Barcode Index Numbers) were assigned to these morphospecies, of which 48 were concordant (i.e., 1 BIN = 1 species), 8 were taxonomically discordant, and 19 were singletons. Twelve species had matching sequences (<2% distance) with conspecifics from distant locations (e.g., North Sea). Seven morphospecies were assigned to multiple, and highly divergent, BINs, including specimens of Corophium multisetosum (18% divergence) and Dexamine spiniventris (16% divergence), which originated from sampling locations on the west coast of Portugal (only about 36 and 250 km apart, respectively). We also found deep divergence (4%-22%) among specimens of seven species from Portugal compared to those from the North Sea and Italy. The detection of evolutionarily meaningful divergence among populations of several amphipod species from southern Europe reinforces the need for a comprehensive re-assessment of the diversity of this faunal group.

On the predictability of event boundaries in discourse: An ERP investigation.

PubMed

Delogu, Francesca; Drenhaus, Heiner; Crocker, Matthew W

2018-02-01

When reading a text describing an everyday activity, comprehenders build a model of the situation described that includes prior knowledge of the entities, locations, and sequences of actions that typically occur within the event. Previous work has demonstrated that such knowledge guides the processing of incoming information by making event boundaries more or less expected. In the present ERP study, we investigated whether comprehenders' expectations about event boundaries are influenced by how elaborately common events are described in the context. Participants read short stories in which a common activity (e.g., washing the dishes) was described either in brief or in an elaborate manner. The final sentence contained a target word referring to a more predictable action marking a fine event boundary (e.g., drying) or a less predictable action, marking a coarse event boundary (e.g., jogging). The results revealed a larger N400 effect for coarse event boundaries compared to fine event boundaries, but no interaction with description length. Between 600 and 1000 ms, however, elaborate contexts elicited a larger frontal positivity compared to brief contexts. This effect was largely driven by less predictable targets, marking coarse event boundaries. We interpret the P600 effect as indexing the updating of the situation model at event boundaries, consistent with Event Segmentation Theory (EST). The updating process is more demanding with coarse event boundaries, which presumably require the construction of a new situation model.

A marker-free system for the analysis of movement disabilities.

PubMed

Legrand, L; Marzani, F; Dusserre, L

1998-01-01

A major step toward improving the treatments of disabled persons may be achieved by using motion analysis equipment. We are developing such a system. It allows the analysis of plane human motion (e.g. gait) without using the tracking of markers. The system is composed of one fixed camera which acquires an image sequence of a human in motion. Then the treatment is divided into two steps: first, a large number of pixels belonging to the boundaries of the human body are extracted at each acquisition time. Secondly, a two-dimensional model of the human body, based on tapered superquadrics, is successively matched with the sets of pixels previously extracted; a specific fuzzy clustering process is used for this purpose. Moreover, an optical flow procedure gives a prediction of the model location at each acquisition time from its location at the previous time. Finally we present some results of this process applied to a leg in motion.

Contrasting evolutionary genome dynamics between domesticated and wild yeasts

PubMed Central

Yue, Jia-Xing; Li, Jing; Aigrain, Louise; Hallin, Johan; Persson, Karl; Oliver, Karen; Bergström, Anders; Coupland, Paul; Warringer, Jonas; Lagomarsino, Marco Consentino; Fischer, Gilles; Durbin, Richard; Liti, Gianni

2017-01-01

Structural rearrangements have long been recognized as an important source of genetic variation with implications in phenotypic diversity and disease, yet their detailed evolutionary dynamics remain elusive. Here, we use long-read sequencing to generate end-to-end genome assemblies for 12 strains representing major subpopulations of the partially domesticated yeast Saccharomyces cerevisiae and its wild relative Saccharomyces paradoxus. These population-level high-quality genomes with comprehensive annotation allow for the first time a precise definition of chromosomal boundaries between cores and subtelomeres and a high-resolution view of evolutionary genome dynamics. In chromosomal cores, S. paradoxus exhibits faster accumulation of balanced rearrangements (inversions, reciprocal translocations and transpositions) whereas S. cerevisiae accumulates unbalanced rearrangements (novel insertions, deletions and duplications) more rapidly. In subtelomeres, both species show extensive interchromosomal reshuffling, with a higher tempo in S. cerevisiae. Such striking contrasts between wild and domesticated yeasts likely reflect the influence of human activities on structural genome evolution. PMID:28416820

Seismicity of the Earth 1900-2012 Sumatra and vicinity

USGS Publications Warehouse

Hayes, Gavin P.; Bernardino, Melissa; Dannemann, Fransiska; Smoczyk, Gregory; Briggs, Richard W.; Benz, Harley M.; Furlong, Kevin P.; Villaseñor, Antonio

2013-01-01

The plate boundary southwest of Sumatra is part of a long tectonic collision zone that extends over 8,000 km from Papua, New Guinea, in the east to the Himalayan front in the west. The Sumatra-Andaman part of the collision zone forms a subduction zone plate boundary, which accommodates convergence between the Indo-Australia and Sunda plates. This convergence is responsible for the intense seismicity in Sumatra. The Sumatra Fault, a major transform structure that bisects Sumatra, accommodates the northwest-increasing lateral component of relative plate motion. Most strain accumulation and release between the two plates occurs along the Sunda megathrust. The increasingly oblique convergence moving northwest is accommodated by crustal seismicity along several transform and normal faults, including the Sumatra Fault. Plate-boundary related deformation is also not restricted to the subduction zone and overriding plate: the Indo-Australian plate actually comprises two somewhat independent plates (India and Australia) that are joined along a broad, actively deforming region that produces seismicity up to several hundred kilometers west of the trench. This deformation is exemplified by the recent April 2012 earthquake sequence, which includes the April 11 M 8.6 and M 8.2 strike-slip events and their subsequent aftershocks. Since 2004, much of the Sunda megathrust between the northern Andaman Islands and Enggano Island, a distance of more than 2,000 km, has ruptured in a series of large subduction zone earthquakes—most rupturing the plate boundary south of Banda Aceh. These events include the great M 9.1 earthquake of December 26, 2004; the M 8.6 Nias Island earthquake of March 28, 2005; and two earthquakes on September 12, 2007, of M 8.5 and M 7.9. On October 25, 2010, a M 7.8 on the shallow portion of the megathrust to the west of the Mentawai Islands caused a substantial tsunami on the west coast of those islands.

A numerical investigation of fine sediment resuspension in the wave boundary layer - effect of hindered settling and bedforms

NASA Astrophysics Data System (ADS)

Hsu, T. J.; Cheng, Z.; Yu, X.

2016-02-01

The wave bottom boundary layer is a major conduit delivering fine terrestrial sediments to the continental margin. Hence, studying the fine sediment resuspension in the wave boundary layer is crucial to the understanding of various components of the earth system, such as carbon cycle. By assuming the settling velocity to be a constant in each simulation, previous turbulence-resolving numerical simulations reveal the existence of three transport modes in the wave boundary layer associated with the sediment availability. As the sediment availability and hence the sediment-induced stable stratification increase, a sequence of transport modes, namely, (I) well-mixed transport, (II) formulation of lutocline resembling a two-layer system, and (III) completely laminarized transport are observed. In general, the settling velocity is a flow variable due to the floc dynamics and hindered settling. This study further investigate the effect of hindered settling. Particularly, for flocs with lower gelling concentrations, the hindered settling effect can play a key role in sustaining large amount of suspended sediment load and results in the laminarized transport (III). For the simulation with a very significant hindered settling effect due to a low gelling concentration, results also indicate the occurrence of gelling ignition, a state in which the erosion rate is always higher than the deposition rate. A condition for the occurrence of gelling ignition is proposed for a range of wave intensities as a function of sediment/floc properties and erodibility parameters. These aforementioned studies are limited to fine sediment transport over a flat bed. However, recent field and laboratory observation show that a small amount of sand fraction can lead to the formation of small bedforms, which can armor the bed while in the meantime enhance near bed turbulence. Preliminary investigation on the effect of bedforms on the resulting transport modes will also be presented.

Magnetostratigraphy of the impact breccias and post-impact carbonates from borehole Yaxcopoil-1, Chicxulub impact crater, Yucatán, Mexico

NASA Astrophysics Data System (ADS)

Rebolledo-Vieyra, Mario; Urrutia-Fucugauchi, Jaime

2004-06-01

We report the magnetostratigraphy of the sedimentary sequence between the impact breccias and the post-impact carbonate sequence conducted on samples recovered by Yaxcopoil-1 (Yax-1). Samples of impact breccias show reverse polarities that span up to ~56 cm into the postimpact carbonate lithologies. We correlate these breccias to those of PEMEX boreholes Yucatán-6 and Chicxulub-1, from which we tied our magnetostratigraphy to the radiometric age from a melt sample from the Yucatán-6 borehole. Thin section analyses of the carbonate samples showed a significant amount of dark minerals and glass shards that we identified as the magnetic carriers; therefore, we propose that the mechanism of magnetic acquisition within the carbonate rocks for the interval studied is detrital remanent magnetism (DRM). With these samples, we constructed the scale of geomagnetic polarities where we find two polarities within the sequence, a reverse polarity event within the impact breccias and the base of the post-impact carbonate sequence (up to 794.07 m), and a normal polarity event in the last ~20 cm of the interval studied. The polarities recorded in the sequence analyzed are interpreted to span from chron 29r to 29n, and we propose that the reverse polarity event lies within the 29r chron. The magnetostratigraphy of the sequence studied shows that the horizon at 794.11 m deep, interpreted as the K/T boundary, lies within the geomagnetic chron 29r, which contains the K/T boundary.

Neogene sequence stratigraphy, Nam Con Son Basin, offshore Vietnam

DOE Office of Scientific and Technical Information (OSTI.GOV)

McMillen, K.J.; Do Van Luu; Lee, E.K.

1996-12-31

An integrated well log, biostratigraphic, and seismic stratigraphic study of Miocene to Recent deltaic sediments deposited in the Nam Con Son Basin offshore from southern Vietnam shows the influence of eustacy and tectonics on sequence development. Sediments consist of Oligocene non-marine rift-basin fill (Cau Formation), early to middle Miocene tide-dominated delta plain to delta front sediments (TB 1.5 to TB 2.5, Due and Thong Formations), and late Miocene to Recent marine shelf sediments (TB. 2.6 to TB 3.1 0, Mang Cau, Nam Con Son, and Bien Dong Formations). Eustacy controlled the timing of key surfaces and sand distribution in themore » tectonically-quiet early Miocene. Tectonic effects on middle to late Miocene sequence development consist of thick transgressive systems tracts due to basin-wide subsidence and transgression, sand distribution in the basin center, and carbonate sedimentation on isolated fault blocks within the basin. Third-order sequence boundaries (SB) are identified by spore peaks, sand stacking patterns, and channel incision. In the basin center, widespread shale beds with coal occur above sequence boundaries followed by transgressive sandstone units. These TST sandstones merge toward the basin margin where they lie on older HST sandstones. Maximum flooding surfaces (MFS) have abundant marine microfossils and mangrove pollen, a change in sand stacking pattern, and often a strong seismic reflection with downlap. Fourth-order genetic-type sequences are also interpreted. The MFS is the easiest marker to identify and correlate on well logs. Fourth-order SB occur within these genetic units but are harder to identify and correlate.« less

Neogene sequence stratigraphy, Nam Con Son Basin, offshore Vietnam

DOE Office of Scientific and Technical Information (OSTI.GOV)

McMillen, K.J.; Do Van Luu; Lee, E.K.

1996-01-01

An integrated well log, biostratigraphic, and seismic stratigraphic study of Miocene to Recent deltaic sediments deposited in the Nam Con Son Basin offshore from southern Vietnam shows the influence of eustacy and tectonics on sequence development. Sediments consist of Oligocene non-marine rift-basin fill (Cau Formation), early to middle Miocene tide-dominated delta plain to delta front sediments (TB 1.5 to TB 2.5, Due and Thong Formations), and late Miocene to Recent marine shelf sediments (TB. 2.6 to TB 3.1 0, Mang Cau, Nam Con Son, and Bien Dong Formations). Eustacy controlled the timing of key surfaces and sand distribution in themore » tectonically-quiet early Miocene. Tectonic effects on middle to late Miocene sequence development consist of thick transgressive systems tracts due to basin-wide subsidence and transgression, sand distribution in the basin center, and carbonate sedimentation on isolated fault blocks within the basin. Third-order sequence boundaries (SB) are identified by spore peaks, sand stacking patterns, and channel incision. In the basin center, widespread shale beds with coal occur above sequence boundaries followed by transgressive sandstone units. These TST sandstones merge toward the basin margin where they lie on older HST sandstones. Maximum flooding surfaces (MFS) have abundant marine microfossils and mangrove pollen, a change in sand stacking pattern, and often a strong seismic reflection with downlap. Fourth-order genetic-type sequences are also interpreted. The MFS is the easiest marker to identify and correlate on well logs. Fourth-order SB occur within these genetic units but are harder to identify and correlate.« less

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

NASA Astrophysics Data System (ADS)

Barakat, Moataz; Dominik, Wilhelm

2010-05-01

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

Kidney segmentation in CT sequences using graph cuts based active contours model and contextual continuity.

PubMed

Zhang, Pin; Liang, Yanmei; Chang, Shengjiang; Fan, Hailun

2013-08-01

Accurate segmentation of renal tissues in abdominal computed tomography (CT) image sequences is an indispensable step for computer-aided diagnosis and pathology detection in clinical applications. In this study, the goal is to develop a radiology tool to extract renal tissues in CT sequences for the management of renal diagnosis and treatments. In this paper, the authors propose a new graph-cuts-based active contours model with an adaptive width of narrow band for kidney extraction in CT image sequences. Based on graph cuts and contextual continuity, the segmentation is carried out slice-by-slice. In the first stage, the middle two adjacent slices in a CT sequence are segmented interactively based on the graph cuts approach. Subsequently, the deformable contour evolves toward the renal boundaries by the proposed model for the kidney extraction of the remaining slices. In this model, the energy function combining boundary with regional information is optimized in the constructed graph and the adaptive search range is determined by contextual continuity and the object size. In addition, in order to reduce the complexity of the min-cut computation, the nodes in the graph only have n-links for fewer edges. The total 30 CT images sequences with normal and pathological renal tissues are used to evaluate the accuracy and effectiveness of our method. The experimental results reveal that the average dice similarity coefficient of these image sequences is from 92.37% to 95.71% and the corresponding standard deviation for each dataset is from 2.18% to 3.87%. In addition, the average automatic segmentation time for one kidney in each slice is about 0.36 s. Integrating the graph-cuts-based active contours model with contextual continuity, the algorithm takes advantages of energy minimization and the characteristics of image sequences. The proposed method achieves effective results for kidney segmentation in CT sequences.

A brief review of some mechanisms causing boundary layer transition at high speeds

NASA Technical Reports Server (NTRS)

Tauber, M. E.

1990-01-01

In high speed flight, the state of the boundary layer can strongly influence the design of vehicles through its effect on skin friction drag and aerodynamic heating. The major mechanisms causing boundary layer transition on high speed vehicles are briefly reviewed and some empirical relations from the unclassified literature are given for the transition Reynolds numbers.

Postapocalypse stratigraphy: Some considerations and proposals

NASA Astrophysics Data System (ADS)

Prosh, E. C.; McCracken, A. D.

1985-01-01

An imminent nuclear apocalypse will be a geologically significant event characterized by widespread extinction and marked by a highly radioactive lower boundary layer. The concept of a fallout-enriched Cenozoic/postapocalypse boundary layer is significant in that such a horizon would constitute an ideal, global isochron that is both readily detectable and correlatable; the only other systemic boundary that appears to be analogous is the Cretaceous/Tertiary boundary. New terminology consistent with the established stratigraphic nomenclature is herein proposed for the major anticipated postapocalypse geochronologic units.

Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition.

PubMed

Penny, D; Hasegawa, M; Waddell, P J; Hendy, M D

1999-03-01

We explore the tree of mammalian mtDNA sequences, using particularly the LogDet transform on amino acid sequences, the distance Hadamard transform, and the Closest Tree selection criterion. The amino acid composition of different species show significant differences, even within mammals. After compensating for these differences, nearest-neighbor bootstrap results suggest that the tree is locally stable, though a few groups show slightly greater rearrangements when a large proportion of the constant sites are removed. Many parts of the trees we obtain agree with those on published protein ML trees. Interesting results include a preference for rodent monophyly. The detection of a few alternative signals to those on the optimal tree were obtained using the distance Hadamard transform (with results expressed as a Lento plot). One rearrangement suggested was the interchange of the position of primates and rodents on the optimal tree. The basic stability of the tree, combined with two calibration points (whale/cow and horse/rhinoceros), together with a distant secondary calibration from the mammal/bird divergence, allows inferences of the times of divergence of putative clades. Allowing for sampling variances due to finite sequence length, most major divergences amongst lineages leading to modern orders, appear to occur well before the Cretaceous/Tertiary (K/T) boundary. Implications arising from these early divergences are discussed, particularly the possibility of competition between the small dinosaurs and the new mammal clades.

A Mitogenomic Phylogeny of Living Primates

PubMed Central

Finstermeier, Knut; Zinner, Dietmar; Brameier, Markus; Meyer, Matthias; Kreuz, Eva; Hofreiter, Michael; Roos, Christian

2013-01-01

Primates, the mammalian order including our own species, comprise 480 species in 78 genera. Thus, they represent the third largest of the 18 orders of eutherian mammals. Although recent phylogenetic studies on primates are increasingly built on molecular datasets, most of these studies have focused on taxonomic subgroups within the order. Complete mitochondrial (mt) genomes have proven to be extremely useful in deciphering within-order relationships even up to deep nodes. Using 454 sequencing, we sequenced 32 new complete mt genomes adding 20 previously not represented genera to the phylogenetic reconstruction of the primate tree. With 13 new sequences, the number of complete mt genomes within the parvorder Platyrrhini was widely extended, resulting in a largely resolved branching pattern among New World monkey families. We added 10 new Strepsirrhini mt genomes to the 15 previously available ones, thus almost doubling the number of mt genomes within this clade. Our data allow precise date estimates of all nodes and offer new insights into primate evolution. One major result is a relatively young date for the most recent common ancestor of all living primates which was estimated to 66-69 million years ago, suggesting that the divergence of extant primates started close to the K/T-boundary. Although some relationships remain unclear, the large number of mt genomes used allowed us to reconstruct a robust primate phylogeny which is largely in agreement with previous publications. Finally, we show that mt genomes are a useful tool for resolving primate phylogenetic relationships on various taxonomic levels. PMID:23874967

Hydrogenophaga crassostreae sp. nov., isolated from a Pacific oyster.

PubMed

Baek, Chaeyun; Kim, Eunji; Shin, Su-Kyoung; Choi, Sungmi; Yi, Hana

2017-10-01

A Gram-negative, motile, rod-shaped, and aerobic bacterial strain, designated LPB0072 T , was isolated from a Pacific oyster (Crassostrea gigas). Autotrophic growth with hydrogen gas was not observed. Cells oxidized thiosulfate to sulfate and reduced nitrate to nitrite. The complete genome sequence of strain LPB0072 T (CP017476) is 4.94 Mb in length and contains 4459 protein-coding genes, with a G+C content of 61.3 mol%. Analysis of the 16S rRNA gene sequence indicated that strain LPB0072 T belongs to the genus Hydrogenophaga, with greatest sequence similarity to the type strain of Hydrogenophaga taeniospiralis (97.5 %). The isoprenoid quinone (Q-8) and the major cellular fatty acids (C16 : 1ω7c and/or C16 : 1ω6c, C16 : 0 and C17 : 1ω6c) identified were concordant with the chemotaxonomic properties of the genus Hydrogenophaga. The average nucleotide identities with closely related species were below the suggested boundary for species delineation, indicating that the isolate is a novel species. Numerous physiological and biochemical features also distinguished the isolate from other known Hydrogenophaga species. Based on the polyphasic data presented in this study, strain LPB0072 T should be classified as a novel species in the genus Hydrogenophaga, and the name Hydrogenophaga crassostreae sp. nov. is proposed. The type strain is LPB0072 T (=KACC 18705 T =JCM 31188 T ).

Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries.

PubMed

Kim, Hyoung Tae; Kim, Jung Sung; Moore, Michael J; Neubig, Kurt M; Williams, Norris H; Whitten, W Mark; Kim, Joo-Hwan

2015-01-01

Earlier research has revealed that the ndh loci have been pseudogenized, truncated, or deleted from most orchid plastomes sequenced to date, including in all available plastomes of the two most species-rich subfamilies, Orchidoideae and Epidendroideae. This study sought to resolve deeper-level phylogenetic relationships among major orchid groups and to refine the history of gene loss in the ndh loci across orchids. The complete plastomes of seven orchids, Oncidium sphacelatum (Epidendroideae), Masdevallia coccinea (Epidendroideae), Sobralia callosa (Epidendroideae), Sobralia aff. bouchei (Epidendroideae), Elleanthus sodiroi (Epidendroideae), Paphiopedilum armeniacum (Cypripedioideae), and Phragmipedium longifolium (Cypripedioideae) were sequenced and analyzed in conjunction with all other available orchid and monocot plastomes. Most ndh loci were found to be pseudogenized or lost in Oncidium, Paphiopedilum and Phragmipedium, but surprisingly, all ndh loci were found to retain full, intact reading frames in Sobralia, Elleanthus and Masdevallia. Character mapping suggests that the ndh genes were present in the common ancestor of orchids but have experienced independent, significant losses at least eight times across four subfamilies. In addition, ndhF gene loss was correlated with shifts in the position of the junction of the inverted repeat (IR) and small single-copy (SSC) regions. The Orchidaceae have unprecedented levels of homoplasy in ndh gene presence/absence, which may be correlated in part with the unusual life history of orchids. These results also suggest that ndhF plays a role in IR/SSC junction stability.

Kinetics and thermodynamics associated with Bi adsorption transitions at Cu and Ni grain boundaries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tai, Kaiping; Feng, Lin; Dillon, Shen J.

The grain boundary diffusivity of Au in Cu and Cu-Bi, and Cu in Ni and Ni-Bi are characterized by secondary ion mass spectroscopy depth profiling. Samples are equilibrated in a Bi containing atmosphere at temperatures above and below the onset of grain boundary adsorption transitions, sometimes called complexion transitions. A simple thermo-kinetic model is used to estimate the relative entropic contributions to the grain boundary energies. The results indicate that the entropy term plays a major role in promoting thermally and chemically induced grain boundary complexion transition.

Molecular biology. Mothers setting boundaries.

PubMed

Thorvaldsen, J L; Bartolomei, M S

2000-06-23

Certain genes are only expressed at one allele, a phenomenon called imprinting. Although it is well established that one allele of certain imprinted genes is silenced through methylation, this does not appear to be the case for all imprinted genes. In a thoughtful Perspective, Thorvaldsen and Bartolomei discuss new findings showing that insertion of insulator elements (boundary regions) between the promoter of a gene and its enhancer (a sequence that boosts gene expression) may be another way in which genes are silenced during imprinting.

Identification of a novel plant amalgavirus (Amalgavirus, Amalgaviridae) genome sequence in Cistus incanus.

PubMed

Goh, C J; Park, D; Lee, J S; Sebastiani, F; Hahn, Y

2018-01-01

Amalgaviridae is a family of double-stranded, monosegmented RNA viruses that are associated with plants, fungi, microsporidians, and animals. A sequence contig derived from the transcriptome of a eudicot, Cistus incanus (the family Cistaceae; commonly known as hoary rockrose), was identified as the genome sequence of a novel plant RNA virus and named Cistus incanus RNA virus 1 (CiRV1). Sequence comparison and phylogenetic analysis indicated that CiRV1 is a novel species of the genus Amalgavirus in the family Amalgaviridae. The CiRV1 genome contig has two overlapping open reading frames (ORFs). ORF1 encodes a putative replication factory matrix-like protein, while ORF2 encodes a RNA-dependent RNA polymerase (RdRp) domain. An ORF1+2 fusion protein, which functions in viral RNA replication, is produced by a +1 programmed ribosomal frameshifting (PRF) mechanism. A +1 PRF motif UUU_CGU, which matches the conserved amalgavirus +1 PRF consensus sequence UUU_CGN, was found at the boundary of CiRV1 ORF1 and ORF2. Comparison of 25 amalgavirus ORF1+2 fusion proteins revealed that only three different positions within a 13-amino acid segment were recurrently used at the boundary, possibly being selected so as not to interfere with correct folding and function of the fusion protein. CiRV1 is the first virus found to be associated with the Cistus species and may be useful for studying amalgaviruses.

ASFinder: a tool for genome-wide identification of alternatively splicing transcripts from EST-derived sequences.

PubMed

Min, Xiang Jia

2013-01-01

Expressed Sequence Tags (ESTs) are a rich resource for identifying Alternatively Splicing (AS) genes. The ASFinder webserver is designed to identify AS isoforms from EST-derived sequences. Two approaches are implemented in ASFinder. If no genomic sequences are provided, the server performs a local BLASTN to identify AS isoforms from ESTs having both ends aligned but an internal segment unaligned. Otherwise, ASFinder uses SIM4 to map ESTs to the genome, then the overlapping ESTs that are mapped to the same genomic locus and have internal variable exon/intron boundaries are identified as AS isoforms. The tool is available at http://proteomics.ysu.edu/tools/ASFinder.html.

Animal selection for whole genome sequencing by quantifying the unique contribution of homozygous haplotypes sequenced

USDA-ARS?s Scientific Manuscript database

Major whole genome sequencing projects promise to identify rare and causal variants within livestock species; however, the efficient selection of animals for sequencing remains a major problem within these surveys. The goal of this project was to develop a library of high accuracy genetic variants f...

Swath sonar mapping of Earth's submarine plate boundaries

NASA Astrophysics Data System (ADS)

Carbotte, S. M.; Ferrini, V. L.; Celnick, M.; Nitsche, F. O.; Ryan, W. B. F.

2014-12-01

The recent loss of Malaysia Airlines flight MH370 in an area of the Indian Ocean where less than 5% of the seafloor is mapped with depth sounding data (Smith and Marks, EOS 2014) highlights the striking lack of detailed knowledge of the topography of the seabed for much of the worlds' oceans. Advances in swath sonar mapping technology over the past 30 years have led to dramatic improvements in our capability to map the seabed. However, the oceans are vast and only an estimated 10% of the seafloor has been mapped with these systems. Furthermore, the available coverage is highly heterogeneous and focused within areas of national strategic priority and community scientific interest. The major plate boundaries that encircle the globe, most of which are located in the submarine environment, have been a significant focus of marine geoscience research since the advent of swath sonar mapping. While the location of these plate boundaries are well defined from satellite-derived bathymetry, significant regions remain unmapped at the high-resolutions provided by swath sonars and that are needed to study active volcanic and tectonic plate boundary processes. Within the plate interiors, some fossil plate boundary zones, major hotspot volcanoes, and other volcanic provinces have been the focus of dedicated research programs. Away from these major tectonic structures, swath mapping coverage is limited to sparse ocean transit lines which often reveal previously unknown deep-sea channels and other little studied sedimentary structures not resolvable in existing low-resolution global compilations, highlighting the value of these data even in the tectonically quiet plate interiors. Here, we give an overview of multibeam swath sonar mapping of the major plate boundaries of the globe as extracted from public archives. Significant quantities of swath sonar data acquired from deep-sea regions are in restricted-access international archives. Open access to more of these data sets would enable global comparisons of plate boundary structures and processes and could facilitate a more coordinated approach to optimizing the future acquisition of these high-value data by the global research community.

Composition and Function of Sulfate-Reducing Prokaryotes in Eutrophic and Pristine Areas of the Florida Everglades†

PubMed Central

Castro, Hector; Reddy, K. R.; Ogram, Andrew

2002-01-01

As a result of agricultural activities in regions adjacent to the northern boundary of the Florida Everglades, a nutrient gradient developed that resulted in physicochemical and ecological changes from the original system. Sulfate input from agricultural runoff and groundwater is present in soils of the Northern Everglades, and sulfate-reducing prokaryotes (SRP) may play an important role in biogeochemical processes such as carbon cycling. The goal of this project was to utilize culture-based and non-culture-based approaches to study differences between the composition of assemblages of SRP in eutrophic and pristine areas of the Everglades. Sulfate reduction rates and most-probable-number enumerations revealed SRP populations and activities to be greater in eutrophic zones than in more pristine soils. In eutrophic regions, methanogenesis rates were higher, the addition of acetate stimulated methanogenesis, and SRP able to utilize acetate competed to a limited degree with acetoclastic methanogens. A surprising amount of diversity within clone libraries of PCR-amplified dissimilatory sulfite reductase (DSR) genes was observed, and the majority of DSR sequences were associated with gram-positive spore-forming Desulfotomaculum and uncultured microorganisms. Sequences associated with Desulfotomaculum fall into two categories: in the eutrophic regions, 94.7% of the sequences related to Desulfotomaculum were associated with those able to completely oxidize substrates, and in samples from pristine regions, all Desulfotomaculum-like sequences were related to incomplete oxidizers. This metabolic selection may be linked to the types of substrates that Desulfotomaculum spp. utilize; it may be that complete oxidizers are more versatile and likelier to proliferate in nutrient-rich zones of the Everglades. Desulfotomaculum incomplete oxidizers may outcompete complete oxidizers for substrates such as hydrogen in pristine zones where diverse carbon sources are less available. PMID:12450837

Colorstratigraphy; A New Stratigraphic Correlation Technique

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

A High Resolution Seismic Sequence Analysis of the Malta Plateau

DTIC Science & Technology

1999-05-01

the SACLANTCEN Programme of Work. The document has been approved for release by The Director, SACLANTCEN. Jan L . Spoelstra Director NATO...the Plio- Quatemary. To the southwest of Sicily, Di Stefano et al. (1993) identified six sequence boundaries and estimated the ages by the...the location of the seismic reflection profiles in Di Stefano et al. (1993) do not overlap any of the profiles in this study and use a lower frequency

Post-boosting of classification boundary for imbalanced data using geometric mean.

PubMed

Du, Jie; Vong, Chi-Man; Pun, Chi-Man; Wong, Pak-Kin; Ip, Weng-Fai

2017-12-01

In this paper, a novel imbalance learning method for binary classes is proposed, named as Post-Boosting of classification boundary for Imbalanced data (PBI), which can significantly improve the performance of any trained neural networks (NN) classification boundary. The procedure of PBI simply consists of two steps: an (imbalanced) NN learning method is first applied to produce a classification boundary, which is then adjusted by PBI under the geometric mean (G-mean). For data imbalance, the geometric mean of the accuracies of both minority and majority classes is considered, that is statistically more suitable than the common metric accuracy. PBI also has the following advantages over traditional imbalance methods: (i) PBI can significantly improve the classification accuracy on minority class while improving or keeping that on majority class as well; (ii) PBI is suitable for large data even with high imbalance ratio (up to 0.001). For evaluation of (i), a new metric called Majority loss/Minority advance ratio (MMR) is proposed that evaluates the loss ratio of majority class to minority class. Experiments have been conducted for PBI and several imbalance learning methods over benchmark datasets of different sizes, different imbalance ratios, and different dimensionalities. By analyzing the experimental results, PBI is shown to outperform other imbalance learning methods on almost all datasets. Copyright © 2017 Elsevier Ltd. All rights reserved.

DB2: a probabilistic approach for accurate detection of tandem duplication breakpoints using paired-end reads.

PubMed

Yavaş, Gökhan; Koyutürk, Mehmet; Gould, Meetha P; McMahon, Sarah; LaFramboise, Thomas

2014-03-05

With the advent of paired-end high throughput sequencing, it is now possible to identify various types of structural variation on a genome-wide scale. Although many methods have been proposed for structural variation detection, most do not provide precise boundaries for identified variants. In this paper, we propose a new method, Distribution Based detection of Duplication Boundaries (DB2), for accurate detection of tandem duplication breakpoints, an important class of structural variation, with high precision and recall. Our computational experiments on simulated data show that DB2 outperforms state-of-the-art methods in terms of finding breakpoints of tandem duplications, with a higher positive predictive value (precision) in calling the duplications' presence. In particular, DB2's prediction of tandem duplications is correct 99% of the time even for very noisy data, while narrowing down the space of possible breakpoints within a margin of 15 to 20 bps on the average. Most of the existing methods provide boundaries in ranges that extend to hundreds of bases with lower precision values. Our method is also highly robust to varying properties of the sequencing library and to the sizes of the tandem duplications, as shown by its stable precision, recall and mean boundary mismatch performance. We demonstrate our method's efficacy using both simulated paired-end reads, and those generated from a melanoma sample and two ovarian cancer samples. Newly discovered tandem duplications are validated using PCR and Sanger sequencing. Our method, DB2, uses discordantly aligned reads, taking into account the distribution of fragment length to predict tandem duplications along with their breakpoints on a donor genome. The proposed method fine tunes the breakpoint calls by applying a novel probabilistic framework that incorporates the empirical fragment length distribution to score each feasible breakpoint. DB2 is implemented in Java programming language and is freely available at http://mendel.gene.cwru.edu/laframboiselab/software.php.

The Impact of Surface Boundary Forcing on Simulation of the 1998 Summer Drought Over the US Midwest Using Factor Separation Technique

NASA Technical Reports Server (NTRS)

Stein, Uri; Fox-Rabinovitz, Michael

1999-01-01

The factor separation (FS) technique has been utilized to evaluate quantitatively the impact of surface boundary forcings on simulation of the 1988 summer drought over the Midwestern part of the U.S. The four surface boundary forcings used are: (1)Sea Surface Temperature (SST), (2) soil moisture, (3) snow cover, and (4) sea ice. The Goddard Earth Observing System(GEOS) General Circulation Model (GCM) is used to simulate the 1988 U.S. drought. A series of sixteen simulations are performed with climatological and real 1988 surface boundary conditions. The major single and mutual synergistic factors/impacts are analyzed. The results show that SST and soil moisture are the major single pro-drought factors. The couple synergistic effect of SST and soil moisture is the major anti-drought factor. The triple synergistic impact of SST, soil moisture, and snow cover is the strongest pro-drought impact and is, therefore, the main contributor to the generation of the drought. The impact of the snow cover and sea ice anomalies for June 1988 on the drought is significant only when combined with the SST and soil moisture anomalies.

Markov models of genome segmentation

NASA Astrophysics Data System (ADS)

Thakur, Vivek; Azad, Rajeev K.; Ramaswamy, Ram

2007-01-01

We introduce Markov models for segmentation of symbolic sequences, extending a segmentation procedure based on the Jensen-Shannon divergence that has been introduced earlier. Higher-order Markov models are more sensitive to the details of local patterns and in application to genome analysis, this makes it possible to segment a sequence at positions that are biologically meaningful. We show the advantage of higher-order Markov-model-based segmentation procedures in detecting compositional inhomogeneity in chimeric DNA sequences constructed from genomes of diverse species, and in application to the E. coli K12 genome, boundaries of genomic islands, cryptic prophages, and horizontally acquired regions are accurately identified.

Novel Strategy for Discrimination of Transcription Factor Binding Motifs Employing Mathematical Neural Network

NASA Astrophysics Data System (ADS)

Sugimoto, Asuka; Sumi, Takuya; Kang, Jiyoung; Tateno, Masaru

2017-07-01

Recognition in biological macromolecular systems, such as DNA-protein recognition, is one of the most crucial problems to solve toward understanding the fundamental mechanisms of various biological processes. Since specific base sequences of genome DNA are discriminated by proteins, such as transcription factors (TFs), finding TF binding motifs (TFBMs) in whole genome DNA sequences is currently a central issue in interdisciplinary biophysical and information sciences. In the present study, a novel strategy to create a discriminant function for discrimination of TFBMs by constituting mathematical neural networks (NNs) is proposed, together with a method to determine the boundary of signals (TFBMs) and noise in the NN-score (output) space. This analysis also leads to the mathematical limitation of discrimination in the recognition of features representing TFBMs, in an information geometrical manifold. Thus, the present strategy enables the identification of the whole space of TFBMs, right up to the noise boundary.

No geochemical evidence for an asteroidal impact at late Devonian mass extinction horizon

NASA Astrophysics Data System (ADS)

McGhee, G. R., Jr.; Gilmore, J. S.; Orth, C. J.; Olsen, E.

1984-04-01

Three sedimentary sequences in New York State (Dunkirk Beach, Walnut Creek Gorge, and Mills Mills) and one sedimentary sequence in Belgium (Sinsin), that cross the Devonian Frasnian-Famennian boundary, were examined for an iridium (Ir) anomaly to determine whether the biotic extinctions at the end of the Cretaceous could have been caused by an asteroidal impact. The sampling at three of the four areas was on 2-cm center points, and 15 to 20 g of sample were collected. The instrumental neutron activation method required 5 g samples, and consequently the distance between samples was less than 1 cm. Though the Devonian samples studied had a high probability of locating an Ir anomaly, none was found. The highest Ir values were between 0.2 and 2 percent of those reported for the marine and terrestrial Ir analyses at the Cretaceous-Tertiary boundary, and Devonian pyrite-rich sediments did not exhibit high Ir concentrations.

Molecular phylogeny for marine turtles based on sequences of the ND4-leucine tRNA and control regions of mitochondrial DNA.

PubMed

Dutton, P H; Davis, S K; Guerra, T; Owens, D

1996-06-01

Marine turtles are divided into two families, the Dermochelyidae and the Cheloniidae. The majority of species are currently placed within the two tribes of the Cheloniidae, the Chelonini and the Carettini, but debate continues over generic and tribal affinities as well as species boundaries. We used nucleotide sequences (907 bp) from the ND4-LEU tRNA region and the control region (526 bp) of mitochondrial DNA to resolve areas of uncertainty in marine turtle (Chelonioidae) systematics. The ND4-LEU tRNA fragment was more conserved than the fragment from the control region, with sequence divergences ranging from 0.026 to 0.148 and 0.067 to 0.267, respectively. Parsimony analysis based only on the ND4-LEU tRNA data suggests that the hawksbill, Eretmochelys imbricata, lies within the tribe Carettni and is closely related to the genus Caretta, but could not resolve the position of the flatback, Natator depressus. A similar analysis based only on the control region sequence data suggested that N. depressus is affiliated with the Chelonini, but failed to resolve the position of E. imbricata and the loggerhead, Caretta caretta. In contrast to these results, the combination of both data sets with published cytochrome b data produced a phylogeny based on 1924 bp of sequence data which resolves the position of E. imbricata relative to Caretta and Lepidochelys and joins N. depressus as sister to the Carettini. Based on the molecular data, the Chelonini contains the Chelonia species, while the Carettini contains the remaining species of Cheloniidae. The control region sequence divergence between Pacific and Atlantic populations of the leatherback, Dermochelys coriacea, was relatively low (0.0081) when compared with the green turtle, Chelonia mydas (0.071-0.074). Atlantic and Pacific populations of Ch. mydas were found to be paraphyletic with respect to the black turtle, Ch. agassizi, suggesting that the current taxonomic designations within the Pacific Chelonia are questionable. This analysis shows the utility of combining sequence data for different regions of mtDNA that by themselves are insufficient to obtain robust phylogenies.

Evidence from central Mexico supporting the Younger Dryas extraterrestrial impact hypothesis.

PubMed

Israde-Alcántara, Isabel; Bischoff, James L; Domínguez-Vázquez, Gabriela; Li, Hong-Chun; DeCarli, Paul S; Bunch, Ted E; Wittke, James H; Weaver, James C; Firestone, Richard B; West, Allen; Kennett, James P; Mercer, Chris; Xie, Sujing; Richman, Eric K; Kinzie, Charles R; Wolbach, Wendy S

2012-03-27

We report the discovery in Lake Cuitzeo in central Mexico of a black, carbon-rich, lacustrine layer, containing nanodiamonds, microspherules, and other unusual materials that date to the early Younger Dryas and are interpreted to result from an extraterrestrial impact. These proxies were found in a 27-m-long core as part of an interdisciplinary effort to extract a paleoclimate record back through the previous interglacial. Our attention focused early on an anomalous, 10-cm-thick, carbon-rich layer at a depth of 2.8 m that dates to 12.9 ka and coincides with a suite of anomalous coeval environmental and biotic changes independently recognized in other regional lake sequences. Collectively, these changes have produced the most distinctive boundary layer in the late Quaternary record. This layer contains a diverse, abundant assemblage of impact-related markers, including nanodiamonds, carbon spherules, and magnetic spherules with rapid melting/quenching textures, all reaching synchronous peaks immediately beneath a layer containing the largest peak of charcoal in the core. Analyses by multiple methods demonstrate the presence of three allotropes of nanodiamond: n-diamond, i-carbon, and hexagonal nanodiamond (lonsdaleite), in order of estimated relative abundance. This nanodiamond-rich layer is consistent with the Younger Dryas boundary layer found at numerous sites across North America, Greenland, and Western Europe. We have examined multiple hypotheses to account for these observations and find the evidence cannot be explained by any known terrestrial mechanism. It is, however, consistent with the Younger Dryas boundary impact hypothesis postulating a major extraterrestrial impact involving multiple airburst(s) and and/or ground impact(s) at 12.9 ka.

Geology and geochemistry of the Middle Proterozoic Eastern Ghat mobile belt and its comparison with the lower crust of the Southern Peninsular shield

NASA Technical Reports Server (NTRS)

Rao, M. V. Subba

1988-01-01

Two prominent rock suites constitute the lithology of the Eastern Ghat mobile belt: (1) the khondalite suite - the metapelites, and (2) the charnockite suite. Later intrusives include ultramafic sequences, anorthosites and granitic gneisses. The chief structural element in the rocks of the Eastern Ghats is a planar fabric (gneissosity), defined by the alignment of platy minerals like flattened quartz, garnet, sillimanite, graphite, etc. The parallelism between the foliation and the lithological layering is related to isoclinal folding. The major structural trend (axial plane foliation trend) observed in the belt is NE-SW. Five major tectonic events have been delineated in the belt. A boundary fault along the western margin of the Eastern Ghats, bordering the low grade terrain has been substantiated by recent gravity and the deep seismic sounding studies. Field evidence shows that the pyroxene granulites (basic granulites) post-date the khondalite suite, but are older than the charnockites as well as the granitic gneisses. Polyphase metamorphism, probably correlatable with different periods of deformation is recorded. The field relations in the Eastern Ghats point to the intense deformation of the terrain, apparently both before, during and after metamorphism.

Role of Transtension in Rifting at the Pacific-North America Plate Boundary

NASA Astrophysics Data System (ADS)

Stock, J. M.

2011-12-01

Transtensional plate motion can be accommodated either in a localized zone of transtensional rifting or over a broader region. Broader zones of deformation can be classified either as diffuse deformation or strain partitioning (one or more major strike-slip shear zones geographically offset from a region of a extensional faulting). The Pacific-North America plate boundary in southwestern North America was transtensional during much of its history and has exhibited the full range of these behaviors at different spatial scales and in different locations, as recorded by fault motions and paleomagnetic rotations. Here we focus on the northern Gulf of California part of the plate boundary (Upper and Lower Delfin basin segments), which has been in a zone of transtensional Pacific-North America plate boundary motion ever since the middle Miocene demise of adjacent Farallon-derived microplates. Prior to the middle Miocene, during the time of microplate activity, this sector of North America experienced basin-and-range normal faults (core complexes) in Sonora. However there is no evidence of continued extensional faulting nor of a Gulf-related topographic depression until after ca 12 Ma when a major ignimbrite (Tuff of San Felipe/ Ignimbrite of Hermosillo) was deposited across the entire region of the future Gulf of California rift in this sector. After 12 Ma, faults disrupted this marker bed in eastern Baja California and western Sonora, and some major NNW-striking right-lateral faults are inferred to have developed near the Sonoran coast causing offset of some of the volcanic facies. However, there are major tectonic rotations of the volcanic rocks in NE Baja California between 12 and 6 Ma, suggesting that the plate boundary motion was still occurring over a broad region. By contrast, after about 6 Ma, diminished rotations in latest Miocene and Pliocene volcanic rocks, as well as fault slip histories, show that plate boundary deformation became localized to a narrower transtensional zone of long offset strike-slip faults and intervening basins (the modern Gulf of California basin and transform fault system). Within and adjacent to this zone the fault patterns continued to evolve, with new plate boundary strike-slip faults breaking into previously intact blocks of continent. These new strike-slip faults were not accompanied by any widespread zones of tectonic rotation. This suggests that if widespread rotations are occurring, plate boundary transtension has not yet localized and the strike-slip faults are not yet accommodating most of the plate boundary slip. The cessation of widespread and significant vertical axis rotations could indicate strain localization and the increasing importance of throughgoing strike-slip faults (a precursor to fully oceanic rifting) along a transtensional plate boundary.

Real-time flutter boundary prediction based on time series models

NASA Astrophysics Data System (ADS)

Gu, Wenjing; Zhou, Li

2018-03-01

For the purpose of predicting the flutter boundary in real time during flutter flight tests, two time series models accompanied with corresponding stability criterion are adopted in this paper. The first method simplifies a long nonstationary response signal as many contiguous intervals and each is considered to be stationary. The traditional AR model is then established to represent each interval of signal sequence. While the second employs a time-varying AR model to characterize actual measured signals in flutter test with progression variable speed (FTPVS). To predict the flutter boundary, stability parameters are formulated by the identified AR coefficients combined with Jury's stability criterion. The behavior of the parameters is examined using both simulated and wind-tunnel experiment data. The results demonstrate that both methods show significant effectiveness in predicting the flutter boundary at lower speed level. A comparison between the two methods is also given in this paper.

Geological and Geophysical Integration Regarding a Structural Evolution Modelling of a Suture Zone Controlled by a Cratonic Buttress - The Case of Dom Feliciano Orogenic Belt, SSE Brazil, Implications for Western Gondwana Assembly

NASA Astrophysics Data System (ADS)

Bruno, H.; Almeida, J.; Heilbron, M. C. P. L.; Salomão, M.

2017-12-01

The matters surrounding the amalgamation of tectonic blocks during the Brasiliano / Pan-African orogeny have been the main subject of study of several works in recent years. The main objective of this work is the hierarchy and discrimination of the boundaries between the known tectonic blocks, integrating geological and geophysical data. The geology of the study area is dominated by Precambrian terranes; Luís Alves Terrane, the vulcanosedimentary sequences of the Itajaí and Campo Alegre Basins, the metasedimentary sequences of the Brusque and Paranaguá Terranes and their granitic suites besides the granitoids of the Florianópolis Terrane. The shear zones and faults that separate these crustal blocks were developed during the Brasiliano / Pan-African orogenic cycle that led to the formation of the supercontinent Gondwana. These tectonic boundaries generally separate blocks of different rheology and crustal thickness. The integration of geological and geophysical data allowed the identification of important structural lineaments and crustal boundaries. The presented geodynamic model suggests that the suture between the block composed of the Brusque, Paranaguá and Florianópolis Terranes and the block composed by the Luís Alves Terrane is the Itajaí Perimbó Shear Zone, and not the Major Gercino Shear Zone as previously suggested. Considering the Itajaí Perimbó Shear Zone as the suture zone, the metassediments of the Brusque Terrane were deposited on the basement of the Florianópolis Terrane, hereby declared as part of the Angola Craton, and are correlated to the metassediments of the Paranaguá Terrane as a passive margin that in approximately ca. 650 My became active margin, functioning as a forearc basin. The oblique collision between the blocks would have occurred with the development of a dextral transpression in the Itajaí Perimbó Shear Zone, separating the Luís Alves Terrane from the Brusque Terrane, a sinistral transcurrence represented by the Palmital Shear Zone separating the Luís Alves Terrane from the Paranaguá Terrane and a frontal thrust, represented by the Icapara and Serra Negra Shear Zones, separating the already amalgamated block from the Luís Alves and Curitiba Terranes of the Paranaguá Terrane.

Mapping cis-Regulatory Domains in the Human Genome UsingMulti-Species Conservation of Synteny

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahituv, Nadav; Prabhakar, Shyam; Poulin, Francis

2005-06-13

Our inability to associate distant regulatory elements with the genes that they regulate has largely precluded their examination for sequence alterations contributing to human disease. One major obstacle is the large genomic space surrounding targeted genes in which such elements could potentially reside. In order to delineate gene regulatory boundaries we used whole-genome human-mouse-chicken (HMC) and human-mouse-frog (HMF) multiple alignments to compile conserved blocks of synteny (CBS), under the hypothesis that these blocks have been kept intact throughout evolution at least in part by the requirement of regulatory elements to stay linked to the genes that they regulate. A totalmore » of 2,116 and 1,942 CBS>200 kb were assembled for HMC and HMF respectively, encompassing 1.53 and 0.86 Gb of human sequence. To support the existence of complex long-range regulatory domains within these CBS we analyzed the prevalence and distribution of chromosomal aberrations leading to position effects (disruption of a genes regulatory environment), observing a clear bias not only for mapping onto CBS but also for longer CBS size. Our results provide a genome wide data set characterizing the regulatory domains of genes and the conserved regulatory elements within them.« less

Insights into the phylogeny and coding potential of microbial dark matter

NASA Astrophysics Data System (ADS)

Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander; Ivanova, Natalia N.; Anderson, Iain J.; Cheng, Jan-Fang; Darling, Aaron; Malfatti, Stephanie; Swan, Brandon K.; Gies, Esther A.; Dodsworth, Jeremy A.; Hedlund, Brian P.; Tsiamis, George; Sievert, Stefan M.; Liu, Wen-Tso; Eisen, Jonathan A.; Hallam, Steven J.; Kyrpides, Nikos C.; Stepanauskas, Ramunas; Rubin, Edward M.; Hugenholtz, Philip; Woyke, Tanja

2013-07-01

Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called `microbial dark matter'. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.

Mitochondrial gene arrangement of the horseshoe crab Limulus polyphemus L.: conservation of major features among arthropod classes

NASA Technical Reports Server (NTRS)

Staton, J. L.; Daehler, L. L.; Brown, W. M.; Jacobs, D. K. (Principal Investigator)

1997-01-01

Numerous complete mitochondrial DNA sequences have been determined for species within two arthropod groups, insects and crustaceans, but there are none for a third, the chelicerates. Most mitochondrial gene arrangements reported for crustaceans and insect species are identical or nearly identical to that of Drosophila yakuba. Sequences across 36 of the gene boundaries in the mitochondrial DNA (mtDNA) of a representative chelicerate. Limulus polyphemus L., also reveal an arrangement like that of Drosophila yakuba. Only the position of the tRNA(LEU)(UUR) gene differs; in Limulus it is between the genes for tRNA(LEU)(CUN) and ND1. This positioning is also found in onychophorans, mollusks, and annelids, but not in insects and crustaceans, and indicates that tRNA(LEU)(CUN)-tRNA(LEU)(UUR)-ND1 was the ancestral gene arrangement for these groups, as suggested earlier. There are no differences in the relative arrangements of protein-coding and ribosomal RNA genes between Limulus and Drosophila, and none have been observed within arthropods. The high degree of similarity of mitochondrial gene arrangements within arthropods is striking, since some taxa last shared a common ancestor before the Cambrian, and contrasts with the extensive mtDNA rearrangements occasionally observed within some other metazoan phyla (e.g., mollusks and nematodes).

Insights into the phylogeny and coding potential of microbial dark matter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander

Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells fromnine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called microbial dark matter. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla.more » We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20percent of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.« less

DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families

PubMed Central

Sander, Adam F.; Lavstsen, Thomas; Rask, Thomas S.; Lisby, Michael; Salanti, Ali; Fordyce, Sarah L.; Jespersen, Jakob S.; Carter, Richard; Deitsch, Kirk W.; Theander, Thor G.; Pedersen, Anders Gorm; Arnot, David E.

2014-01-01

Many bacterial, viral and parasitic pathogens undergo antigenic variation to counter host immune defense mechanisms. In Plasmodium falciparum, the most lethal of human malaria parasites, switching of var gene expression results in alternating expression of the adhesion proteins of the Plasmodium falciparum-erythrocyte membrane protein 1 class on the infected erythrocyte surface. Recombination clearly generates var diversity, but the nature and control of the genetic exchanges involved remain unclear. By experimental and bioinformatic identification of recombination events and genome-wide recombination hotspots in var genes, we show that during the parasite’s sexual stages, ectopic recombination between isogenous var paralogs occurs near low folding free energy DNA 50-mers and that these sequences are heavily concentrated at the boundaries of regions encoding individual Plasmodium falciparum-erythrocyte membrane protein 1 structural domains. The recombinogenic potential of these 50-mers is not parasite-specific because these sequences also induce recombination when transferred to the yeast Saccharomyces cerevisiae. Genetic cross data suggest that DNA secondary structures (DSS) act as inducers of recombination during DNA replication in P. falciparum sexual stages, and that these DSS-regulated genetic exchanges generate functional and diverse P. falciparum adhesion antigens. DSS-induced recombination may represent a common mechanism for optimizing the evolvability of virulence gene families in pathogens. PMID:24253306

National Borders Effectively Halt the Spread of Rabies: The Current Rabies Epidemic in China Is Dislocated from Cases in Neighboring Countries

PubMed Central

Guo, Zhenyang; Tao, Xiaoyan; Yin, Cuiping; Han, Na; Yu, Jinning; Li, Hao; Liu, Haizhou; Fang, Wei; Adams, James; Wang, Jun; Liang, Guodong; Tang, Qing; Rayner, Simon

2013-01-01

China has seen a massive resurgence of rabies cases in the last 15 years with more than 25,000 human fatalities. Initial cases were reported in the southwest but are now reported in almost every province. There have been several phylogenetic investigations into the origin and spread of the virus within China but few reports investigating the impact of the epidemic on neighboring countries. We therefore collected nucleoprotein sequences from China and South East Asia and investigated their phylogenetic and phylogeographic relationship. Our results indicate that within South East Asia, isolates mainly cluster according to their geographic origin. We found evidence of sporadic exchange of strains between neighboring countries, but it appears that the major strain responsible for the current Chinese epidemic has not been exported. This suggests that national geographical boundaries and border controls are effective at halting the spread of rabies from China into adjacent regions. We further investigated the geographic structure of Chinese sequences and found that the current epidemic is dominated by variant strains that were likely present at low levels in previous domestic epidemics. We also identified epidemiological linkages between high incidence provinces consistent with observations based on surveillance data from human rabies cases. PMID:23383359

National borders effectively halt the spread of rabies: the current rabies epidemic in China is dislocated from cases in neighboring countries.

PubMed

Guo, Zhenyang; Tao, Xiaoyan; Yin, Cuiping; Han, Na; Yu, Jinning; Li, Hao; Liu, Haizhou; Fang, Wei; Adams, James; Wang, Jun; Liang, Guodong; Tang, Qing; Rayner, Simon

2013-01-01

China has seen a massive resurgence of rabies cases in the last 15 years with more than 25,000 human fatalities. Initial cases were reported in the southwest but are now reported in almost every province. There have been several phylogenetic investigations into the origin and spread of the virus within China but few reports investigating the impact of the epidemic on neighboring countries. We therefore collected nucleoprotein sequences from China and South East Asia and investigated their phylogenetic and phylogeographic relationship. Our results indicate that within South East Asia, isolates mainly cluster according to their geographic origin. We found evidence of sporadic exchange of strains between neighboring countries, but it appears that the major strain responsible for the current Chinese epidemic has not been exported. This suggests that national geographical boundaries and border controls are effective at halting the spread of rabies from China into adjacent regions. We further investigated the geographic structure of Chinese sequences and found that the current epidemic is dominated by variant strains that were likely present at low levels in previous domestic epidemics. We also identified epidemiological linkages between high incidence provinces consistent with observations based on surveillance data from human rabies cases.

The atmospheric boundary layer — advances in knowledge and application

NASA Astrophysics Data System (ADS)

Garratt, J. R.; Hess, G. D.; Physick, W. L.; Bougeault, P.

1996-02-01

We summarise major activities and advances in boundary-layer knowledge in the 25 years since 1970, with emphasis on the application of this knowledge to surface and boundary-layer parametrisation schemes in numerical models of the atmosphere. Progress in three areas is discussed: (i) the mesoscale modelling of selected phenomena; (ii) numerical weather prediction; and (iii) climate simulations. Future trends are identified, including the incorporation into models of advanced cloud schemes and interactive canopy schemes, and the nesting of high resolution boundary-layer schemes in global climate models.

Comments on the Parameters and Processes that Affect the Preservation Potential and Style of Oblique-Divergent Plate Boundaries

NASA Astrophysics Data System (ADS)

Umhoefer, P. J.

2014-12-01

Oblique-divergent or transtensional zones present particular challenges in ancient belts because of the poor preservation potential of the thinned continental crust and young oceanic crust. Many oblique belts will preferentially preserve their boundary zones that lie within continents rather than the main plate boundary zone, which will be at a much lower elevation and composed of denser crust. Zones of tectonic escape or strike-slip overprinting of arcs or plateaus deform continental crust and may be better preserved. Here I highlight parameters and processes that have major effects on oblique divergent belts. Strain partitioning is common, but not ubiquitous, along and across oblique boundaries; the causes of partitioning are not always clear and make this especially vexing for work in ancient belts. Partitioning causes complexity in the patterns of structures at all scales. Inherited structures commonly determine the orientation and style of structures along oblique boundaries and can control the pattern of faults across transtensional belts. Regionally, inherited trends of arcs or other 1000-km-scale features can control boundary structures. Experiments and natural examples suggest that oblique boundary zones contain less of a record of strike-slip faulting and more extensional structures. The obliquity of divergence produces predictable families of structures that typify (i) strike-slip dominated zones (obliquity <~20°), (ii) mixed zones (~20° - ~35°), and (iii) extension dominated zones (>~35°). The combination of partitioning and mixed structures in oblique zones means that the boundaries of belts with large-magnitude strike-slip faulting will commonly preserve little of no record of that faulting history. Plate boundaries localize strain onto the main plate boundary structures from the broader plate boundary and therefore the boundary zones commonly preserve the earlier structures more than later structures, a major problem in interpreting ancient belts. Sediment input is critical in some oblique plate boundaries because these belts become more pronounced sediment sinks over time. The evolving topography of oblique boundaries means that they have great variability of sediment flux into differing parts of the system; large rivers enter these belts only in special circumstances.

The Azimuthally Averaged Boundary Layer Structure of a Numerically Simulated Major Hurricane

DTIC Science & Technology

2015-08-14

layer in which the effects of sur- face friction are associated with significant departures from gradient wind balance. The boundary layer in the... effects of surface friction are associated with significant departures from gradient wind balance. More specifically, we follow Key Points: The...comprises a balance between three horizontal forces: Coriolis , pressure gradient, and friction. The boundary layer flow is characterized by a large Reynolds

Integrated biostratigraphic and sequence stratigraphic framework for Upper Cretaceous strata of the eastern Gulf Coastal Plain, USA

USGS Publications Warehouse

Mancini, E.A.; Puckett, T.M.; Tew, B.H.

1996-01-01

Upper Cretaceous (Santonian-Maastrichtian stages) strata of the eastern US Gulf Coastal Plain represent a relatively complete section of marine to nonmarine mixed siliciclastic and carbonate sediments. This section includes three depositional sequences which display characteristic systems tracts and distinct physical defining surfaces. The marine lithofacies are rich in calcareous nannoplankton and planktonic foraminifera which can be used for biostratigraphic zonation. Integration of this zonation with the lithostratigraphy and sequence stratigraphy of these strata results in a framework that can be used for local and regional intrabasin correlation and potentially for global interbasin correlation. Only the synchronous maximum flooding surfaces of these depositional sequences, however, have chronostratigraphic significance. The sequence boundaries and initial flooding surfaces are diachronous, and their use for correlation can produce conflicting results. The availability of high resolution biostratigraphy is critical for global correlation of depositional sequences. ?? 1996 Academic Press Limited.

Source modeling of the 2015 Mw 7.8 Nepal (Gorkha) earthquake sequence: Implications for geodynamics and earthquake hazards

NASA Astrophysics Data System (ADS)

McNamara, D. E.; Yeck, W. L.; Barnhart, W. D.; Schulte-Pelkum, V.; Bergman, E.; Adhikari, L. B.; Dixit, A.; Hough, S. E.; Benz, H. M.; Earle, P. S.

2017-09-01

The Gorkha earthquake on April 25th, 2015 was a long anticipated, low-angle thrust-faulting event on the shallow décollement between the India and Eurasia plates. We present a detailed multiple-event hypocenter relocation analysis of the Mw 7.8 Gorkha Nepal earthquake sequence, constrained by local seismic stations, and a geodetic rupture model based on InSAR and GPS data. We integrate these observations to place the Gorkha earthquake sequence into a seismotectonic context and evaluate potential earthquake hazard. Major results from this study include (1) a comprehensive catalog of calibrated hypocenters for the Gorkha earthquake sequence; (2) the Gorkha earthquake ruptured a 150 × 60 km patch of the Main Himalayan Thrust (MHT), the décollement defining the plate boundary at depth, over an area surrounding but predominantly north of the capital city of Kathmandu (3) the distribution of aftershock seismicity surrounds the mainshock maximum slip patch; (4) aftershocks occur at or below the mainshock rupture plane with depths generally increasing to the north beneath the higher Himalaya, possibly outlining a 10-15 km thick subduction channel between the overriding Eurasian and subducting Indian plates; (5) the largest Mw 7.3 aftershock and the highest concentration of aftershocks occurred to the southeast the mainshock rupture, on a segment of the MHT décollement that was positively stressed towards failure; (6) the near surface portion of the MHT south of Kathmandu shows no aftershocks or slip during the mainshock. Results from this study characterize the details of the Gorkha earthquake sequence and provide constraints on where earthquake hazard remains high, and thus where future, damaging earthquakes may occur in this densely populated region. Up-dip segments of the MHT should be considered to be high hazard for future damaging earthquakes.

Source modeling of the 2015 Mw 7.8 Nepal (Gorkha) earthquake sequence: Implications for geodynamics and earthquake hazards

USGS Publications Warehouse

McNamara, Daniel E.; Yeck, William; Barnhart, William D.; Schulte-Pelkum, V.; Bergman, E.; Adhikari, L. B.; Dixit, Amod; Hough, S.E.; Benz, Harley M.; Earle, Paul

2017-01-01

The Gorkha earthquake on April 25th, 2015 was a long anticipated, low-angle thrust-faulting event on the shallow décollement between the India and Eurasia plates. We present a detailed multiple-event hypocenter relocation analysis of the Mw 7.8 Gorkha Nepal earthquake sequence, constrained by local seismic stations, and a geodetic rupture model based on InSAR and GPS data. We integrate these observations to place the Gorkha earthquake sequence into a seismotectonic context and evaluate potential earthquake hazard.Major results from this study include (1) a comprehensive catalog of calibrated hypocenters for the Gorkha earthquake sequence; (2) the Gorkha earthquake ruptured a ~ 150 × 60 km patch of the Main Himalayan Thrust (MHT), the décollement defining the plate boundary at depth, over an area surrounding but predominantly north of the capital city of Kathmandu (3) the distribution of aftershock seismicity surrounds the mainshock maximum slip patch; (4) aftershocks occur at or below the mainshock rupture plane with depths generally increasing to the north beneath the higher Himalaya, possibly outlining a 10–15 km thick subduction channel between the overriding Eurasian and subducting Indian plates; (5) the largest Mw 7.3 aftershock and the highest concentration of aftershocks occurred to the southeast the mainshock rupture, on a segment of the MHT décollement that was positively stressed towards failure; (6) the near surface portion of the MHT south of Kathmandu shows no aftershocks or slip during the mainshock. Results from this study characterize the details of the Gorkha earthquake sequence and provide constraints on where earthquake hazard remains high, and thus where future, damaging earthquakes may occur in this densely populated region. Up-dip segments of the MHT should be considered to be high hazard for future damaging earthquakes.

AUREOL-3 observations of new boundaries in the auroral ion precipitation

NASA Technical Reports Server (NTRS)

Bosqued, Jean M.; Ashour-Abdalla, Maha; El Alaoui, Mostafa; Zelenyj, Lev M.; Berthlier, Annick

1993-01-01

Interesting and well-separated structures in the 1-20 keV ion precipitation pattern have been revealed by an analysis of more than 50 crossings of the nightside (21-03 MLT) auroral zone by the AUREOL-3 satellite. First, velocity-dispersed ion structures (VDIS) are crossed near the poleward edge of the oval, and are the best ionospheric signature of ion beams flowing along the plasma sheet boundary layer. Proceeding equatorward, a large majority of VDIS events are bounded by a new and interesting narrow band of strongly reduced precipitation, or a gap, which delineates VDIS from the diffuse precipitation region connected to the CPS. A statistical analysis shows that the gap has an extent of about 1-2 deg, which is almost independent of magnetic activity; its location, about 70 deg ILAT, shifts significantly equatorward with higher magnetic activity levels. Intense electron arcs are observed near the equatorward edge of the gap. An important result is that the overall sequence of VDIS-gap-CPS can be explained in terms of orbital dynamics in the tail. The gap in precipitation appears as the counterpart of the 'wall' regime in the equatorial plane, in which a cross-tail current carried by energetic ions is strongly enhanced between 8 and 12 R(E). This region has important consequences for the development of substorms.

Segmentation and tracking in echocardiographic sequences: active contours guided by optical flow estimates

NASA Technical Reports Server (NTRS)

Mikic, I.; Krucinski, S.; Thomas, J. D.

1998-01-01

This paper presents a method for segmentation and tracking of cardiac structures in ultrasound image sequences. The developed algorithm is based on the active contour framework. This approach requires initial placement of the contour close to the desired position in the image, usually an object outline. Best contour shape and position are then calculated, assuming that at this configuration a global energy function, associated with a contour, attains its minimum. Active contours can be used for tracking by selecting a solution from a previous frame as an initial position in a present frame. Such an approach, however, fails for large displacements of the object of interest. This paper presents a technique that incorporates the information on pixel velocities (optical flow) into the estimate of initial contour to enable tracking of fast-moving objects. The algorithm was tested on several ultrasound image sequences, each covering one complete cardiac cycle. The contour successfully tracked boundaries of mitral valve leaflets, aortic root and endocardial borders of the left ventricle. The algorithm-generated outlines were compared against manual tracings by expert physicians. The automated method resulted in contours that were within the boundaries of intraobserver variability.

Long aftershock sequences within continents and implications for earthquake hazard assessment.

PubMed

Stein, Seth; Liu, Mian

2009-11-05

One of the most powerful features of plate tectonics is that the known plate motions give insight into both the locations and average recurrence interval of future large earthquakes on plate boundaries. Plate tectonics gives no insight, however, into where and when earthquakes will occur within plates, because the interiors of ideal plates should not deform. As a result, within plate interiors, assessments of earthquake hazards rely heavily on the assumption that the locations of small earthquakes shown by the short historical record reflect continuing deformation that will cause future large earthquakes. Here, however, we show that many of these recent earthquakes are probably aftershocks of large earthquakes that occurred hundreds of years ago. We present a simple model predicting that the length of aftershock sequences varies inversely with the rate at which faults are loaded. Aftershock sequences within the slowly deforming continents are predicted to be significantly longer than the decade typically observed at rapidly loaded plate boundaries. These predictions are in accord with observations. So the common practice of treating continental earthquakes as steady-state seismicity overestimates the hazard in presently active areas and underestimates it elsewhere.

A conservative assessment of the major genetic causes of idiopathic chronic pancreatitis: data from a comprehensive analysis of PRSS1, SPINK1, CTRC and CFTR genes in 253 young French patients.

PubMed

Masson, Emmanuelle; Chen, Jian-Min; Audrézet, Marie-Pierre; Cooper, David N; Férec, Claude

2013-01-01

Idiopathic chronic pancreatitis (ICP) has traditionally been defined as chronic pancreatitis in the absence of any obvious precipitating factors (e.g. alcohol abuse) and family history of the disease. Studies over the past 15 years have revealed that ICP has a highly complex genetic architecture involving multiple gene loci. Here, we have attempted to provide a conservative assessment of the major genetic causes of ICP in a sample of 253 young French ICP patients. For the first time, conventional types of mutation (comprising coding sequence variants and variants at intron/exon boundaries) and gross genomic rearrangements were screened for in all four major pancreatitis genes, PRSS1, SPINK1, CTRC and CFTR. For the purposes of the study, synonymous, intronic and 5'- or 3'-untranslated region variants were excluded from the analysis except where there was persuasive evidence of functional consequences. The remaining sequence variants/genotypes were classified into causative, contributory or neutral categories by consideration of (i) their allele frequencies in patient and normal control populations, (ii) their presumed or experimentally confirmed functional effects, (iii) the relative importance of their associated genes in the pathogenesis of chronic pancreatitis and (iv) gene-gene interactions wherever applicable. Adoption of this strategy allowed us to assess the pathogenic relevance of specific variants/genotypes to their respective carriers to an unprecedented degree. The genetic cause of ICP could be assigned in 23.7% of individuals in the study group. A strong genetic susceptibility factor was also present in an additional 24.5% of cases. Taken together, up to 48.2% of the studied ICP patients were found to display evidence of a genetic basis for their pancreatitis. Whereas these particular proportions may not be extrapolable to all ICP patients, the approach employed should serve as a useful framework for acquiring a better understanding of the role of genetic factors in causing this oligogenic disease.

Preferred-rupture propagation to the hangingwall of the shallow part of the out-of-sequence thrust: Ishido Fault in Boso Peninsula, central Japan

NASA Astrophysics Data System (ADS)

Yamamoto, Y.; Fukuyama, M.; Ujiie, K.; Hirose, T.; Hamada, Y.; Kitamura, M.; Kamiya, N.

2016-12-01

Although earthquake ruptures in shallow portion of plate boundary have recently been identified (e.g. Tohoku, Nankai, etc.), their mechanisms why the shallow portion of plate boundary composed mainly of clay minerals can accumulate strain and make seismic slip are under controversial. An ancient out-of-sequence thrust which divided the early and late Miocene accretionary complexes in the Boso Peninsula, central Japan records rupture propagation to the shallow portion of accretionary prism (< 2 km). The fault core is composed of black-colored thin (<1 mm) pseudotachylite and fluidized fault gouge. The former is characterized by homogeneous glassy matrix including fragments of quartz/feldspar, submicron-sized Fe-rich spherules, and vesicles. Based on the mineralogy of the host rock and EDS analyses of matrices, origin of the pseudotachylite was apparently frictional melting of smectite containing Fe. Fe-rich spherules formed by rapid cooling of pseudotachylite. On the other hand, overturned fault-related drag fold developed in the footwall, within about 30 m. Although some Riedel sheared normal faults developed in the overturned footwall, no other brittle deformations were identified. These occurrences imply coexistence of low- and high-speed slips along the same thrust fault. The whole-rock major and trace elemental analyses using XRF and ICP-MS show that mudstone in the hangingwall has similar chemical composition to those of pseudotachylite and fluidized fault gouge with REE enriched patterns, whereas the footwall has different chemical characteristics with relatively flat REE pattern and low LOI. Therefore, the protolith of pseudotachylite and fluidized fault gouge is mudstone in the hangingwall. These data imply that rupture propagation preferably occurred in the hangingwall along the fault zone. The footwall was also deformed apparently during slow-slip deformation leading to formation of the overturn, whereas only the hangingwall, just side of the fault zone, slipped under high-speed shear.

Independent Origin and Global Distribution of Distinct Plasmodium vivax Duffy Binding Protein Gene Duplications

PubMed Central

Hostetler, Jessica B.; Lo, Eugenia; Kanjee, Usheer; Amaratunga, Chanaki; Suon, Seila; Sreng, Sokunthea; Mao, Sivanna; Yewhalaw, Delenasaw; Mascarenhas, Anjali; Kwiatkowski, Dominic P.; Ferreira, Marcelo U.; Rathod, Pradipsinh K.; Yan, Guiyun; Fairhurst, Rick M.; Duraisingh, Manoj T.; Rayner, Julian C.

2016-01-01

Background Plasmodium vivax causes the majority of malaria episodes outside Africa, but remains a relatively understudied pathogen. The pathology of P. vivax infection depends critically on the parasite’s ability to recognize and invade human erythrocytes. This invasion process involves an interaction between P. vivax Duffy Binding Protein (PvDBP) in merozoites and the Duffy antigen receptor for chemokines (DARC) on the erythrocyte surface. Whole-genome sequencing of clinical isolates recently established that some P. vivax genomes contain two copies of the PvDBP gene. The frequency of this duplication is particularly high in Madagascar, where there is also evidence for P. vivax infection in DARC-negative individuals. The functional significance and global prevalence of this duplication, and whether there are other copy number variations at the PvDBP locus, is unknown. Methodology/Principal Findings Using whole-genome sequencing and PCR to study the PvDBP locus in P. vivax clinical isolates, we found that PvDBP duplication is widespread in Cambodia. The boundaries of the Cambodian PvDBP duplication differ from those previously identified in Madagascar, meaning that current molecular assays were unable to detect it. The Cambodian PvDBP duplication did not associate with parasite density or DARC genotype, and ranged in prevalence from 20% to 38% over four annual transmission seasons in Cambodia. This duplication was also present in P. vivax isolates from Brazil and Ethiopia, but not India. Conclusions/Significance PvDBP duplications are much more widespread and complex than previously thought, and at least two distinct duplications are circulating globally. The same duplication boundaries were identified in parasites from three continents, and were found at high prevalence in human populations where DARC-negativity is essentially absent. It is therefore unlikely that PvDBP duplication is associated with infection of DARC-negative individuals, but functional tests will be required to confirm this hypothesis. PMID:27798646

Experimental verification of free-space singular boundary conditions in an invisibility cloak

NASA Astrophysics Data System (ADS)

Wu, Qiannan; Gao, Fei; Song, Zhengyong; Lin, Xiao; Zhang, Youming; Chen, Huanyang; Zhang, Baile

2016-04-01

A major issue in invisibility cloaking, which caused intense mathematical discussions in the past few years but still remains physically elusive, is the plausible singular boundary conditions associated with the singular metamaterials at the inner boundary of an invisibility cloak. The perfect cloaking phenomenon, as originally proposed by Pendry et al for electromagnetic waves, cannot be treated as physical before a realistic inner boundary of a cloak is demonstrated. Although a recent demonstration has been done in a waveguide environment, the exotic singular boundary conditions should apply to a general environment as in free space. Here we fabricate a metamaterial surface that exhibits the singular boundary conditions and demonstrate its performance in free space. Particularly, the phase information of waves reflected from this metamaterial surface is explicitly measured, confirming the singular responses of boundary conditions for an invisibility cloak.

Numerical Solution of Time-Dependent Problems with a Fractional-Power Elliptic Operator

NASA Astrophysics Data System (ADS)

Vabishchevich, P. N.

2018-03-01

A time-dependent problem in a bounded domain for a fractional diffusion equation is considered. The first-order evolution equation involves a fractional-power second-order elliptic operator with Robin boundary conditions. A finite-element spatial approximation with an additive approximation of the operator of the problem is used. The time approximation is based on a vector scheme. The transition to a new time level is ensured by solving a sequence of standard elliptic boundary value problems. Numerical results obtained for a two-dimensional model problem are presented.

Sandstone petrographic evidence and the Chugach-Prince William terrane boundary in southern Alaska

USGS Publications Warehouse

Dumoulin, Julie A.

1988-01-01

The contact between the Upper Cretaceous Valdez Group and the Paleocene and Eocene Orca Group has been inferred to be the boundary between the Chugach and the Prince William tectonostratigraphic terranes. Sandstone petrographic data from the Prince William Sound area show no compositional discontinuity across this contact. These data are best explained by considering the Valdez and Orca Groups to be part of a single terrane - a thick flysch sequence derived primarily from a progressively unroofing magmatic arc with increasing input from subduction-complex sources through time.

Sequential deformation of plains along Tessera boundaries on Venus: Evidence from Alpha Regio

NASA Technical Reports Server (NTRS)

Gilmore, M. S.; Head, James W., III

1992-01-01

Tesserae are regions of elevated terrain characterized by two or more sets of ridges and grooves that intersect orthogonally. Tesserae comprise 15-20 percent of the surface of Venus, but the nature of their formation and evolution is not well understood; processes proposed to account for their characteristics are many and varied. Two types of tessera boundaries have been described: type 1 are generally embayed by plains; and type 2 boundaries are characterized by being linear at the 100-km scale and often associated with steep scarps or tectonic features. Margins such as the western edge of Alpha have been described as type 2. Some of the tessera have boundaries that display deformation of both the edge of the tessera and the adjoining plains. This study focuses on the western edge of Alpha Regio in an effort to characterize on occurrence of this type of boundary and assess the implications of the style in general. Using Magellan SAR imagery, lineament lengths, orientations, and spacing were measured for ten 50 x 60 km areas spanning 500 km of the western boundary. Structural characteristics and orientations were compared to stratigraphic units in order to assess the sequence and style of deformation.

An adjoint view on flux consistency and strong wall boundary conditions to the Navier–Stokes equations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stück, Arthur, E-mail: arthur.stueck@dlr.de

2015-11-15

Inconsistent discrete expressions in the boundary treatment of Navier–Stokes solvers and in the definition of force objective functionals can lead to discrete-adjoint boundary treatments that are not a valid representation of the boundary conditions to the corresponding adjoint partial differential equations. The underlying problem is studied for an elementary 1D advection–diffusion problem first using a node-centred finite-volume discretisation. The defect of the boundary operators in the inconsistently defined discrete-adjoint problem leads to oscillations and becomes evident with the additional insight of the continuous-adjoint approach. A homogenisation of the discretisations for the primal boundary treatment and the force objective functional yieldsmore » second-order functional accuracy and eliminates the defect in the discrete-adjoint boundary treatment. Subsequently, the issue is studied for aerodynamic Reynolds-averaged Navier–Stokes problems in conjunction with a standard finite-volume discretisation on median-dual grids and a strong implementation of noslip walls, found in many unstructured general-purpose flow solvers. Going out from a base-line discretisation of force objective functionals which is independent of the boundary treatment in the flow solver, two improved flux-consistent schemes are presented; based on either body wall-defined or farfield-defined control-volumes they resolve the dual inconsistency. The behaviour of the schemes is investigated on a sequence of grids in 2D and 3D.« less

Dichotomy Boundary at Aeolis Mensae, Mars: Fretted Terrain Developed in a Sedimentary Deposit

NASA Astrophysics Data System (ADS)

Irwin, R. P., III; Watters, T. R.; Howard, A. D.; Maxwell, T. A.; Craddock, R. A.

2003-03-01

Fretted terrain in Aeolis Mensae, Mars, developed in a sedimentary deposit. A thick, massive unit with a capping layer or duricrust overlies a more durable layered sequence. Wind, collapse, and minor fluvial activity contributed to degradation.

Memory as embodiment: The case of modality and serial short-term memory.

PubMed

Macken, Bill; Taylor, John C; Kozlov, Michail D; Hughes, Robert W; Jones, Dylan M

2016-10-01

Classical explanations for the modality effect-superior short-term serial recall of auditory compared to visual sequences-typically recur to privileged processing of information derived from auditory sources. Here we critically appraise such accounts, and re-evaluate the nature of the canonical empirical phenomena that have motivated them. Three experiments show that the standard account of modality in memory is untenable, since auditory superiority in recency is often accompanied by visual superiority in mid-list serial positions. We explain this simultaneous auditory and visual superiority by reference to the way in which perceptual objects are formed in the two modalities and how those objects are mapped to speech motor forms to support sequence maintenance and reproduction. Specifically, stronger obligatory object formation operating in the standard auditory form of sequence presentation compared to that for visual sequences leads both to enhanced addressability of information at the object boundaries and reduced addressability for that in the interior. Because standard visual presentation does not lead to such object formation, such sequences do not show the boundary advantage observed for auditory presentation, but neither do they suffer loss of addressability associated with object information, thereby affording more ready mapping of that information into a rehearsal cohort to support recall. We show that a range of factors that impede this perceptual-motor mapping eliminate visual superiority while leaving auditory superiority unaffected. We make a general case for viewing short-term memory as an embodied, perceptual-motor process. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Depositional environments, sequence stratigraphy, and trap configuration of lower Wolfcampian clastics along eastern edge of Midland basin, west Texas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stewart, N.R.; Reuter, S.G.

1989-03-01

The Lower Permian (lower Wolfcampian) along the eastern edge of the Midland basin, west Texas, is characterized by ramp-type shelf margins. During eustatic lowstand, nearshore sedimentation shifted drastically to the west into a basinal setting below the Pennsylvanian (Canyon) shelf margin. Core descriptions demonstrate that lowstand systems tract (LST) and transgressive systems tract (TST) siliciclastics were deposited in deltaic and coastal-plain environments. Prodelta, delta-front, and stream-mouth bar facies are associated with the LST. Coastal-plain and distributary channels are preserved in the TST. The sequence stratigraphic framework indicates type 1 sequence boundaries at 287 Ma, 282 Ma, and 280 Ma inmore » the lower Wolfcampian clastics. This lower Wolfcampian package of sedimentary rocks overlies the Pennsylvanian and is capped by the 279-Ma middle Wolfcampian unconformity. All three sequence boundaries and associated systems tract deposits exhibit a prograding stacking pattern within the sequence stratigraphic framework. Basinally restricted prograding LST deltaic rocks are overlain by backstepping TST deltaics and highstand systems tract (HST) outer marine shales. Production in lower Wolfcampian clastic fields is associated with fine-grained quartzarenites up to 45 ft thick which were deposited in stream-mouth bars. Delta-front and prodelta low-permeability shales encase the reservoir facies, forming lateral permeability barriers. HST outer marine shales deposited over the stream-mouth-bar sandstones act as a top seal, creating a stratigraphic trap and providing source for the high-BTU gas and oil produced from these basinally restricted LST deltaics.« less

Late Miocene-Early Pliocene reactivation of the Main Boundary Thrust: Evidence from the seismites in southeastern Kumaun Himalaya, India

NASA Astrophysics Data System (ADS)

Mishra, Anurag; Srivastava, Deepak C.; Shah, Jyoti

2013-05-01

Tectonic history of the Himalaya is punctuated by successive development of the faults that run along the boundaries between different lithotectonic terrains. The Main Boundary Fault, defining the southern limit of the Lesser Himalayan terrain, is tectonically most active. A review of published literature reveals that the nature and age of reactivation events on the Main Boundary Fault is one of the poorly understood aspects of the Himalayan orogen. By systematic outcrop mapping of the seismites, this study identifies a Late Miocene-Early Pliocene reactivation on the Main Boundary Thrust in southeast Kumaun Himalaya. Relatively friable and cohesionless Neogene sedimentary sequences host abundant soft-sediment deformation structures in the vicinity of the Main Boundary Thrust. Among a large variety of structures, deformed cross-beds, liquefaction pockets, slump folds, convolute laminations, sand dykes, mushroom structures, fluid escape structures, flame and load structures and synsedimentary faults are common. The morphological attributes, the structural association and the distribution pattern of the soft-sediment deformation structures with respect to the Main Boundary Fault strongly suggest their development by seismically triggered liquefaction and fluidization. Available magnetostratigraphic age data imply that the seismites were developed during a Late Miocene-Early Pliocene slip on the Main Boundary Thrust. The hypocenter of the main seismic event may lie on the Main Boundary Thrust or to the north of the study area on an unknown fault or the Basal Detachment Thrust.

Globally optimal grouping for symmetric closed boundaries by combining boundary and region information.

PubMed

Stahl, Joachim S; Wang, Song

2008-03-01

Many natural and man-made structures have a boundary that shows a certain level of bilateral symmetry, a property that plays an important role in both human and computer vision. In this paper, we present a new grouping method for detecting closed boundaries with symmetry. We first construct a new type of grouping token in the form of symmetric trapezoids by pairing line segments detected from the image. A closed boundary can then be achieved by connecting some trapezoids with a sequence of gap-filling quadrilaterals. For such a closed boundary, we define a unified grouping cost function in a ratio form: the numerator reflects the boundary information of proximity and symmetry and the denominator reflects the region information of the enclosed area. The introduction of the region-area information in the denominator is able to avoid a bias toward shorter boundaries. We then develop a new graph model to represent the grouping tokens. In this new graph model, the grouping cost function can be encoded by carefully designed edge weights and the desired optimal boundary corresponds to a special cycle with a minimum ratio-form cost. We finally show that such a cycle can be found in polynomial time using a previous graph algorithm. We implement this symmetry-grouping method and test it on a set of synthetic data and real images. The performance is compared to two previous grouping methods that do not consider symmetry in their grouping cost functions.

Magnetic anomalies in East Antarctica: a window on major tectonic provinces and their boundaries

USGS Publications Warehouse

Golynsky, A.V.

2007-01-01

An analysis of aeromagnetic data compiled within the Antarctic Digital Magnetic Anomaly Project (ADMAP) yields significant new insight into major tectonic provinces of East Antarctica. Several previously unknown crustal blocks are imaged in the deep interior of the continent, which are interpreted as cratonic nuclei. These cratons are fringed by a large and continuous orogenic belt between Coats Land and Princess Elizabeth Land, with possible branches in the deeper interior of East Antarctica. Most of the crustal provinces and boundaries identified in this study are only in part exposed. More detailed analyses of these crustal provinces and their tectonic boundaries would require systematic acquisition of additional high-resolution magnetic data, because at present the ADMAP database is largely inadequate to address many remaining questions regarding Antarctica’s tectonic evolution.

FIRE aircraft observations of horizontal and vertical transport in marine stratocumulus

NASA Technical Reports Server (NTRS)

Paluch, Ilga R.; Lenschow, Donald H.

1990-01-01

A major goal of research on marine stratocumulus is to try to understand the processes that generate and dissipate them. One approach to studying this problem is to investigate the boundary layer structure in the vicinity of a transition from a cloudy to a cloud-free region to document the differences in structure on each side of the transition. Since stratiform clouds have a major impact on the radiation divergence in the boundary layer, the transition from a cloudy to a clear boundary layer is a region of large horizontal inhomogeneity in air temperature and turbulence intensity. This leads to a considerable difference in horizontal and vertical transports between the cloudy and cloud-free regions. Measurements are used from the NCAR Electra aircraft during flights 5 (7 July 1987) and 10 (18 July 1987) of FIRE for this purpose. Flight 5 coincided with a LANDSAT overflight, and was designed to investigate the transition across a well-defined N-S cloud boundary, since the LANDSAT image can document the cloud cover in considerable detail. Turbulence legs were flown about 60 km on both sides of the cloud boundary. Flight 10 was flown at night in an area of scattered small cumuli and broken cloud patches.

Definition of boundary and initial conditions in the analysis of saturated ground-water flow systems - An introduction

USGS Publications Warehouse

Franke, O. Lehn; Reilly, Thomas E.; Bennett, Gordon D.

1987-01-01

Accurate definition of boundary and initial conditions is an essential part of conceptualizing and modeling ground-water flow systems. This report describes the properties of the seven most common boundary conditions encountered in ground-water systems and discusses major aspects of their application. It also discusses the significance and specification of initial conditions and evaluates some common errors in applying this concept to ground-water-system models. An appendix is included that discusses what the solution of a differential equation represents and how the solution relates to the boundary conditions defining the specific problem. This report considers only boundary conditions that apply to saturated ground-water systems.

Discordance between morphological and molecular species boundaries among Caribbean species of the reef sponge Callyspongia.

PubMed

DeBiasse, Melissa B; Hellberg, Michael E

2015-02-01

Sponges are among the most species-rich and ecologically important taxa on coral reefs, yet documenting their diversity is difficult due to the simplicity and plasticity of their morphological characters. Genetic attempts to identify species are hampered by the slow rate of mitochondrial sequence evolution characteristic of sponges and some other basal metazoans. Here we determine species boundaries of the Caribbean coral reef sponge genus Callyspongia using a multilocus, model-based approach. Based on sequence data from one mitochondrial (COI), one ribosomal (28S), and two single-copy nuclear protein-coding genes, we found evolutionarily distinct lineages were not concordant with current species designations in Callyspongia. While C. fallax,C. tenerrima, and C. plicifera were reciprocally monophyletic, four taxa with different morphologies (C. armigera,C. longissima,C. eschrichtii, and C. vaginalis) formed a monophyletic group and genetic distances among these taxa overlapped distances within them. A model-based method of species delimitation supported collapsing these four into a single evolutionary lineage. Variation in spicule size among these four taxa was partitioned geographically, not by current species designations, indicating that in Callyspongia, these key taxonomic characters are poor indicators of genetic differentiation. Taken together, our results suggest a complex relationship between morphology and species boundaries in sponges.

Discordance between morphological and molecular species boundaries among Caribbean species of the reef sponge Callyspongia

PubMed Central

DeBiasse, Melissa B; Hellberg, Michael E

2015-01-01

Sponges are among the most species-rich and ecologically important taxa on coral reefs, yet documenting their diversity is difficult due to the simplicity and plasticity of their morphological characters. Genetic attempts to identify species are hampered by the slow rate of mitochondrial sequence evolution characteristic of sponges and some other basal metazoans. Here we determine species boundaries of the Caribbean coral reef sponge genus Callyspongia using a multilocus, model-based approach. Based on sequence data from one mitochondrial (COI), one ribosomal (28S), and two single-copy nuclear protein-coding genes, we found evolutionarily distinct lineages were not concordant with current species designations in Callyspongia. While C. fallax,C. tenerrima, and C. plicifera were reciprocally monophyletic, four taxa with different morphologies (C. armigera,C. longissima,C. eschrichtii, and C. vaginalis) formed a monophyletic group and genetic distances among these taxa overlapped distances within them. A model-based method of species delimitation supported collapsing these four into a single evolutionary lineage. Variation in spicule size among these four taxa was partitioned geographically, not by current species designations, indicating that in Callyspongia, these key taxonomic characters are poor indicators of genetic differentiation. Taken together, our results suggest a complex relationship between morphology and species boundaries in sponges. PMID:25691989

A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights

PubMed Central

Qin, Qi-Long; Xie, Bin-Bin; Zhang, Xi-Ying; Chen, Xiu-Lan; Zhou, Bai-Cheng; Zhou, Jizhong; Oren, Aharon

2014-01-01

Genomic information has already been applied to prokaryotic species definition and classification. However, the contribution of the genome sequence to prokaryotic genus delimitation has been less studied. To gain insights into genus definition for the prokaryotes, we attempted to reveal the genus-level genomic differences in the current prokaryotic classification system and to delineate the boundary of a genus on the basis of genomic information. The average nucleotide sequence identity between two genomes can be used for prokaryotic species delineation, but it is not suitable for genus demarcation. We used the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance. A comprehensive genomic survey indicated that the POCP can serve as a robust genomic index for establishing the genus boundary for prokaryotic groups. Basically, two species belonging to the same genus would share at least half of their proteins. In a specific lineage, the genus and family/order ranks showed slight or no overlap in terms of POCP values. A prokaryotic genus can be defined as a group of species with all pairwise POCP values higher than 50%. Integration of whole-genome data into the current taxonomy system can provide comprehensive information for prokaryotic genus definition and delimitation. PMID:24706738

Algorithm based on regional separation for automatic grain boundary extraction using improved mean shift method

NASA Astrophysics Data System (ADS)

Zhenying, Xu; Jiandong, Zhu; Qi, Zhang; Yamba, Philip

2018-06-01

Metallographic microscopy shows that the vast majority of metal materials are composed of many small grains; the grain size of a metal is important for determining the tensile strength, toughness, plasticity, and other mechanical properties. In order to quantitatively evaluate grain size in metals, grain boundaries must be identified in metallographic images. Based on the phenomenon of grain boundary blurring or disconnection in metallographic images, this study develops an algorithm based on regional separation for automatically extracting grain boundaries by an improved mean shift method. Experimental observation shows that the grain boundaries obtained by the proposed algorithm are highly complete and accurate. This research has practical value because the proposed algorithm is suitable for grain boundary extraction from most metallographic images.

Dinoflagellate and calcareous nannofossil response to sea-level change in Cretaceous-Tertiary boundary sections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Habib, D.; Moshkovitz, S.; Kramer, C.

1992-02-01

Stratigraphic sections in south-central Alabama were studied to test palynological evidence of sea-level change across the Cretaceous-Tertiary boundary. New evidence from both calcareous nannofossils and dinoflagellate cysts places the regional disconformity in Alabama (Type 1 sequence boundary) virtually at the K-T boundary. This suggests that sea-level fall may have contributed to mass-extinction event. Dinoflagellate diversity varies between systems tract components of coastal onlap. This parameter is useful for interpreting sea-level change in this part of the section, because dinoflagellates did not participate in the mass extinction. The iridium spikes in the roadcut near Braggs are of earliest Danian age andmore » correlate in relative magnitude with the lower values reported from directly above the K-T boundary in the Gubbio stratotype section. Iridium was concentrated in marine flooding surfaces in episodes of higher productivity of algal organic matter at the time when the iridium-enriched ocean encroached on the shelf during the first Cenozoic episode of sea-level rise.« less

Seismic analysis of clinoform depositional sequences and shelf-margin trajectories in Lower Cretaceous (Albian) strata, Alaska North Slope

USGS Publications Warehouse

Houseknecht, D.W.; Bird, K.J.; Schenk, C.J.

2009-01-01

Lower Cretaceous strata beneath the Alaska North Slope include clinoform depositional sequences that filled the western Colville foreland basin and overstepped the Beaufort rift shoulder. Analysis of Albian clinoform sequences with two-dimensional (2D) seismic data resulted in the recognition of seismic facies inferred to represent lowstand, transgressive and highstand systems tracts. These are stacked to produce shelf-margin trajectories that appear in low-resolution seismic data to alternate between aggradational and progradational. Higher-resolution seismic data reveal shelf-margin trajectories that are more complex, particularly in net-aggradational areas, where three patterns commonly are observed: (1) a negative (downward) step across the sequence boundary followed by mostly aggradation in the lowstand systems tract (LST), (2) a positive (upward) step across the sequence boundary followed by mostly progradation in the LST and (3) an upward backstep across a mass-failure d??collement. These different shelf-margin trajectories are interpreted as (1) fall of relative sea level below the shelf edge, (2) fall of relative sea level to above the shelf edge and (3) mass-failure removal of shelf-margin sediment. Lowstand shelf margins mapped using these criteria are oriented north-south in the foreland basin, indicating longitudinal filling from west to east. The shelf margins turn westward in the north, where the clinoform depositional system overstepped the rift shoulder, and turn eastward in the south, suggesting progradation of depositional systems from the ancestral Brooks Range into the foredeep. Lowstand shelf-margin orientations are consistently perpendicular to clinoform-foreset-dip directions. Although the Albian clinoform sequences of the Alaska North Slope are generally similar in stratal geometry to clinoform sequences elsewhere, they are significantly thicker. Clinoform-sequence thickness ranges from 600-1000 m in the north to 1700-2000 m in the south, reflecting increased accommodation from the rift shoulder into the foredeep. The unusually thick clinoform sequences suggest significant subsidence followed by rapid sediment influx. No claim to original US government works. Journal Compilation ?? Blackwell Publishing Ltd, European Association of Geoscientists & Engineers and International Association of Sedimentologists.

Spatio-Temporal Structure, Path Characteristics, and Perceptual Grouping in Immediate Serial Spatial Recall

PubMed Central

De Lillo, Carlo; Kirby, Melissa; Poole, Daniel

2016-01-01

Immediate serial spatial recall measures the ability to retain sequences of locations in short-term memory and is considered the spatial equivalent of digit span. It is tested by requiring participants to reproduce sequences of movements performed by an experimenter or displayed on a monitor. Different organizational factors dramatically affect serial spatial recall but they are often confounded or underspecified. Untangling them is crucial for the characterization of working-memory models and for establishing the contribution of structure and memory capacity to spatial span. We report five experiments assessing the relative role and independence of factors that have been reported in the literature. Experiment 1 disentangled the effects of spatial clustering and path-length by manipulating the distance of items displayed on a touchscreen monitor. Long-path sequences segregated by spatial clusters were compared with short-path sequences not segregated by clusters. Recall was more accurate for sequences segregated by clusters independently from path-length. Experiment 2 featured conditions where temporal pauses were introduced between or within cluster boundaries during the presentation of sequences with the same paths. Thus, the temporal structure of the sequences was either consistent or inconsistent with a hierarchical representation based on segmentation by spatial clusters but the effect of structure could not be confounded with effects of path-characteristics. Pauses at cluster boundaries yielded more accurate recall, as predicted by a hierarchical model. In Experiment 3, the systematic manipulation of sequence structure, path-length, and presence of path-crossings of sequences showed that structure explained most of the variance, followed by the presence/absence of path-crossings, and path-length. Experiments 4 and 5 replicated the results of the previous experiments in immersive virtual reality navigation tasks where the viewpoint of the observer changed dynamically during encoding and recall. This suggested that the effects of structure in spatial span are not dependent on perceptual grouping processes induced by the aerial view of the stimulus array typically afforded by spatial recall tasks. These results demonstrate the independence of coding strategies based on structure from effects of path characteristics and perceptual grouping in immediate serial spatial recall. PMID:27891101

Multilocus Phylogeography of the Treefrog Scinax eurydice (Anura, Hylidae) Reveals a Plio-Pleistocene Diversification in the Atlantic Forest.

PubMed

Menezes, Lucas; Canedo, Clarissa; Batalha-Filho, Henrique; Garda, Adrian Antonio; Gehara, Marcelo; Napoli, Marcelo Felgueiras

2016-01-01

We aim to evaluate the genetic structure of an Atlantic Forest amphibian species, Scinax eurydice, testing the congruence among patterns identified and proposed by the literature for Pleistocene refugia, microrefugia, and geographic barriers to gene flow such as major rivers. Furthermore, we aim to evaluate predictions of such barriers and refugia on the genetic structure of the species, such as presence/absence of dispersal, timing since separation, and population expansions/contractions. We sequenced mitochondrial and nuclear genetic markers on 94 tissue samples from 41 localities. We inferred a gene tree and estimated genetic distances using mtDNA sequences. We then ran population clustering and assignment methods, AMOVA, and estimated migration rates among populations identified through mtDNA and nDNA analyses. We used a dated species tree, skyline plots, and summary statistics to evaluate concordance between population's distributions and geographic barriers and Pleistocene refugia. Scinax eurydice showed high mtDNA divergences and four clearly distinct mtDNA lineages. Species tree and population assignment tests supported the existence of two major clades corresponding to northeastern and southeastern Atlantic Forest in Brazil, each one composed of two other clades. Lineage splitting events occurred from late Pliocene to Pleistocene. We identified demographic expansions in two clades, and inexistent to low levels of migrations among different populations. Genetic patterns and demographic data support the existence of two northern Refuge and corroborate microrefugia south of the Doce/Jequitinhonha Rivers biogeographic divide. The results agree with a scenario of recent demographic expansion of lowland taxa. Scinax eurydice comprises a species complex, harboring undescribed taxa consistent with Pleistocene refugia. Two rivers lie at the boundaries among populations and endorse their role as secondary barriers to gene flow.

Species boundaries and possible hybridization between the black mongoose (Galerella nigrata) and the slender mongoose (Galerella sanguinea).

PubMed

Rapson, Sara A; Goldizen, Anne W; Seddon, Jennifer M

2012-12-01

Major climatic oscillations since the mid-Miocene climatic optimum are known to have played a key role in promoting speciation events. In this study we use molecular data to elucidate the evolutionary history of Galerella nigrata and link its divergence to known major climatic events. A total of 51 samples from G. nigrata and 17 from Galerella sanguinea were used to provide the first molecular evidence that G. nigrata may be a species in its own right. Both mitochondrial cytochrome b and the nuclear ß-fibrinogen intron seven sequences of G. nigrata form distinct monophyletic clades, separate from its sister species G. sanguinea. We estimate the divergence of these two species to have occurred 3.85-4.27 million years ago, coinciding with a period of the Plio-Pleistocene that was characterised by cooling global temperatures and strong aridity in southern Africa. However, evidence for potential hybridization between the two species was documented for ten individuals using phenotypic (pelage colouration) and/or molecular (nuclear and mtDNA sequences and microsatellite loci) data. There appeared to be a bias towards unidirectional hybridization with all potential hybrids showing mtDNA haplotypes from G. nigrata. We suggest that as the desert expanded across Namibia, G. sanguinea likely retreated with the savanna, leaving some mongooses stranded on the granite inselbergs of north-western Namibia. Subsequent adaptation of these mongooses to local conditions on granite inselbergs could have led to ecological speciation. Secondary contact zones would have been re-established with subsequent global warming events. It appears that the two species have not yet undergone complete reproductive isolation. Copyright © 2012 Elsevier Inc. All rights reserved.

Multilocus Phylogeography of the Treefrog Scinax eurydice (Anura, Hylidae) Reveals a Plio-Pleistocene Diversification in the Atlantic Forest

PubMed Central

Menezes, Lucas; Canedo, Clarissa; Batalha-Filho, Henrique; Garda, Adrian Antonio; Gehara, Marcelo; Napoli, Marcelo Felgueiras

2016-01-01

We aim to evaluate the genetic structure of an Atlantic Forest amphibian species, Scinax eurydice, testing the congruence among patterns identified and proposed by the literature for Pleistocene refugia, microrefugia, and geographic barriers to gene flow such as major rivers. Furthermore, we aim to evaluate predictions of such barriers and refugia on the genetic structure of the species, such as presence/absence of dispersal, timing since separation, and population expansions/contractions. We sequenced mitochondrial and nuclear genetic markers on 94 tissue samples from 41 localities. We inferred a gene tree and estimated genetic distances using mtDNA sequences. We then ran population clustering and assignment methods, AMOVA, and estimated migration rates among populations identified through mtDNA and nDNA analyses. We used a dated species tree, skyline plots, and summary statistics to evaluate concordance between population’s distributions and geographic barriers and Pleistocene refugia. Scinax eurydice showed high mtDNA divergences and four clearly distinct mtDNA lineages. Species tree and population assignment tests supported the existence of two major clades corresponding to northeastern and southeastern Atlantic Forest in Brazil, each one composed of two other clades. Lineage splitting events occurred from late Pliocene to Pleistocene. We identified demographic expansions in two clades, and inexistent to low levels of migrations among different populations. Genetic patterns and demographic data support the existence of two northern Refuge and corroborate microrefugia south of the Doce/Jequitinhonha Rivers biogeographic divide. The results agree with a scenario of recent demographic expansion of lowland taxa. Scinax eurydice comprises a species complex, harboring undescribed taxa consistent with Pleistocene refugia. Two rivers lie at the boundaries among populations and endorse their role as secondary barriers to gene flow. PMID:27248688

Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries

PubMed Central

Moore, Michael J.; Neubig, Kurt M.; Williams, Norris H.; Whitten, W. Mark; Kim, Joo-Hwan

2015-01-01

Earlier research has revealed that the ndh loci have been pseudogenized, truncated, or deleted from most orchid plastomes sequenced to date, including in all available plastomes of the two most species-rich subfamilies, Orchidoideae and Epidendroideae. This study sought to resolve deeper-level phylogenetic relationships among major orchid groups and to refine the history of gene loss in the ndh loci across orchids. The complete plastomes of seven orchids, Oncidium sphacelatum (Epidendroideae), Masdevallia coccinea (Epidendroideae), Sobralia callosa (Epidendroideae), Sobralia aff. bouchei (Epidendroideae), Elleanthus sodiroi (Epidendroideae), Paphiopedilum armeniacum (Cypripedioideae), and Phragmipedium longifolium (Cypripedioideae) were sequenced and analyzed in conjunction with all other available orchid and monocot plastomes. Most ndh loci were found to be pseudogenized or lost in Oncidium, Paphiopedilum and Phragmipedium, but surprisingly, all ndh loci were found to retain full, intact reading frames in Sobralia, Elleanthus and Masdevallia. Character mapping suggests that the ndh genes were present in the common ancestor of orchids but have experienced independent, significant losses at least eight times across four subfamilies. In addition, ndhF gene loss was correlated with shifts in the position of the junction of the inverted repeat (IR) and small single-copy (SSC) regions. The Orchidaceae have unprecedented levels of homoplasy in ndh gene presence/absence, which may be correlated in part with the unusual life history of orchids. These results also suggest that ndhF plays a role in IR/SSC junction stability. PMID:26558895

Biostratigraphy of Cretaceous-Paleogene marine succession, foraminiferal changes across the K/T boundary, sequence stratigraphy and response to sedimentary cyclicity in the Haymana Basin (Central Anatolia, Turkey)

NASA Astrophysics Data System (ADS)

Amirov, Elnur

2016-04-01

The aim of this study is to establish the planktonic foraminiferal biozonation, to construct the sequence stratigraphical framework and to determine the foraminiferal response to sedimentary cyclicity in the sedimentary sequence spanning Upper Cretaceous-Paleocene in the Haymana basin (Central Anatolia, Turkey). In order to achieve this study, the stratigraphic section was measured from sedimentary sequence of the Haymana, Beyobası and Yeşilyurt formations. The sedimentary sequence is mainly characterized by flyschoidal sequence that is composed of alternating of siliciclastic and carbonate units. On the account of the detailed taxonomic study of planktonic foraminifers, the biostratigraphic framework was established for the Maastrichtian-Paleocene interval. The biozonation includes 7 zones; Pseudoguembelina hariaensis, Pα, P1, P2, P3, P4 and P5 zones. The Cretaceous-Paleogene (K/P) boundary was delineated between the samples HEA-105 and 106. In order to construct the sequence-stratigraphical framework, the A, B, C and D-type meter-scale cycles were identified. Based on the stacking patterns of them, six depositional sequences, six third and two second order cycles were determined. Third order cycles coincide with the Global Sea Level Change Curve. On the account of the conducted petrographic analysis sandstone, mudstone, marl, limestone and muddy-limestone lithofacies were recorded in the studied samples. In order to demonstrate the response of foraminifers to cyclicity, quantitative analysis has been carried out by counting the individuals of planktonic, benthonic foraminifers and ostracods. The best response to sedimentary cyclicity was revealed from planktonic foraminifers. The average abundance of planktonic foraminifers increases in the transgressive systems tract and decreases in the highstand systems tract. Foraminifera are the most abundant marine protozoa in the benthic, epipelagic and pelagic realm. Because of the complexity and diversity of habitats, especially in the pelagic realm, planktonic foraminifera show high biodiversity and abundance as an effect of their different ecological requirements. Microfaunal analysis displays significant presence of foraminifers and an insignificant presence of ostracoda shells which represented by genera Leptocythere, Caspiella, Xestoleberis and etc. The foraminiferal assemblages of this sequence were determined in detail and quantitative analysis of them was carried out. By detail investigation of microfauna and determination of foraminifer species under the microscope, it was possible to pinpoint the C/P boundary in the studied section, which is indicating the mass extinctions of Cretaceous foraminifers represented by genera Archaeoglobigerina, Contusotruncana, Gansserina, Globigerinelloides, Globotruncana, Globorotalia, Hedbergella, Heterohelix, Planoglobulina and appearance of new small and non-keeled Danian species, represented by genera such as Chiloguembelina, Eoglobigerina, Globoconusa, Globanomalina, Igorina, Parvularugoglobigerina, Parasubbotina, Subbotina, Woodringina and etc. As a result of precise conducted research the significant bioevent has been revealed, namely that Hedbergella holmdelensis became extinct in Pα Zone.

COI haplotype groups in Mesocriconema (Nematoda: Criconematidae) and their morphospecies associations.

PubMed

Powers, T O; Bernard, E C; Harris, T; Higgins, R; Olson, M; Lodema, M; Mullin, P; Sutton, L; Powers, K S

2014-07-03

Without applying an a priori bias for species boundaries, specimen identities in the plant-parasitic nematode genus Mesocriconema were evaluated by examining mitochondrial COI nucleotide sequences, morphology, and biogeography. A total of 242 specimens that morphologically conformed to the genus were individually photographed, measured, and amplified by a PCR primer set to preserve the linkage between specimen morphology and a specific DNA barcode sequence. Specimens were extracted from soil samples representing 45 locations across 23 ecoregions in North America. Dendrograms constructed by neighbor-joining, maximum likelihood, and Bayesian Inference using a 721-bp COI barcode were used to group COI haplotypes. Each tree-building approach resulted in 24 major haplotype groups within the dataset. The distinctiveness of these groups was evaluated by node support, genetic distance, absence of intermediates, and several measures of distinctiveness included in software used for the exploration of species boundaries. Five of the 24 COI haplotype groups corresponded to morphologically characterized, Linnaean species. Morphospecies conforming to M. discus, Discocriconemella inarata, M. rusticum, M. onoense, and M. kirjanovae were represented by groups composed of multiple closely related or identical COI haplotypes. In other cases, morphospecies names could be equally applied to multiple haplotype groups that were genetically distant from each other. Identification based on morphology alone resulted in M. curvatum and M. ornatum species designations applied to seven and three groups, respectively. Morphological characters typically used for species level identification were demonstrably variable within haplotype groups, suggesting caution in assigning species names based on published compendia that solely consider morphological characters. Morphospecies classified as M. xenoplax formed a monophyletic group composed of seven genetically distinct COI subgroups. The species Discocriconemella inarata is transferred to Mesocriconema inaratum based on its phylogenetic position on the COI tree as well as previous phylogenetic analyses using 18S, ITS1, and cytochrome b nucleotide sequences. This study indicates that some of the species considered cosmopolitan in their distribution are actually multispecies polyphyletic groupings and an accurate assessment of Mesocriconema species distributions will benefit from molecular determination of haplotype relationships. The groups revealed by COI analysis should provide a useful framework for the evaluation of additional Mesocriconema species and will improve the reliability of designating taxonomic units in studies of nematode biodiversity. 

The analytical solution for drug delivery system with nonhomogeneous moving boundary condition

NASA Astrophysics Data System (ADS)

Saudi, Muhamad Hakimi; Mahali, Shalela Mohd; Harun, Fatimah Noor

2017-08-01

This paper discusses the development and the analytical solution of a mathematical model based on drug release system from a swelling delivery device. The mathematical model is represented by a one-dimensional advection-diffusion equation with nonhomogeneous moving boundary condition. The solution procedures consist of three major steps. Firstly, the application of steady state solution method, which is used to transform the nonhomogeneous moving boundary condition to homogeneous boundary condition. Secondly, the application of the Landau transformation technique that gives a significant impact in removing the advection term in the system of equation and transforming the moving boundary condition to a fixed boundary condition. Thirdly, the used of separation of variables method to find the analytical solution for the resulted initial boundary value problem. The results show that the swelling rate of delivery device and drug release rate is influenced by value of growth factor r.

Pressure and tension waves from bubble collapse near a solid boundary: A numerical approach.

PubMed

Lechner, Christiane; Koch, Max; Lauterborn, Werner; Mettin, Robert

2017-12-01

The acoustic waves being generated during the motion of a bubble in water near a solid boundary are calculated numerically. The open source package OpenFOAM is used for solving the Navier-Stokes equation and extended to include nonlinear acoustic wave effects via the Tait equation for water. A bubble model with a small amount of gas is chosen, the gas obeying an adiabatic law. A bubble starting from a small size with high internal pressure near a flat, solid boundary is studied. The sequence of events from bubble growth via axial microjet formation, jet impact, annular nanojet formation, torus-bubble collapse, and bubble rebound to second collapse is described. The different pressure and tension waves with their propagation properties are demonstrated.

Without Boundaries: An Inquiry into Deaf Epistemologies through a Metaparadigm

ERIC Educational Resources Information Center

Wang, Ye

2010-01-01

The ongoing debate on Deaf epistemologies reflects two major paradigms in deaf education: positivism and constructivism. The present article investigates Deaf epistemologies through a metaparadigm, which should blur the boundaries among different paradigms and connect the epistemological inquiry to instructional practice for d/Deaf students. The…

Coincidence or not? Interconnected gas/fluid migration and ocean-atmosphere oscillations in the Levant Basin

NASA Astrophysics Data System (ADS)

Lazar, Michael; Lang, Guy; Schattner, Uri

2016-08-01

A growing number of studies on shallow marine gas/fluid systems from across the globe indicate their abundance throughout geological epochs. However, these episodic events have not been fully integrated into the fundamental concepts of continental margin development, which are thought to be dictated by three elements: tectonics, sedimentation and eustasy. The current study focuses on the passive sector of the Levant Basin on the eastern Mediterranean continental margin where these elements are well constrained, in order to isolate the contribution of gas/fluid systems. Single-channel, multichannel and 3D seismic reflection data are interpreted in terms of variance, chaos, envelope and sweetness attributes. Correlation with the Romi-1 borehole and sequence boundaries constrains interpretation of seismic stratigraphy. Results show a variety of fluid- or gas-related features such as seafloor and subsurface pockmarks, volumes of acoustic blanking, bright spots, conic pinnacle mounds, gas chimneys and high sweetness zones that represent possible secondary reservoirs. It is suggested that gas/fluid migrate upwards along lithological conduits such as falling-stage systems tracts and sequence boundaries during both highstands and lowstands. In all, 13 mid-late Pleistocene sequence boundaries are accompanied by independent evidence of 13 eustatic sea-level drops. Whether this connection is coincidental or not requires further research. These findings fill gaps between previously reported sporadic appearances throughout the Levant Basin and margin and throughout geological time from the Messinian until the present day, and create a unified framework for understanding the system as a whole. Repetitive appearance of these features suggests that their role in the morphodynamics of continental margins is more important than previously thought and thus may constitute one of the key elements of continental margin development.

The buckling response of symmetrically laminated composite plates having a trapezoidal planform area. M.S. Thesis Interim Report No. 98, Aug. 1990 - May 1994

NASA Technical Reports Server (NTRS)

Radloff, H. D., II; Hyer, M. W.; Nemeth, M. P.

1994-01-01

The focus of this work is the buckling response of symmetrically laminated composite plates having a planform area in the shape of an isosceles trapezoid. The loading is assumed to be inplane and applied perpendicular to the parallel ends of the plate. The tapered edges of the plate are assumed to have simply supported boundary conditions, while the parallel ends are assumed to have either simply supported or clamped boundary conditions. A semi-analytic closed-form solution based on energy principles and the Trefftz stability criterion is derived and solutions are obtained using the Rayleigh-Ritz method. Intrinsic in this solution is a simplified prebuckling analysis which approximates the inplane force resultant distributions by the forms Nx=P/W(x) and Ny=Nxy=0, where P is the applied load and W(x) is the plate width which, for the trapezoidal planform, varies linearly with the lengthwise coordinate x. The out-of-plane displacement is approximated by a double trigonometric series. This analysis is posed in terms of four nondimensional parameters representing orthotropic and anisotropic material properties, and two nondimensional parameters representing geometric properties. For comparison purposes, a number of specific plate geometry, ply orientation, and stacking sequence combinations are investigated using the general purpose finite element code ABAQUS. Comparison of buckling coefficients calculated using the semi-analytical model and the finite element model show agreement within 5 percent, in general, and within 15 percent for the worst cases. In order to verify both the finite element and semi-analytical analyses, buckling loads are measured for graphite/epoxy plates having a wide range of plate geometries and stacking sequences. Test fixtures, instrumentation system, and experimental technique are described. Experimental results for the buckling load, the buckled mode shape, and the prebuckling plate stiffness are presented and show good agreement with the analytical results regarding the buckling load and the prebuckling plate stiffness. However, the experimental results show that for some cases the analysis underpredicts the number of halfwaves in the buckled mode shape. In the context of the definitions of taper ratio and aspect ratio used in this study, it is concluded that the buckling load always increases as taper ratio increases for a given aspect ratio for plates having simply supported boundary conditions on the parallel ends. There are combinations of plate geometry and ply stackling sequences, however, that reverse this trend for plates having clamped boundary conditions on the parallel ends such that an increase in the taper ratio causes a decrease in the buckling load. The clamped boundary conditions on the parallel ends of the plate are shown to increase the buckling load compared to simply supported boundary conditions. Also, anisotropy (the D16 and D26 terms) is shown to decrease the buckling load and skew the buckled mode shape for both the simply supported and clamped boundary conditions.

Shape classification of malignant lymphomas and leukemia by morphological watersheds and ARMA modeling

NASA Astrophysics Data System (ADS)

Celenk, Mehmet; Song, Yinglei; Ma, Limin; Zhou, Min

2003-05-01

A new algorithm that can be used to automatically recognize and classify malignant lymphomas and lukemia is proposed in this paper. The algorithm utilizes the morphological watershed to extract boundaries of cells from their grey-level images. It generates a sequence of Euclidean distances by selecting pixels in clockwise direction on the boundary of the cell and calculating the Euclidean distances of the selected pixels from the centroid of the cell. A feature vector associated with each cell is then obtained by applying the auto-regressive moving-average (ARMA) model to the generated sequence of Euclidean distances. The clustering measure J3=trace{inverse(Sw-1)Sm} involving the within (Sw) and mixed (Sm) class-scattering matrices is computed for both cell classes to provide an insight into the extent to which different cell classes in the training data are separated. Our test results suggest that the algorithm is highly accurate for the development of an interactive, computer-assisted diagnosis (CAD) tool.

Characterization of the bovine pseudoautosomal boundary: Documenting the evolutionary history of mammalian sex chromosomes

PubMed Central

Van Laere, Anne-Sophie; Coppieters, Wouter; Georges, Michel

2008-01-01

Here, we report the sequence characterization of the bovine pseudoautosomal boundary (PAB) and its neighborhood. We demonstrate that it maps to the 5′ end of the GPR143 gene, which has concomitantly lost upstream noncoding exons on the Y chromosome. We show that the bovine PAB was created ∼20.7 million years ago by illegitimate intrachromatid recombination between inverted, ruminant-specific Bov-tA repeats. Accordingly, we demonstrate that cattle share their PAB with all other examined ruminants including sheep, but not with cetaceans or more distantly related mammals. We provide evidence that, since its creation, the ancestral ruminant PAB has been displaced by attrition, which occurs at variable rates in different species, and that it is capable of retreat by attrition erasure. We have estimated the ratio of male to female mutation rates in the Bovidae family as ∼1.7, and we provide evidence that the mutation rate is higher in the recombining pseudoautosomal region than in the adjacent, nonrecombining gonosome-specific sequences. PMID:18981267

Cyclothem [“digital”] correlation and biostratigraphy across the global Moscovian-Kasimovian-Gzhelian stage boundary interval (Middle-Upper Pennsylvanian) in North America and eastern Europe

NASA Astrophysics Data System (ADS)

Heckel, Philip H.; Alekseev, Aleksandr S.; Barrick, James E.; Boardman, Darwin R.; Goreva, Natalya V.; Nemyrovska, Tamara I.; Ueno, Katsumi; Villa, Elisa; Work, David M.

2007-07-01

The long-standing difficulty of correlating Pennsylvanian strata among provincial faunal regions is resolved by effecting “digital” correlation of major glacial-eustatic cyclothems that represent high-stands when certain species achieved more global distribution than usual. In the late Moscovian-early Gzhelian (late Desmoinesian-early Virgilian) succession in the midcontinent United States, several major cyclothems are correlated, by both conodont species in common and cyclothem scale, with cyclothems in Russia (Moscow Basin) and Ukraine (Donets Basin), and the remaining cyclothems fit into the framework by position and scale. In this way the suggested event marker for the global Kasimovian-Gzhelian stage boundary (first appearance of Idiognathodus simulator) is supported, while possible event markers for the Moscovian-Kasimovian boundary await further evaluation.

Development of a Vorticity-Velocity Navier-Stokes Formulation for the Study of Compressibility Effects on Dynamic Stall

NASA Technical Reports Server (NTRS)

Ghia, K. N.; Ghia, U.

1996-01-01

The first major area of this study was to develop a vorticity-velocity formulation and numerical solution algorithms suitable for the analyses of incompressible as well as low-to- moderate-speed compressible flows. Research performed towards contributing to the determination of the appropriate vorticity and dilation creation boundary conditions suggested to temporarily set aside this approach and use a primitive-variable approach other than the pseudo-compressibility approach used. The second major area of study was initiated to comprehensively examine the INS-2D and INS-3D programs from the point of view of boundary conditions. The research carried out was documented in the form of two technical papers which are included in Appendices A and B; the boundary-condition related issues for INS-3D are briefly mentioned.

Optimal boundary conditions for ORCA-2 model

NASA Astrophysics Data System (ADS)

Kazantsev, Eugene

2013-08-01

A 4D-Var data assimilation technique is applied to ORCA-2 configuration of the NEMO in order to identify the optimal parametrization of boundary conditions on the lateral boundaries as well as on the bottom and on the surface of the ocean. The influence of boundary conditions on the solution is analyzed both within and beyond the assimilation window. It is shown that the optimal bottom and surface boundary conditions allow us to better represent the jet streams, such as Gulf Stream and Kuroshio. Analyzing the reasons of the jets reinforcement, we notice that data assimilation has a major impact on parametrization of the bottom boundary conditions for u and v. Automatic generation of the tangent and adjoint codes is also discussed. Tapenade software is shown to be able to produce the adjoint code that can be used after a memory usage optimization.

Pre-Alpine (Variscan) Inheritance: A Key for the Location of the Future Valaisan Basin (Western Alps)

NASA Astrophysics Data System (ADS)

Ballèvre, M.; Manzotti, P.; Dal Piaz, G. V.

2018-03-01

The boundary between the Helvetic and the Penninic (=Briançonnais) Zones has long been recognized as a major fault ("Penninic Front") in the Western Alps. A narrow oceanic domain has been postulated at least along part of this boundary (the Valaisan Basin). However, the information provided by the pre-Triassic basement has not been fully exploited and will be discussed here in detail. The igneous and metamorphic history of the pre-Triassic basement shows significant differences between the External Massifs from the Helvetic Zone, with abundant Late Carboniferous granites, and the basement of the Briançonnais Zone, including the Internal Massifs (Dora-Maira, Gran Paradiso, and Monte Rosa), devoid of Carboniferous granites. A major coal-bearing basin, the "Zone Houillère," opened along this boundary. This limnic intramontane basin has never been properly investigated. The Zone Houillère is not comparable with the external, paralic, flexural, basins on both sides of the Variscan belt but shows similarities with the Saar-Saale Basin. Like the latter, we interpret the Zone Houillère as a transtensional basin opened along a major, crustal-scale, fault zone, namely, the East Variscan Shear Zone. The Permian magmatism and sedimentation displays contrasting distributions, being absent or very localized in the Helvetic Zone, and widespread in the Penninic Zone. The above data indicate that the structural inheritance from the Variscan belt plays a major role in defining the future location of the Valaisan Basin, that is, the boundary between the European paleomargin and the Briançonnais microcontinent.

Boundaries for martensitic transition of 7Li under pressure

DOE PAGES

Schaeffer, Anne Marie; Cai, Weizhao; Olejnik, Ella; ...

2015-08-14

We report that physical properties of lithium under extreme pressures continuously reveal unexpected features. These include a sequence of structural transitions to lower symmetry phases, metal-insulator-metal transition, superconductivity with one of the highest elemental transition temperatures, and a maximum followed by a minimum in its melting line. The instability of the bcc structure of lithium is well established by the presence of a temperature-driven martensitic phase transition. The boundaries of this phase, however, have not been previously explored above 3 GPa. All higher pressure phase boundaries are either extrapolations or inferred based on indirect evidence. Here we explore the pressuremore » dependence of the martensitic transition of lithium up to 7 GPa using a combination of neutron and X-ray scattering. We find a rather unexpected deviation from the extrapolated boundaries of the hR3 phase of lithium. Furthermore, there is evidence that, above ~3 GPa, once in fcc phase, lithium does not undergo a martensitic transition.« less

Motion of 1/3⟨111⟩ dislocations on Σ3 {112} twin boundaries in nanotwinned copper

NASA Astrophysics Data System (ADS)

Lu, N.; Du, K.; Lu, L.; Ye, H. Q.

2014-01-01

The atomic structure of Σ3 {112} ITBs in nanotwinned Cu is investigated by using aberration-corrected high resolution transmission electron microscopy (HRTEM) and in situ HRTEM observations. The Σ3 {112} ITBs are consisted of periodically repeated three partial dislocations. The in situ HRTEM results show that 1/3[111] partial dislocation moves on the Σ3 {112} incoherent twin boundary (ITB), which was accompanied by a migration of the ITB. A dislocation reaction mechanism is proposed for the motion of 1/3[111] Frank partial dislocation, in which the 1/3[111] partial dislocation exchanges its position with twin boundary dislocations in sequence. In this way, the 1/3[111] dislocation can move on the incoherent twin boundary in metals with low stacking fault energy. Meanwhile, the ITB will migrate in its normal direction accordingly. These results provide insight into the reaction mechanism of 1/3[111] dislocations and ITBs and the associated migration of ITBs.

Spatiotemporal motion boundary detection and motion boundary velocity estimation for tracking moving objects with a moving camera: a level sets PDEs approach with concurrent camera motion compensation.

PubMed

Feghali, Rosario; Mitiche, Amar

2004-11-01

The purpose of this study is to investigate a method of tracking moving objects with a moving camera. This method estimates simultaneously the motion induced by camera movement. The problem is formulated as a Bayesian motion-based partitioning problem in the spatiotemporal domain of the image quence. An energy functional is derived from the Bayesian formulation. The Euler-Lagrange descent equations determine imultaneously an estimate of the image motion field induced by camera motion and an estimate of the spatiotemporal motion undary surface. The Euler-Lagrange equation corresponding to the surface is expressed as a level-set partial differential equation for topology independence and numerically stable implementation. The method can be initialized simply and can track multiple objects with nonsimultaneous motions. Velocities on motion boundaries can be estimated from geometrical properties of the motion boundary. Several examples of experimental verification are given using synthetic and real-image sequences.

Molecular Characterization of Epiphytic Bacterial Communities on Charophycean Green Algae

PubMed Central

Fisher, Madeline M.; Wilcox, Lee W.; Graham, Linda E.

1998-01-01

Epiphytic bacterial communities within the sheath material of three filamentous green algae, Desmidium grevillii, Hyalotheca dissiliens, and Spondylosium pulchrum (class Charophyceae, order Zygnematales), collected from a Sphagnum bog were characterized by PCR amplification, cloning, and sequencing of 16S ribosomal DNA. A total of 20 partial sequences and nine different sequence types were obtained, and one sequence type was recovered from the bacterial communities on all three algae. By phylogenetic analysis, the cloned sequences were placed into several major lineages of the Bacteria domain: the Flexibacter/Cytophaga/Bacteroides phylum and the α, β, and γ subdivisions of the phylum Proteobacteria. Analysis at the subphylum level revealed that the majority of our sequences were not closely affiliated with those of known, cultured taxa, although the estimated evolutionary distances between our sequences and their nearest neighbors were always less than 0.1 (i.e., greater than 90% similar). This result suggests that the majority of sequences obtained in this study represent as yet phenotypically undescribed bacterial species and that the range of bacterial-algal interactions that occur in nature has not yet been fully described. PMID:9797295

The Cretaceous-Tertiary boundary interval in Badlands National Park, South Dakota

USGS Publications Warehouse

Stoffer, Philip W.; Messina, Paula; Chamberlain, John A.; Terry, Dennis O.

2001-01-01

A marine K-T boundary interval has been identified throughout the Badlands National Park region of South Dakota. Data from marine sediments suggest that deposits from two asteroid impacts (one close, one far away) may be preserved in the Badlands. These impact-generated deposits may represent late Maestrichtian events or possibly the terminal K-T event. Interpretation is supported by paleontological correlation, sequence stratigraphy, magnetostratigraphy, and strontium isotope geochronology. This research is founded on nearly a decade of NPS approved field work in Badlands National Park and a foundation of previously published data and interpretations. The K-T boundary occurs within or near the base of a stratigraphic interval referred to as the "Interior Zone." We interpret the stratigraphy of the Interior Zone as a series of distinct, recognizable lithologic members and units from oldest to youngest, an upper weathered interval of the Elk Butte Member of the Pierre Shale (early late Maestrichtian), a complete (albeit condensed) interval of Fox Hill Formation, a pedogenically altered K-T Boundary "Disturbed Zone," and a generally unresolved sequence of marine to marginal marine units ranging in age from possibly latest Maestrichtian to late Paleocene (the "Yellow Mounds"), that underlie a basal red clay unit (the late Eocene overbank channel facies of the Chamberlain Pass Formation at the base of the White River Group). Within this sequence is a series of unconformities that all display some degree of subaerial weathering and erosion. The dating of marine fossils above and below these unconformities are in line with generally accepted global sea-level changes recognized for the late Campanian through early Eocene. Within the greater framework of regional geology, these findings support that the Western Interior Seaway and subsequent Cannonball Seaway were dependently linked to the changing base-level controlled by sea-level of the global ocean through the Gulf of Mexico and possibly the Arctic Ocean. The variation of facies preserved in Late Cretaceous strata in the Badlands National Park area were in part controlled by local or regional tectonic blocks that were either rising or sinking contemporaneous with deposition.

Muscovite-Dehydration Melting: A Textural Study of a Key Reaction in Transforming Continental Margin Strata Into a Migmatitic Orogenic Core

NASA Astrophysics Data System (ADS)

Dyck, B. J.; St Onge, M. R.; Waters, D. J.; Searle, M. P.

2015-12-01

Metamorphosed continental margin sedimentary sequences, which comprise the dominant tectonostratigraphic assemblage exposed in orogenic hinterlands, are crucial to understanding the architecture and evolution of collisional mountain belts. This study explores the textural effect of anatexis in amphibolite-grade conditions and documents the mineral growth mechanisms that control nucleation and growth of K-feldspar, sillimanite and silicate melt. The constrained textural evolution follows four stages: 1) Nucleation - K-feldspar is documented to nucleate epitaxially on isomorphic plagioclase in quartzofeldspathic (psammitic) domains, whereas sillimanite nucleates in the Al-rich (pelitic) domain, initially on [001] mica planes. The first melt forms at the site of muscovite breakdown. 2) Chemically driven growth - In the quartzofeldspathic domain, K-feldspar progressively replaces plagioclase by a K+ - Na+ cation transfer reaction, driven by the freeing of muscovite-bound K+ during breakdown of the mica. Sillimanite forms intergrowths with the remaining hydrous melt components, contained initially in ovoid clots. 3) Merge and coarsening - With an increase in pressure, melt and sillimanite migrate away from clots along grain boundaries. A melt threshold is reached once the grain-boundary network is wetted by melt, increasing the length-scale of diffusion, resulting in grain boundary migration and grain-size coarsening. The melt threshold denotes the transition to an open-system on the lithology scale, where melt is a transient phase. 4) Residual melt crystallization - Residual melt crystallizes preferentially on existing peritectic grains as anatectic quartz, plagioclase, and K-feldspar. As the system cools and closes, grain growth forces melt into the intersections of grain-boundaries, recognized as irregular shaped melt films, or as intergrowths of the volatile-rich phases (i.e. Tur-Ms-Ap). In the Himalayan metamorphic core these processes result in the formation of: pelitic K-feldspar augen gneiss, stockwork leucogranites, and an effective strengthening of the hinterland, as evidenced by a switch in tectonic deformation style, from thin-skinned cover sequence thrust imbrication and folding to out-of-sequence basement-involved thick-skinned thrusting and folding.

HR-EBSD as a new tool for quantifying geometrically necessary dislocations in quartz: Application to chessboard subgrain boundaries

NASA Astrophysics Data System (ADS)

Wallis, D.; Parsons, A. J.; Hansen, L. N.

2017-12-01

Chessboard subgrains in quartz, with boundaries composed of {m}[c] edge dislocations, are widely used as evidence for high-temperature deformation and have been suggested to form only in β-quartz. However, the origins and dislocation structure of chessboard subgrains remain poorly constrained and, without precise constraints on axes of misorientations across subgrain boundaries, other subgrain types formed at lower temperatures can be misidentified as chessboard subgrains. The technique most commonly employed to investigate subgrain structures, electron backscatter diffraction, can only resolve misorientation angles and axes for a portion of the substructure. This limitation hinders detailed interpretation of the dislocation types, densities, and processes that generate characteristic subgrain structures. We overcome these limitations by employing high-angular resolution electron backscatter diffraction (HR-EBSD), which employs cross-correlation of diffraction patterns to achieve angular resolution on the order of 0.01° with well-constrained misorientation axes. We analyse chessboard subgrains in samples from the Greater Himalayan Sequence, Nepal, which were deformed along well constrained pressure-temperature paths confined to the stability field of α-quartz. HR-EBSD analysis demonstrates that the subgrain boundaries consist of two sets. One set consists primarily of {m}[c] edge dislocations and the other consists of dislocations primarily with Burgers vectors. Apparent densities of geometrically necessary dislocations vary from > 1013 m-2 within some subgrain boundaries to < 1012 m-2 within subgrain interiors. This analysis provides new insight into the structure of chessboard subgrain boundaries, and a new tool to distinguish them from superficially similar deformation microstructures formed by other dislocation types at lower temperatures. Application of HR-EBSD to quartz from the Greater Himalayan Sequence confirms the activity of {m}[c] slip in the α-quartz stability field and demonstrates that formation of chessboard subgrains is not restricted to the stability field of β-quartz. Most importantly, this study demonstrates the potential of HR-EBSD as an improved method for analysis of quartz microstructures used as indicators of deformation conditions.

The observation of possible reconnection events in the boundary changes of solar coronal holes

NASA Technical Reports Server (NTRS)

Kahler, S. W.; Moses, J. Daniel

1989-01-01

Coronal holes are large scale regions of magnetically open fields which are easily observed in solar soft X-ray images. The boundaries of coronal holes are separatrices between large scale regions of open and closed magnetic fields where one might expect to observe evidence of solar magnetic reconnection. Previous studies by Nolte and colleagues using Skylab X-ray images established that large scale (greater than or equal to 9 x 10(4) km) changes in coronal hole boundaries were due to coronal processes, i.e., magnetic reconnection, rather than to photospheric motions. Those studies were limited to time scales of about one day, and no conclusion could be drawn about the size and time scales of the reconnection process at hole boundaries. Sequences of appropriate Skylab X-ray images were used with a time resolution of about 90 min during times of the central meridian passages of the coronal hole labelled Coronal Hole 1 to search for hole boundary changes which can yield the spatial and temporal scales of coronal magnetic reconnection. It was found that 29 of 32 observed boundary changes could be associated with bright points. The appearance of the bright point may be the signature of reconnection between small scale and large scale magnetic fields. The observed boundary changes contributed to the quasi-rigid rotation of Coronal Hole 1.

Salt marsh hydrology data web site facilitates research

NASA Astrophysics Data System (ADS)

Gardner, L. R.; Reeves, H. W.

The interface between maritime forests and inter-tidal salt marshes along the southeastern coast of the United States is a major ecological boundary characterized by a sequence of botanical zones that typically consist of pine/ oak forest>Iva>Juncus>Salicornia>Spartina. In addition to questions regarding the physical and chemical factors that govern this ecotone, this interface is of interest because of the potential for groundwater flow to transfer nutrients and pollutants from developed uplands to the adjacent marshes. The interface is also of interest because it is presumably migrating upslope as a result of ongoing sea level rise and concomitant aquifer salinization.A new Web site, http://links.baruch.sc.edu/data/GRNDWATER/data/data.htm, contains long-term and spatially dense measurements of groundwater heads and salinity from a network of nested piezometers that has been installed along three forest-marsh transects across the Crab Haul Creek finger marsh basin at the North Inlet-Winyah Bay National Estuarine Research Reserve in Georgetown County South Carolina (Figure 1).

Relative ages of lava flows at Alba Patera, Mars

NASA Technical Reports Server (NTRS)

Schneeberger, Dale M.; Pieri, David C.

1987-01-01

Many large lava flows on the flanks of Alba Patera are astonishing in their volume and length. As a suite, these flows suggest tremendously voluminous and sustained eruptions, and provide dimensional boundary conditions typically a factor of 100 larger than terrestrial flows. One of the most striking features associated with Alba Patera is the large, radially oriented lava flows that exhibit a variety of flow morphologies. These include sheet flows, tube fed and tube channel flows, and undifferentiated flows. Three groups of flows were studied; flows on the northwest flank, southeast flank, and the intracaldera region. The lava flows discussed probably were erupted as a group during the same major volcanic episode as suggested by the data presented. Absolute ages are poorly constrained for both the individual flows and shield, due in part to disagreement as to which absolute age curve is representative for Mars. A relative age sequence is implied but lacks precision due to the closeness of the size frequency curves.

Solving the Problem of Linear Viscoelasticity for Piecewise-Homogeneous Anisotropic Plates

NASA Astrophysics Data System (ADS)

Kaloerov, S. A.; Koshkin, A. A.

2017-11-01

An approximate method for solving the problem of linear viscoelasticity for thin anisotropic plates subject to transverse bending is proposed. The method of small parameter is used to reduce the problem to a sequence of boundary problems of applied theory of bending of plates solved using complex potentials. The general form of complex potentials in approximations and the boundary conditions for determining them are obtained. Problems for a plate with elliptic elastic inclusions are solved as an example. The numerical results for a plate with one, two elliptical (circular), and linear inclusions are analyzed.

Habitable zones around main sequence stars

NASA Technical Reports Server (NTRS)

Kasting, James F.; Whitmire, Daniel P.; Reynolds, Ray T.

1993-01-01

A mechanism for stabilizing climate on the earth and other earthlike planets is described, and the physical processes that define the inner and outer boundaries of the habitable zone (HZ) around the sun and main sequence stars are discussed. Physical constraints on the HZ obtained from Venus and Mars are taken into account. A 1D climate model is used to estimate the width of the HZ and the continuously habitable zone around the sun, and the analysis is extended to other main sequence stars. Whether other stars have planets and where such planets might be located with respect to the HZ is addressed. The implications of the findings for NASA's SETI project are considered.

Assessing DNA Barcodes for Species Identification in North American Reptiles and Amphibians in Natural History Collections.

PubMed

Chambers, E Anne; Hebert, Paul D N

2016-01-01

High rates of species discovery and loss have led to the urgent need for more rapid assessment of species diversity in the herpetofauna. DNA barcoding allows for the preliminary identification of species based on sequence divergence. Prior DNA barcoding work on reptiles and amphibians has revealed higher biodiversity counts than previously estimated due to cases of cryptic and undiscovered species. Past studies have provided DNA barcodes for just 14% of the North American herpetofauna, revealing the need for expanded coverage. This study extends the DNA barcode reference library for North American herpetofauna, assesses the utility of this approach in aiding species delimitation, and examines the correspondence between current species boundaries and sequence clusters designated by the BIN system. Sequences were obtained from 730 specimens, representing 274 species (43%) from the North American herpetofauna. Mean intraspecific divergences were 1% and 3%, while average congeneric sequence divergences were 16% and 14% in amphibians and reptiles, respectively. BIN assignments corresponded with current species boundaries in 79% of amphibians, 100% of turtles, and 60% of squamates. Deep divergences (>2%) were noted in 35% of squamate and 16% of amphibian species, and low divergences (<2%) occurred in 12% of reptiles and 23% of amphibians, patterns reflected in BIN assignments. Sequence recovery declined with specimen age, and variation in recovery success was noted among collections. Within collections, barcodes effectively flagged seven mislabeled tissues, and barcode fragments were recovered from five formalin-fixed specimens. This study demonstrates that DNA barcodes can effectively flag errors in museum collections, while BIN splits and merges reveal taxa belonging to deeply diverged or hybridizing lineages. This study is the first effort to compile a reference library of DNA barcodes for herpetofauna on a continental scale.

Assessing DNA Barcodes for Species Identification in North American Reptiles and Amphibians in Natural History Collections

PubMed Central

Chambers, E. Anne; Hebert, Paul D. N.

2016-01-01

Background High rates of species discovery and loss have led to the urgent need for more rapid assessment of species diversity in the herpetofauna. DNA barcoding allows for the preliminary identification of species based on sequence divergence. Prior DNA barcoding work on reptiles and amphibians has revealed higher biodiversity counts than previously estimated due to cases of cryptic and undiscovered species. Past studies have provided DNA barcodes for just 14% of the North American herpetofauna, revealing the need for expanded coverage. Methodology/Principal Findings This study extends the DNA barcode reference library for North American herpetofauna, assesses the utility of this approach in aiding species delimitation, and examines the correspondence between current species boundaries and sequence clusters designated by the BIN system. Sequences were obtained from 730 specimens, representing 274 species (43%) from the North American herpetofauna. Mean intraspecific divergences were 1% and 3%, while average congeneric sequence divergences were 16% and 14% in amphibians and reptiles, respectively. BIN assignments corresponded with current species boundaries in 79% of amphibians, 100% of turtles, and 60% of squamates. Deep divergences (>2%) were noted in 35% of squamate and 16% of amphibian species, and low divergences (<2%) occurred in 12% of reptiles and 23% of amphibians, patterns reflected in BIN assignments. Sequence recovery declined with specimen age, and variation in recovery success was noted among collections. Within collections, barcodes effectively flagged seven mislabeled tissues, and barcode fragments were recovered from five formalin-fixed specimens. Conclusions/Significance This study demonstrates that DNA barcodes can effectively flag errors in museum collections, while BIN splits and merges reveal taxa belonging to deeply diverged or hybridizing lineages. This study is the first effort to compile a reference library of DNA barcodes for herpetofauna on a continental scale. PMID:27116180

­Oligo-Miocene Monazite Ages in the Lesser Himalaya Sequence, Arunachal Pradesh, India; Geological Content of Age Variations

NASA Astrophysics Data System (ADS)

Clarke, G. L.; Bhowmik, S. K.; Ireland, T. R.; Aitchison, J. C.; Chapman, S. L.; Kent, L.

2016-12-01

A telescoped and inverted greenschist-upper amphibolite facies sequence in the in the Siyom Valley of eastern Arunachal Pradesh is tectonically overlain by an upright (grade decreasing upward) granulite to lower amphibolite facies sequence. Such grade relationships would normally attribute the boundary to a Main Central Thrust (MCT) structure, and predict a change from underlying Lesser Himalaya Sequence (LHS) to Greater Himalaya Sequence rocks across the boundary. However, all pelitic and psammitic samples have similar detrital zircon age spectra, involving c. 2500, 1750-1500, 1200 and 1000 Ma Gondwanan populations correlated with the LHS. Isograds are broadly parallel to a penetrative NW-dipping S2 foliation, developed contemporaneously with the inversion. Garnet growth in garnet, staurolite and kyanite zone schists beneath the thrust commenced at P>8 kbar and T≈550°C, before syn- to post-S2 heating of staurolite and kyanite zone rocks to T≈640°C at P≈8.5 kbar, most probably at c. 18.5 Ma. Kyanite-rutile-garnet migmatite immediately above the thrust records peak conditions of P≈10 kbar and T≈750°C and c. 21.5 Ma monazite ages. Complexity in c. 21-1000 Ma monazite ages in overlying amphibolite facies schists reflects the patchy recrystallization of detrital grains, intra-grain complexity being dependent on whole rock composition, metamorphic grade and evolition. Slip on a SE-propagating thrust was likely contemporaneous with early Miocene metamorphism, based on the distribution of structure, metamorphic textures, and overlap of age relationships. It is inferred to have initially controlled the uplift of granulite to mid-crustal levels between 22 and 19 Ma, thermal relaxation within a disrupted LHS metamorphic profile inducing a post-S2 thermal peak in lower grade footwall rocks.

Testing Astronomical and 40Ar/39Ar Timescales for the K/Pg Boundary Interval Using High-Resolution Magnetostratigraphy and U-Pb Geochronology in the Denver Basin of Colorado

NASA Astrophysics Data System (ADS)

Clyde, W.; Bowring, S. A.; Johnson, K. R.; Ramezani, J.; Jones, M. M.

2015-12-01

Accurate and precise calibration of the Geomagnetic Polarity Timescale (GPTS) in absolute time is critical for resolving rates of geological and biological processes which in turn help constrain the underlying causes of those processes. Numerical calibration of the GPTS was traditionally carried out by interpolation between a limited number of 40Ar/39Ar dated volcanic ash deposits from superpositional sequences with well-defined magnetostratigraphies. More recently, the Neogene part of the GPTS has been calibrated using high-resolution astrochronological methods, however the application of these approaches to pre-Neogene parts of the timescale is controversial given the uncertainties in relevant orbital parameters this far back in time and differing interpretations of local cyclostratigraphic records. The Cretaceous-Paleogene (K/Pg) boundary interval is a good example, where various astronomical and 40Ar/39Ar calibrations have been proposed with varying degrees of agreement. The Denver Basin (Colorado, USA) contains one of the most complete stratigraphic sequences across the K/Pg boundary in the world, preserving evidence of bolide impact as well as biotic extinction and recovery in a thick stratigraphic package that is accessible by both core and outcrop. We present a series of high-precision U-Pb age determinations from interbedded volcanic ash deposits within a tightly constrained magnetobiostratigraphic framework across the K/Pg boundary in the Denver Basin. This new timeline provides a precise absolute age for the K/Pg boundary, constrains the ages of magnetic polarity Chrons C28 to C30, and provides a direct and independent test of early Paleogene astronomical and 40Ar/39Ar based timescales. Temporal calibration of fossil pollen evidence of the "fern spike" in the Denver Basin shows that plant extinctions peaked within ~50-500 years of the bolide impact and primary productivity recovered ~500-5000 years after the impact.

Identification of Genomic Insertion and Flanking Sequence of G2-EPSPS and GAT Transgenes in Soybean Using Whole Genome Sequencing Method.

PubMed

Guo, Bingfu; Guo, Yong; Hong, Huilong; Qiu, Li-Juan

2016-01-01

Molecular characterization of sequence flanking exogenous fragment insertion is essential for safety assessment and labeling of genetically modified organism (GMO). In this study, the T-DNA insertion sites and flanking sequences were identified in two newly developed transgenic glyphosate-tolerant soybeans GE-J16 and ZH10-6 based on whole genome sequencing (WGS) method. More than 22.4 Gb sequence data (∼21 × coverage) for each line was generated on Illumina HiSeq 2500 platform. The junction reads mapped to boundaries of T-DNA and flanking sequences in these two events were identified by comparing all sequencing reads with soybean reference genome and sequence of transgenic vector. The putative insertion loci and flanking sequences were further confirmed by PCR amplification, Sanger sequencing, and co-segregation analysis. All these analyses supported that exogenous T-DNA fragments were integrated in positions of Chr19: 50543767-50543792 and Chr17: 7980527-7980541 in these two transgenic lines. Identification of genomic insertion sites of G2-EPSPS and GAT transgenes will facilitate the utilization of their glyphosate-tolerant traits in soybean breeding program. These results also demonstrated that WGS was a cost-effective and rapid method for identifying sites of T-DNA insertions and flanking sequences in soybean.

Road boundary detection

NASA Technical Reports Server (NTRS)

Sowers, J.; Mehrotra, R.; Sethi, I. K.

1989-01-01

A method for extracting road boundaries using the monochrome image of a visual road scene is presented. The statistical information regarding the intensity levels present in the image along with some geometrical constraints concerning the road are the basics of this approach. Results and advantages of this technique compared to others are discussed. The major advantages of this technique, when compared to others, are its ability to process the image in only one pass, to limit the area searched in the image using only knowledge concerning the road geometry and previous boundary information, and dynamically adjust for inconsistencies in the located boundary information, all of which helps to increase the efficacy of this technique.

Mitigating trans-boundary movement of Bemisia tabaci (Hemiptera: Aleyrodidae) on Mentha sp. by pre-shipping treaments of biopesticides

USDA-ARS?s Scientific Manuscript database

Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a major pest of several important crops including vegetables, cereals, fruits, and ornamentals grown worldwide. One important mode of its dispersal is through the trans-boundary movement of infested plant materials. In order to prevent the sprea...

Boundary Maintenance in Evangelical Christian Higher Education: A Case Study of the Council for Christian Colleges & Universities

ERIC Educational Resources Information Center

Patterson, James A.

2005-01-01

This essay, utilizing the "kaleidoscope" image of historian Timothy Smith, reflects on issues affecting evangelical identity and boundaries in the major professional association for Christian higher education, the Council for Christian Colleges & Universities (CCCU). Since the CCCU was birthed by a smaller organization, the Christian College…

Evolution of the Puente Hills Thrust Fault

NASA Astrophysics Data System (ADS)

Bergen, K. J.; Shaw, J. H.; Dolan, J. F.

2013-12-01

This study aims to assess the evolution of the blind Puente Hills thrust fault system (PHT) by determining its age of initiation, lateral propagation history, and changes in slip rate over time. The PHT presents one of the largest seismic hazards in the United States, given its location beneath downtown Los Angeles. The PHT is comprised of three fault segments: the Los Angeles (LA), Santa Fe Springs (SFS), and Coyote Hills (CH). The LA and SFS segments are characterized by growth stratigraphy where folds formed by uplift on the fault segments have been continually buried by sediment from the Los Angeles and San Gabriel rivers. The CH segment has developed topography and is characterized by onlapping growth stratigraphy. This depositional setting gives us the unique opportunity to measure uplift on the LA and SFS fault segments, and minimum uplift on the CH fault segment, as the difference in sediment thicknesses across the buried folds. We utilize depth converted oil industry seismic reflection data to image the fold geometries. Identifying time-correlative stratigraphic markers for slip rate determination in the basin has been a problem for researchers in the past, however, as the faunal assemblages observed in wells are time-transgressive by nature. To overcome this, we utilize the sequence stratigraphic model and well picks of Ponti et al. (2007) as a basis for mapping time-correlative sequence boundaries throughout our industry seismic reflection data from the present to the Pleistocene. From the Pleistocene to Miocene we identify additional sequence boundaries in our seismic reflection data from imaged sequence geometries and by correlating industry well formation tops. The sequence and formation top picks are then used to build 3-dimensional surfaces in the modeling program Gocad. From these surfaces we measure the change in thicknesses across the folds to obtain uplift rates between each sequence boundary. Our results show three distinct phases of deformation on the LA and SFS segments: an early period characterized by fault-propagation or structural wedge kinematics that terminates in the early Pleistocene, followed by a period of quiescence. The faults were subsequently reactivated in the middle Pleistocene and propagated upward to detachments, with the deformation characterized by fold-bend folding kinematics. Slip on the LA segment decreases to the West, suggesting lateral growth in that direction. Our work highlights the need to assess along-strike variability in slip rate when assessing the seismic hazard of a compressional fault, as marginal sites may significantly underestimate fault activity. Ponti, D. J. et al. A 3-Dimensional Model of Water-Bearing Sequences in the Dominguez Gap Region, Long Beach, California. US Geological Survey Open-File Report 1013 (2007).

Rescaled earthquake recurrence time statistics: application to microrepeaters

NASA Astrophysics Data System (ADS)

Goltz, Christian; Turcotte, Donald L.; Abaimov, Sergey G.; Nadeau, Robert M.; Uchida, Naoki; Matsuzawa, Toru

2009-01-01

Slip on major faults primarily occurs during `characteristic' earthquakes. The recurrence statistics of characteristic earthquakes play an important role in seismic hazard assessment. A major problem in determining applicable statistics is the short sequences of characteristic earthquakes that are available worldwide. In this paper, we introduce a rescaling technique in which sequences can be superimposed to establish larger numbers of data points. We consider the Weibull and log-normal distributions, in both cases we rescale the data using means and standard deviations. We test our approach utilizing sequences of microrepeaters, micro-earthquakes which recur in the same location on a fault. It seems plausible to regard these earthquakes as a miniature version of the classic characteristic earthquakes. Microrepeaters are much more frequent than major earthquakes, leading to longer sequences for analysis. In this paper, we present results for the analysis of recurrence times for several microrepeater sequences from Parkfield, CA as well as NE Japan. We find that, once the respective sequence can be considered to be of sufficient stationarity, the statistics can be well fitted by either a Weibull or a log-normal distribution. We clearly demonstrate this fact by our technique of rescaled combination. We conclude that the recurrence statistics of the microrepeater sequences we consider are similar to the recurrence statistics of characteristic earthquakes on major faults.

General design method for 3-dimensional, potential flow fields. Part 2: Computer program DIN3D1 for simple, unbranched ducts

NASA Technical Reports Server (NTRS)

Stanitz, J. D.

1985-01-01

The general design method for three-dimensional, potential, incompressible or subsonic-compressible flow developed in part 1 of this report is applied to the design of simple, unbranched ducts. A computer program, DIN3D1, is developed and five numerical examples are presented: a nozzle, two elbows, an S-duct, and the preliminary design of a side inlet for turbomachines. The two major inputs to the program are the upstream boundary shape and the lateral velocity distribution on the duct wall. As a result of these inputs, boundary conditions are overprescribed and the problem is ill posed. However, it appears that there are degrees of compatibility between these two major inputs and that, for reasonably compatible inputs, satisfactory solutions can be obtained. By not prescribing the shape of the upstream boundary, the problem presumably becomes well posed, but it is not clear how to formulate a practical design method under this circumstance. Nor does it appear desirable, because the designer usually needs to retain control over the upstream (or downstream) boundary shape. The problem is further complicated by the fact that, unlike the two-dimensional case, and irrespective of the upstream boundary shape, some prescribed lateral velocity distributions do not have proper solutions.

Paleolimnology of Lake Tanganyika, East Africa, over the past 100 k yr

USGS Publications Warehouse

Scholz, C.A.; King, J.W.; Ellis, G.S.; Swart, Peter K.; Stager, J.C.; Colman, Steven M.

2003-01-01

New sediment core data from a unique slow-sedimentation rate site in Lake Tanganyika contain a much longer and continuous record of limnological response to climate change than have been previously observed in equatorial regions of central Africa. The new core site was first located through an extensive seismic reflection survey over the Kavala Island Ridge (KIR), a sedimented basement high that separates the Kigoma and Kalemie Basins in Lake Tanganyika. Proxy analyses of paleoclimate response carried out on core T97-52V include paleomagnetic and index properties, TOC and isotopic analyses of organic carbon, and diatom and biogenic silica analyses. A robust age model based on 11 radiocarbon (AMS) dates indicates a linear, continuous sedimentation rate nearly an order of magnitude slower here compared to other core sites around the lake. This age model indicates continuous sedimentation over the past 79 k yr, and a basal age in excess of 100 k yr. The results of the proxy analyses for the past ??? 20 k yr are comparable to previous studies focused on that interval in Lake Tanganyika, and show that the lake was about 350 m lower than present at the Last Glacial Maximum (LGM). Repetitive peaks in TOC and corresponding drops in ??13C over the past 79 k yr indicate periods of high productivity and mixing above the T97-52V core site, probably due to cooler and perhaps windier conditions. From ??? 80 through ??? 58 k yr the ??13C values are relatively negative (-26 to -28???) suggesting predominance of algal contributions to bottom sediments at this site during this time. Following this interval there is a shift to higher values of ??13C, indicating a possible shift to C-4 pathway-dominated grassland-type vegetation in the catchment, and indicating cooler, dryer conditions from ??? 55 k yr through the LGM. Two seismic sequence boundaries are observed at shallow stratigraphic levels in the seismic reflection data, and the upper boundary correlates to a major discontinuity near the base of T97-52V. We interpret these discontinuities to reflect major, prolonged drops in lake level below the core site (393 m), with the lower boundary correlating to marine oxygen isotope Stage 6. This suggests that the previous glacial period was considerably cooler and more arid in the equatorial tropics than was the last glacial period.

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

NASA Astrophysics Data System (ADS)

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

2013-05-01

Chicxulub crater is one the three largest known impact craters on Earth, formed 66 Ma-old, with multi-ring basin morphology. Crater is located in northwestern Yucatan, southern Gulf of Mexico, with rim diameter of 200 km and crater center at Chicxulub Perto in the coastline. It is buried beneath the carbonate and evaporitic Cenozoic sequence. Study of the structure requires geophysics and drilling, with several boreholes drilled in the peninsula. The Yaxcopoil-1 borehole was drilled south of Merida, about 62 km from center, as part of the Chicxulub Scientific Drilling Program. One of the main objectives was to determine the role of the Chicxulub impact event in the K/Pg mass extinction and boundary events. We present a sedimentological and petrological study of the carbonate sequence in the interval from 404 m to 792 m overlying the K/Pg boundary. The well reached a depth of 1510.6 m. In this interval, we identified twelve units marked by different lithological and sedimentological changes, and supplemented by thin section analysis. Facies are composed mainly of marls, argillaceous, limestones, dolomitized limestones, calcareous breccias and calcarenites with shales thin beds. From the microfacies study we observed several major changes in the microfacies. From bottom of the sequence several textural changes cyclic from mudstone to bioclastic planktic foraminiferal wackestone, bioclastic packstone and some bioclastic grainstone. Two textures dominated in the calcareous sequence: bioclastic wackestone and packstone microfacies. From the microfacies study, we derived inferences on stable environmental conditions. We observed benthic and planktic foraminiferal layers. The benthic foraminifera strongly depend on environmental parameters, such as nutrient supply or oxygenation of the sea bottom water in the Paleocene and Eocene. Changes suggest occurrence of a progradational event, with a relative increase in sea level very slowly, with the sediment enough to overcome the elevation. In the last meters of Unit 2 (778-772 m), a series of thin layers of marl and calcareous shale interbedded with wackestone are interpreted as a transgressive event. In the first few meters of Unit 3 provides greater energy currents causing variations in the grain size. Petrographic observations show that planktonic and benthic facies are arranged as intermittent flows in parts of the unit, which points to flow currents. Predominance of coarse-grained facies rich in carbonates possibly indicates a prograding event into deep areas. In the sequence several possible changes in sea level are recorded, especially from Unit 5 to 8 Unit, where a possible limit between the Paleocene and Eocene is located between Unit 6 and Unit 7, at about 660 m. Biostratigraphy was obtained by zones corresponding to P4 and P5. In Unit 8 contains the first record of turbidite or storm deposits outer shelf environments that could be related to platform progradation. The Paleocene-Eocene thermal maximum represents a period of global warming and sea level rise. The sedimentological and micropaleontological changes may be correlated with the faunal turnover in the Gulf of Mexico, providing a complementary tool for biostratigraphic inferences.

Tracking the India-Arabia Transform Plate Boundary during Paleogene Times.

NASA Astrophysics Data System (ADS)

Rodriguez, M.; Huchon, P.; Chamot-Rooke, N. R. A.; Fournier, M.; Delescluse, M.

2014-12-01

The Zagros and Himalaya mountain belts are the most prominent reliefs built by continental collision. They respectively result from Arabia and India collision with Eurasia. Convergence motions at mountain belts induced most of plate reorganization events in the Indian Ocean during the Cenozoic. Although critical for paleogeographic reconstructions, the way relative motion between Arabia and India was accommodated prior to the formation of the Sheba ridge in the Gulf of Aden remains poorly understood. The India-Arabia plate-boundary belongs to the category of long-lived (~90-Ma) oceanic transform faults, thus providing a good case study to investigate the role of major kinematic events over the structural evolution of a long-lived transform system. A seismic dataset crossing the Owen Fracture Zone, the Owen Basin, and the Oman Margin was acquired to track the past locations of the India-Arabia plate boundary. We highlight the composite age of the Owen Basin basement, made of Paleocene oceanic crust drilled on its eastern part, and composed of pre-Maastrichtian continental crust overlaid by Early Paleocene ophiolites on its western side. A major transform fault system crossing the Owen Basin juxtaposed these two slivers of lithosphere of different ages, and controlled the uplift of marginal ridges along the Oman Margin. This transform system deactivated ~40 Ma ago, coeval with the onset of ultra-slow spreading at the Carlsberg Ridge. The transform boundary then jumped to the edge of the present-day Owen Ridge during the Late Eocene-Oligocene period, before seafloor spreading began at the Sheba Ridge. This migration of the plate boundary involved the transfer of a part of the Indian oceanic lithosphere accreted at the Carlsberg Ridge to the Arabian plate. The episode of plate transfer at the India-Arabia plate boundary during the Late Eocene-Oligocene interval is synchronous with a global plate reorganization event corresponding to geological events at the Zagros and Himalaya belts. The Owen Ridge uplifted later, in Late Miocene times, and is unrelated to any major migration of the India-Arabia boundary.

Expanding the World of Marine Bacterial and Archaeal Clades

PubMed Central

Yilmaz, Pelin; Yarza, Pablo; Rapp, Josephine Z.; Glöckner, Frank O.

2016-01-01

Determining which microbial taxa are out there, where they live, and what they are doing is a driving approach in marine microbial ecology. The importance of these questions is underlined by concerted, large-scale, and global ocean sampling initiatives, for example the International Census of Marine Microbes, Ocean Sampling Day, or Tara Oceans. Given decades of effort, we know that the large majority of marine Bacteria and Archaea belong to about a dozen phyla. In addition to the classically culturable Bacteria and Archaea, at least 50 “clades,” at different taxonomic depths, exist. These account for the majority of marine microbial diversity, but there is still an underexplored and less abundant portion remaining. We refer to these hitherto unrecognized clades as unknown, as their boundaries, names, and classifications are not available. In this work, we were able to characterize up to 92 of these unknown clades found within the bacterial and archaeal phylogenetic diversity currently reported for marine water column environments. We mined the SILVA 16S rRNA gene datasets for sequences originating from the marine water column. Instead of the usual subjective taxa delineation and nomenclature methods, we applied the candidate taxonomic unit (CTU) circumscription system, along with a standardized nomenclature to the sequences in newly constructed phylogenetic trees. With this new phylogenetic and taxonomic framework, we performed an analysis of ICoMM rRNA gene amplicon datasets to gain insights into the global distribution of the new marine clades, their ecology, biogeography, and interaction with oceanographic variables. Most of the new clades we identified were interspersed by known taxa with cultivated members, whose genome sequences are available. This result encouraged us to perform metabolic predictions for the novel marine clades using the PICRUSt approach. Our work also provides an update on the taxonomy of several phyla and widely known marine clades as our CTU approach breaks down these randomly lumped clades into smaller objectively calculated subgroups. Finally, all taxa were classified and named following standards compatible with the Bacteriological Code rules, enhancing their digitization, and comparability with future microbial ecological and taxonomy studies. PMID:26779174

Astronomical Pacing of Relative Sea Level through OAE2 from the Expanded SH#1 Core, Southern Utah

NASA Astrophysics Data System (ADS)

Jones, M. M.; Sageman, B. B.; Oakes, R. L.; Bralower, T. J.; Parker, A. L.; Leckie, R. M.

2017-12-01

Proximal marine strata of the North American Western Interior Basin (WIB) preserve a rich record of faunal turnover linked to Oceanic Anoxic Event 2 (OAE2 - 94 Ma), a pronounced Late Cretaceous carbon cycle perturbation interpreted to reflect global warming and possible ocean acidification. To develop a more robust synthesis of paleobiologic and geochemical datasets spanning this major Earth-life transition, we drilled a 131-meter core (SH#1) on the Kaiparowits Plateau of southern Utah, recovering the Cenomanian-Turonian Boundary (CTB) interval of the Tropic Shale. A 17.5-meter positive excursion in high-resolution bulk carbon isotope chemostratigraphy (δ13Corg) of SH#1 characterizes the most expanded and detailed record of OAE2 recovered from the WIB. Additionally, we detect statistically significant evidence for astronomical cycles in a companion δ13Ccarb dataset, using advanced spectral techniques (evolutive average spectral misfit). Bandpass filtering and tracing of the short eccentricity cycle (97 ka) permit development of a floating astronomical time scale (ATS) for the CTB interval. The presence of radioisotopic dates within the time series provides an independent check on astrochronologic interpretations. We attribute some depleted δ13Ccarb values in SH#1, which cyclically punctuate the OAE2 excursion, to preferential carbonate diagenesis driven by periodic sea level oscillations. Accordingly, major flooding surfaces in SH#1 correlate well to an existing sequence stratigraphic framework from shoreface facies of the Markagunt Plateau ( 100 km west). Comparing the ATS and sequence stratigraphic surfaces in SH#1, we observe that stable eccentricity cycles (405 ka) pace stratigraphic sequences and associated saw-toothed trends in sedimentation rate estimates through OAE2. Furthermore, short eccentricity cycles pace nested parasequences. These results confirm astronomical and, therefore, climatic pacing of relative sea level trends during OAE2 in the WIB. The ATS, δ13C chemostratigraphy, and basin-wide correlation of the CTB interval provide an expanded, temporally-resolved record of OAE2 within the chronostratigraphic framework of the WIB, and help to resolve rates of paleobiologic and paleoenvironmental change in the context of oscillating relative sea levels.

Stratigraphy and age estimate of Neogene shallow marine fossiliferous deposits in Brunei Darussalam (Ambug Hill, Tutong district)

NASA Astrophysics Data System (ADS)

Kocsis, László; Briguglio, Antonino; Roslim, Amajida; Razak, Hazirah; Ćorić, Stjepan; Frijia, Gianluca

2018-06-01

The Ambug Hill in Brunei is an exceptional geological site where a series of siliciclastic rocks crops out with some layers extremely rich in marine fossils. Such fossiliferous outcrops are extremely rare in the northern part of Borneo and their description is of primary importance as their fossil content can be used to correlate the regional depositional sequences with global biostratigraphic zonations. In this work we present for the first time a detailed sedimentary profile completed with Sr-isotopes and biostratigraphic dating. The succession is divided into four sedimentary units. The first unit comprises bioturbated sandstone followed by a second unit of clay-silt rich levels whose first 9.5 m contain rich marine fossil assemblages. Calcareous nannoplankton data indicate a Late Tortonian - Early Messinian (NN11) age, which is confirmed by Sr-isotope dating derived from bivalves giving a numerical age range from 8.3 to 6.2 My. After a major emersion surface, the third sedimentary unit of sand- and siltstone lacks suitable fossils for bio- and isotope stratigraphy. The age of emersion and the related sedimentary gap can be either correlated with the Me1 (7.25 My) or the Me2 (5.73 My) sequence boundary. A fourth, thin sedimentary unit is recognized on the top of the profile with silt- and claystone beds without age diagnostic remains and calcareous fossils.

The Joint Effects of Background Selection and Genetic Recombination on Local Gene Genealogies

PubMed Central

Zeng, Kai; Charlesworth, Brian

2011-01-01

Background selection, the effects of the continual removal of deleterious mutations by natural selection on variability at linked sites, is potentially a major determinant of DNA sequence variability. However, the joint effects of background selection and genetic recombination on the shape of the neutral gene genealogy have proved hard to study analytically. The only existing formula concerns the mean coalescent time for a pair of alleles, making it difficult to assess the importance of background selection from genome-wide data on sequence polymorphism. Here we develop a structured coalescent model of background selection with recombination and implement it in a computer program that efficiently generates neutral gene genealogies for an arbitrary sample size. We check the validity of the structured coalescent model against forward-in-time simulations and show that it accurately captures the effects of background selection. The model produces more accurate predictions of the mean coalescent time than the existing formula and supports the conclusion that the effect of background selection is greater in the interior of a deleterious region than at its boundaries. The level of linkage disequilibrium between sites is elevated by background selection, to an extent that is well summarized by a change in effective population size. The structured coalescent model is readily extendable to more realistic situations and should prove useful for analyzing genome-wide polymorphism data. PMID:21705759

Transcriptome-derived evidence supports recent polyploidization and a major phylogeographic division in Trithuria submersa (Hydatellaceae, Nymphaeales).

PubMed

Marques, Isabel; Montgomery, Sean A; Barker, Michael S; Macfarlane, Terry D; Conran, John G; Catalán, Pilar; Rieseberg, Loren H; Rudall, Paula J; Graham, Sean W

2016-04-01

Relatively little is known about species-level genetic diversity in flowering plants outside the eudicots and monocots, and it is often unclear how to interpret genetic patterns in lineages with whole-genome duplications. We addressed these issues in a polyploid representative of Hydatellaceae, part of the water-lily order Nymphaeales. We examined a transcriptome of Trithuria submersa for evidence of recent whole-genome duplication, and applied transcriptome-derived microsatellite (expressed-sequence tag simple-sequence repeat (EST-SSR)) primers to survey genetic variation in populations across its range in mainland Australia. A transcriptome-based Ks plot revealed at least one recent polyploidization event, consistent with fixed heterozygous genotypes representing underlying sets of homeologous loci. A strong genetic division coincides with a trans-Nullarbor biogeographic boundary. Patterns of 'allelic' variation (no more than two variants per EST-SSR genotype) and recently published chromosomal evidence are consistent with the predicted polyploidization event and substantial homozygosity underlying fixed heterozygote SSR genotypes, which in turn reflect a selfing mating system. The Nullarbor Plain is a barrier to gene flow between two deep lineages of T. submersa that may represent cryptic species. The markers developed here should also be useful for further disentangling species relationships, and provide a first step towards future genomic studies in Trithuria. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Comparative sequence stratigraphy of low-latitude versus high-latitude lacustrine rift basins: Seismic data examples from the East African and Baikal rifts

USGS Publications Warehouse

Scholz, C.A.; Moore, T.C.; Hutchinson, D.R.; Golmshtok, A. Ja; Klitgord, Kim D.; Kurotchkin, A.G.

1998-01-01

Lakes Baikal, Malawi and Tanganyika are the world's three largest rift valley lakes and are the classic modem examples of lacustrine rift basins. All the rift lakes are segmented into half-graben basins, and seismic reflection datasets reveal how this segmentation controls the filling of the rift basins through time. In the early stages of rifting, basins are fed primarily by flexural margin and axial margin drainage systems. At the climax of syn-rift sedimentation, however, when the basins are deeply subsided, almost all the margins are walled off by rift shoulder uplifts, and sediment flux into the basins is concentrated at accommodation zone and axial margin river deltas. Flexural margin unconformities are commonplace in the tropical lakes but less so in high-latitude Lake Baikal. Lake levels are extremely dynamic in the tropical lakes and in low-latitude systems in general because of the predominance of evaporation in the hydrologic cycle in those systems. Evaporation is minimized in relation to inflow in the high-latitude Lake Baikal and in most high-latitude systems, and consequently, major sequence boundaries tend to be tectonically controlled in that type of system. The acoustic stratigraphies of the tropical lakes are dominated by high-frequency and high-amplitude lake level shifts, whereas in high-latitude Lake Baikal, stratigraphic cycles are dominated by tectonism and sediment-supply variations.

Sentinel Hill Core Test 1: Facies Descriptions and Stratigraphic Reinterpretations of the Prince Creek and Schrader Bluff Formations, North Slope, Alaska

USGS Publications Warehouse

Flores, Romeo M.; Stricker, Gary D.; Decker, Paul L.; Myers, Mark D.

2007-01-01

The Sentinel Hill Core Test 1 well penetrated an intertonguing sequence of (1) the marine Schrader Bluff Formation in the depth intervals 950?1,180 ft and 690?751 ft, which consists of shoreface and offshore deposits that accumulated along a storm-dominated, barred shoreline; and (2) the nonmarine Prince Creek Formation in the depth intervals 751?950 ft and surface to 690 ft, which consists of fluvial channel, crevasse splay, backswamp, and ash fall deposits. The strata range in age from early Campanian to early Maastrichtian. An erosional contact at a depth of 690 ft at the base of the upper unit of the Prince Creek Formation is interpreted as a major regional sequence boundary, and the overlying conglomeratic fluvial channel deposits are interpreted to have accumulated in a paleovalley. In its more proximal reaches along the Colville River, channels of this paleovalley cut down 75 ft into the lowermost Prince Creek Formation and the uppermost Schrader Bluff Formation. Farther offshore, the equivalent surface to the aforementioned paleovalley appears to be a subtle discontinuity between middle and lower Schrader Bluff Formation shelfal marine strata. Still farther offshore, the equivalent paleovalley surface is interpreted as a marine mass-wasting surface that locally cuts through the lowermost Schrader Bluff Formation and into the underlying Seabee Formation.

Early Pleistocene occurrence of Acheulian technology in North China

NASA Astrophysics Data System (ADS)

Li, Xingwen; Ao, Hong; Dekkers, Mark J.; Roberts, Andrew P.; Zhang, Peng; Lin, Shan; Huang, Weiwen; Hou, Yamei; Zhang, Weihua; An, Zhisheng

2017-01-01

Acheulian tools with their associated level of cognizance heralded a major threshold in the evolution of hominin technology, culture and behavior. Thus, unraveling occurrence ages of Acheulian technology across different regions worldwide constitutes a key aspect of understanding the archeology of early human evolution. Here we present a magneto-cyclochronology for the Acheulian assemblage from Sanmenxia Basin, Loess Plateau, North China. Our results place a sequence of stable normal and reversed paleomagnetic polarities within a regional lithostratigraphic context. The Acheulian assemblage is dated to be older than the Matuyama-Brunhes boundary at 0.78 Ma, and is found in strata that are probably equivalent to a weak paleosol subunit within loess layer L9 in the Chinese loess-paleosol sequence, which corresponds to marine isotope stage (MIS) 23, a relatively subdued interglacial period with age range of ∼0.89-0.92 Ma. This age of ∼0.9 Ma implies that Acheulian stone tools were unambiguously present in North China during the Early Pleistocene. It distinctly enlarges the geographic distribution of Acheulian technology and brings its occurrence in North China back into the Early Pleistocene, which is contemporaneous with its first emergence in Europe. Combined with other archeological records, the larger area over which Acheulian technology existed in East Asia during the terminal Early Pleistocene has important implications for understanding early human occupation of North China.

Accurate indel prediction using paired-end short reads

PubMed Central

2013-01-01

Background One of the major open challenges in next generation sequencing (NGS) is the accurate identification of structural variants such as insertions and deletions (indels). Current methods for indel calling assign scores to different types of evidence or counter-evidence for the presence of an indel, such as the number of split read alignments spanning the boundaries of a deletion candidate or reads that map within a putative deletion. Candidates with a score above a manually defined threshold are then predicted to be true indels. As a consequence, structural variants detected in this manner contain many false positives. Results Here, we present a machine learning based method which is able to discover and distinguish true from false indel candidates in order to reduce the false positive rate. Our method identifies indel candidates using a discriminative classifier based on features of split read alignment profiles and trained on true and false indel candidates that were validated by Sanger sequencing. We demonstrate the usefulness of our method with paired-end Illumina reads from 80 genomes of the first phase of the 1001 Genomes Project ( http://www.1001genomes.org) in Arabidopsis thaliana. Conclusion In this work we show that indel classification is a necessary step to reduce the number of false positive candidates. We demonstrate that missing classification may lead to spurious biological interpretations. The software is available at: http://agkb.is.tuebingen.mpg.de/Forschung/SV-M/. PMID:23442375

The joint effects of background selection and genetic recombination on local gene genealogies.

PubMed

Zeng, Kai; Charlesworth, Brian

2011-09-01

Background selection, the effects of the continual removal of deleterious mutations by natural selection on variability at linked sites, is potentially a major determinant of DNA sequence variability. However, the joint effects of background selection and genetic recombination on the shape of the neutral gene genealogy have proved hard to study analytically. The only existing formula concerns the mean coalescent time for a pair of alleles, making it difficult to assess the importance of background selection from genome-wide data on sequence polymorphism. Here we develop a structured coalescent model of background selection with recombination and implement it in a computer program that efficiently generates neutral gene genealogies for an arbitrary sample size. We check the validity of the structured coalescent model against forward-in-time simulations and show that it accurately captures the effects of background selection. The model produces more accurate predictions of the mean coalescent time than the existing formula and supports the conclusion that the effect of background selection is greater in the interior of a deleterious region than at its boundaries. The level of linkage disequilibrium between sites is elevated by background selection, to an extent that is well summarized by a change in effective population size. The structured coalescent model is readily extendable to more realistic situations and should prove useful for analyzing genome-wide polymorphism data.

Investigation of intraplate seismicity near the sites of the 2012 major strike-slip earthquakes in the eastern Indian Ocean through a passive-source OBS experiment

NASA Astrophysics Data System (ADS)

Guo, L.; Lin, J.; Yang, H.

2017-12-01

The 11 April 2012 Mw8.6 earthquake off the coast of Sumatra in the eastern Indian Ocean was the largest strike-slip earthquake ever recorded. The 2012 mainshock and its aftershock sequences were associated with complex slip partitioning and earthquake interactions of an oblique convergent system, in a new plate boundary zone between the Indian and Australian plates. The detail processes of the earthquake interactions and correlation with seafloor geological structure, however, are still poorly known. During March-April 2017, an array of broadband OBS (ocean bottom seismometer) were deployed, for the first time, near the epicenter region of the 2012 earthquake sequence. During post-expedition data processing, we identified 70 global earthquakes from the National Earthquake Information Center (NEIC) catalog that occurred during our OBS deployment period. We then picked P and S waves in the seismic records and analyzed their arrival times. We further identified and analyzed multiple local earthquakes and examined their relationship to the observed seafloor structure (fracture zones, seafloor faults, etc.) and the state of stresses in this region of the eastern Indian Ocean. The ongoing analyses of the data obtained from this unique seismic experiment are expected to provide important constraints on the large-scale intraplate deformation in this part of the eastern Indian Ocean.

Additive erosion reduction influences in the turbulent boundary layer

NASA Astrophysics Data System (ADS)

Buckingham, A. C.

1981-05-01

Results of a sequence of flow, heat and mass transfer calculations are presented which theoretically characterize the erosive environment at the wall surface of refractory metal coated and uncoated gun barrels. The theoretical results include analysis of the wall surface temperature, heat flux, and shear stress time histories on thin (10 mil.) Cr, Mo, Nb, and Ta plated steel barrel walls as uncoated steel walls. The calculations combine effects of a number of separate processes which were previously (and purposely) studied individually. These include solid particle additive concentrations, gas wall thermochemical influences, and transient turbulent wall boundary layer flow with multicomponent molecular diffusion and reactions from interaction of propellant combustion and the eroding surface. The boundary layer model includes particulate additive concentrations as well as propellant combustion products, considered for the present to be in the local thermochemical equilibrium.

Incorporating Inquiry-Based Learning in the Calculus Sequence: A Most Challenging Endeavour

ERIC Educational Resources Information Center

McLoughlin, M. Padraig M. M.

2009-01-01

A course in the Calculus sequence is arguably the most difficult course in which inquiry-based learning (IBL) can be achieved with any degree of success within the curriculum in part due to: (1) the plethora of majors taking Calculus to which the sequence relates to their majors in what is considered an "applied" manner; and (2) the…

The Impact of the Atlantic Cold Tongue on West African Monsoon Onset in Regional Model Simulations for 1998-2002

NASA Technical Reports Server (NTRS)

Druyan, Leonard M.; Fulakeza, Matthew B.

2014-01-01

The Atlantic cold tongue (ACT) develops during spring and early summer near the Equator in the Eastern Atlantic Ocean and Gulf of Guinea. The hypothesis that the ACT accelerates the timing of West African monsoon (WAM) onset is tested by comparing two regional climate model (RM3) simulation ensembles. Observed sea surface temperatures (SST) that include the ACT are used to force a control ensemble. An idealized, warm SST perturbation is designed to represent lower boundary forcing without the ACT for the experiment ensemble. Summer simulations forced by observed SST and reanalysis boundary conditions for each of five consecutive years are compared to five parallel runs forced by SST with the warm perturbation. The article summarizes the sequence of events leading to the onset of the WAM in the Sahel region. The representation of WAM onset in RM3 simulations is examined and compared to Tropical Rainfall Measuring Mission (TRMM), Global Precipitation Climatology Project (GPCP) and reanalysis data. The study evaluates the sensitivity of WAM onset indicators to the presence of the ACT by analysing the differences between the two simulation ensembles. Results show that the timing of major rainfall events and therefore theWAM onset in the Sahel are not sensitive to the presence of the ACT. However, the warm SST perturbation does increase downstream rainfall rates over West Africa as a consequence of enhanced specific humidity and enhanced northward moisture flux in the lower troposphere.

The influence of context boundaries on memory for the sequential order of events.

PubMed

DuBrow, Sarah; Davachi, Lila

2013-11-01

Episodic memory allows people to reexperience the past by recovering the sequences of events that characterize those prior experiences. Although experience is continuous, people are able to selectively retrieve and reexperience more discrete episodes from their past, raising the possibility that some elements become tightly related to each other in memory, whereas others do not. The current series of experiments was designed to ask how shifts in context during an experience influence how people remember the past. Specifically, we asked how context shifts influence the ability to remember the relative order of past events, a hallmark of episodic memory. We found that memory for the order of events was enhanced within, rather than across, context shifts, or boundaries (Experiment 1). Next, we showed that this relative enhancement in order memory was eliminated when across-item associative processing was disrupted (Experiment 2), suggesting that context shifts have a selective effect on sequential binding. Finally, we provide evidence that the act of making order memory judgments involves the reactivation of representations that bridged the tested items (Experiment 3). Together, these data suggest that boundaries may serve to parse continuous experience into sequences of contextually related events and that this organization facilitates remembering the temporal order of events that share the same context. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Construction of a small Mus musculus repetitive DNA library: identification of a new satellite sequence in Mus musculus.

PubMed Central

Pietras, D F; Bennett, K L; Siracusa, L D; Woodworth-Gutai, M; Chapman, V M; Gross, K W; Kane-Haas, C; Hastie, N D

1983-01-01

We report the construction of a small library of recombinant plasmids containing Mus musculus repetitive DNA inserts. The repetitive cloned fraction was derived from denatured genomic DNA by reassociation to a Cot value at which repetitive, but not unique, sequences have reannealed followed by exhaustive S1 nuclease treatment to degrade single stranded DNA. Initial characterizations of this library by colony filter hybridizations have led to the identification of a previously undetected M. musculus minor satellite as well as to clones containing M. musculus major satellite sequences. This new satellite is repeated 10-20 times less than the major satellite in the M. musculus genome. It has a repeat length of 130 nucleotides compared with the M. musculus major satellite with a repeat length of 234 nucleotides. Sequence analysis of the minor satellite has shown that it has a 29 base pair region with extensive homology to one of the major satellite repeating subunits. We also show by in situ hybridization that this minor satellite sequence is located at the centromeres and possibly the arms of at least half the M musculus chromosomes. Sequences related to the minor satellite have been found in the DNA of a related Mus species, Mus spretus, and may represent the major satellite of that species. Images PMID:6314268

Quantifying assemblage turnover and species contributions at ecologic boundaries.

PubMed

Hayek, Lee-Ann C; Wilson, Brent

2013-01-01

Not all boundaries, whether stratigraphical or geographical, are marked by species-level changes in community composition. For example, paleodata for some sites do not show readily discernible glacial-interglacial contrasts. Rather, the proportional abundances of species can vary subtly between glacials and interglacials. This paper presents a simple quantitative measure of assemblage turnover (assemblage turnover index, ATI) that uses changes in species' proportional abundances to identify intervals of community change. A second, functionally-related index (conditioned-on-boundary index, CoBI) identifies species contributions to the total assemblage turnover. With these measures we examine benthonic foraminiferal assemblages to assess glacial/interglacial contrasts at abyssal depths. Our results indicate that these measures, ATI and CoBI, have potential as sequence stratigraphic tools in abyssal depth deposits. Many peaks in the set of values of ATI coincide with terminations at the end of glaciations and delineate peak-bounded ATI intervals (PATIs) separated by boundaries that approximate to glacial terminations and to transgressions at neritic depths. These measures, however, can be used to evaluate the assemblage turnover and composition at any defined ecological or paleoecological boundary. The section used is from Ocean Drilling Program (OPD) Hole 994C, drilled on the Blake Ridge, offshore SE USA.

Quantifying Assemblage Turnover and Species Contributions at Ecologic Boundaries

PubMed Central

Hayek, Lee-Ann C.; Wilson, Brent

2013-01-01

Not all boundaries, whether stratigraphical or geographical, are marked by species-level changes in community composition. For example, paleodata for some sites do not show readily discernible glacial-interglacial contrasts. Rather, the proportional abundances of species can vary subtly between glacials and interglacials. This paper presents a simple quantitative measure of assemblage turnover (assemblage turnover index, ATI) that uses changes in species' proportional abundances to identify intervals of community change. A second, functionally-related index (conditioned-on-boundary index, CoBI) identifies species contributions to the total assemblage turnover. With these measures we examine benthonic foraminiferal assemblages to assess glacial/interglacial contrasts at abyssal depths. Our results indicate that these measures, ATI and CoBI, have potential as sequence stratigraphic tools in abyssal depth deposits. Many peaks in the set of values of ATI coincide with terminations at the end of glaciations and delineate peak-bounded ATI intervals (PATIs) separated by boundaries that approximate to glacial terminations and to transgressions at neritic depths. These measures, however, can be used to evaluate the assemblage turnover and composition at any defined ecological or paleoecological boundary. The section used is from Ocean Drilling Program (OPD) Hole 994C, drilled on the Blake Ridge, offshore SE USA. PMID:24130679

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou Huanqiang; School of Physical Sciences, University of Queensland, Brisbane, Queensland 4072; Barthel, Thomas

We investigate boundary critical phenomena from a quantum-information perspective. Bipartite entanglement in the ground state of one-dimensional quantum systems is quantified using the Renyi entropy S{sub {alpha}}, which includes the von Neumann entropy ({alpha}{yields}1) and the single-copy entanglement ({alpha}{yields}{infinity}) as special cases. We identify the contribution of the boundaries to the Renyi entropy, and show that there is an entanglement loss along boundary renormalization group (RG) flows. This property, which is intimately related to the Affleck-Ludwig g theorem, is a consequence of majorization relations between the spectra of the reduced density matrix along the boundary RG flows. We also pointmore » out that the bulk contribution to the single-copy entanglement is half of that to the von Neumann entropy, whereas the boundary contribution is the same.« less

An improved procedure for determining grain boundary diffusion coefficients from averaged concentration profiles

NASA Astrophysics Data System (ADS)

Gryaznov, D.; Fleig, J.; Maier, J.

2008-03-01

Whipple's solution of the problem of grain boundary diffusion and Le Claire's relation, which is often used to determine grain boundary diffusion coefficients, are examined for a broad range of ratios of grain boundary to bulk diffusivities Δ and diffusion times t. Different reasons leading to errors in determining the grain boundary diffusivity (DGB) when using Le Claire's relation are discussed. It is shown that nonlinearities of the diffusion profiles in lnCav-y6/5 plots and deviations from "Le Claire's constant" (-0.78) are the major error sources (Cav=averaged concentration, y =coordinate in diffusion direction). An improved relation (replacing Le Claire's constant) is suggested for analyzing diffusion profiles particularly suited for small diffusion lengths (short times) as often required in diffusion experiments on nanocrystalline materials.

Genetic Diversity and Phylogenetic Analysis of the Iranian Leishmania Parasites Based on HSP70 Gene PCR-RFLP and Sequence Analysis.

PubMed

Nemati, Sara; Fazaeli, Asghar; Hajjaran, Homa; Khamesipour, Ali; Anbaran, Mohsen Falahati; Bozorgomid, Arezoo; Zarei, Fatah

2017-08-01

Despite the broad distribution of leishmaniasis among Iranians and animals across the country, little is known about the genetic characteristics of the causative agents. Applying both HSP70 PCR-RFLP and sequence analyses, this study aimed to evaluate the genetic diversity and phylogenetic relationships among Leishmania spp. isolated from Iranian endemic foci and available reference strains. A total of 36 Leishmania isolates from almost all districts across the country were genetically analyzed for the HSP70 gene using both PCR-RFLP and sequence analysis. The original HSP70 gene sequences were aligned along with homologous Leishmania sequences retrieved from NCBI, and subjected to the phylogenetic analysis. Basic parameters of genetic diversity were also estimated. The HSP70 PCR-RFLP presented 3 different electrophoretic patterns, with no further intraspecific variation, corresponding to 3 Leishmania species available in the country, L. tropica, L. major, and L. infantum. Phylogenetic analyses presented 5 major clades, corresponding to 5 species complexes. Iranian lineages, including L. major, L. tropica, and L. infantum, were distributed among 3 complexes L. major, L. tropica, and L. donovani. However, within the L. major and L. donovani species complexes, the HSP70 phylogeny was not able to distinguish clearly between the L. major and L. turanica isolates, and between the L. infantum, L. donovani, and L. chagasi isolates, respectively. Our results indicated that both HSP70 PCR-RFLP and sequence analyses are medically applicable tools for identification of Leishmania species in Iranian patients. However, the reduced genetic diversity of the target gene makes it inevitable that its phylogeny only resolves the major groups, namely, the species complexes.

Paleoclimatic analyses of middle Eocene through Oligocene planktic foraminiferal faunas

USGS Publications Warehouse

Keller, G.

1983-01-01

Quantitative faunal analyses and oxygen isotope ranking of individual planktic foraminiferal species from deep sea sequences of three oceans are used to make paleoceanographic and paleoclimatic inferences. Species grouped into surface, intermediate and deep water categories based on ??18O values provide evidence of major changes in water-mass stratification, and individual species abundances indicate low frequency cool-warm oscillations. These data suggest that relatively stable climatic phases with minor cool-warm oscillations of ???0.5 m.y. frequency are separated by rapid cooling events during middle Eocene to early Oligocene time. Five major climatic phases are evident in the water-mass stratification between middle Eocene through Oligocene time. Phase changes occur at P14/P15, P15/P16, P20/P21 and P21/P22 Zone boundaries and are marked by major faunal turnovers, rapid cooling in the isotope record, hiatuses and changes in the eustatic sea level. A general cooling trend between middle Eocene to early late Oligocene is indicated by the successive replacement of warm middle Eocene surface water species by cooler late Eocene intermediate water species and still cooler Oligocene intermediate and deep water species. Increased water-mass stratification in the latest Eocene (P17), indicated by the coexistence of surface, intermediate and deep dwelling species groups, suggest that increased thermal gradients developed between the equator and poles nearly coincident with the development of the psychrosphere. This pattern may be related to significant ice accumulation between late Eocene and early late Oligocene time. ?? 1983.

Rendezvous terminal phase automatic braking sequencing and targeting. [for space shuttle orbiter

NASA Technical Reports Server (NTRS)

Kachmar, P. M.

1973-01-01

The purpose of the rendezvous terminal phase braking program is to provide the means of automatically bringing the primary orbiter within desired station keeping boundaries relative to the target satellite. A detailed discussion is presented on the braking program and its navigation, targeting, and guidance functions.

The Papillomavirus Episteme: a major update to the papillomavirus sequence database.

PubMed

Van Doorslaer, Koenraad; Li, Zhiwen; Xirasagar, Sandhya; Maes, Piet; Kaminsky, David; Liou, David; Sun, Qiang; Kaur, Ramandeep; Huyen, Yentram; McBride, Alison A

2017-01-04

The Papillomavirus Episteme (PaVE) is a database of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. This update describes the addition of major new features. The papillomavirus genomes within PaVE have been further annotated, and now includes the major spliced mRNA transcripts. Viral genes and transcripts can be visualized on both linear and circular genome browsers. Evolutionary relationships among PaVE reference protein sequences can be analysed using multiple sequence alignments and phylogenetic trees. To assist in viral discovery, PaVE offers a typing tool; a simplified algorithm to determine whether a newly sequenced virus is novel. PaVE also now contains an image library containing gross clinical and histopathological images of papillomavirus infected lesions. Database URL: https://pave.niaid.nih.gov/. Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

The Role of ICT in Bridge-Building and Social Inclusion: Theory, Policy and Practice Issues

ERIC Educational Resources Information Center

Austin, Roger

2006-01-01

This paper reports on the evaluation of a major programme which is using telecommunications to link teachers and pupils both across the political boundary between Northern Ireland and the Republic of Ireland and across the boundaries of "mainstream" schooling and those children in "special schools". The paper examines the…

Digital geologic and geophysical data of Bangladesh

USGS Publications Warehouse

Persits, Feliks M.; Wandrey, C.J.; Milici, R.C.; Manwar, Abdullah

1997-01-01

The data set for these maps includes arcs, polygons, and labels that outline and describe the general geologic age and geophysical fields of Bangladesh. Political boundaries are provided to show the general location of administrative regions and state boundaries. Major base topographic data like cities, rivers, etc. were derived from the same paper map source as the geology.

Allostratigraphy of the U.S. middle Atlantic continental margin; characteristics, distribution, and depositional history of principal unconformity-bounded upper Cretaceous and Cenozoic sedimentary units

USGS Publications Warehouse

Poag, C. Wylie; Ward, Lauck W.

1993-01-01

Publication of Volumes 93 and 95 ('The New Jersey Transect') of the Deep Sea Drilling Project's Initial Reports completed a major phase of geological and geophysical research along the middle segment of the U. S. Atlantic continental margin. Relying heavily on data from these and related published records, we have integrated outcrop, borehole, and seismic-reflection data from this large area (500,000 km^2 ) to define the regional allostratigraphic framework for Upper Cretaceous and Cenozoic sedimentary rocks. The framework consists of 12 alloformations, which record the Late Cretaceous and Cenozoic depositional history of the contiguous Baltimore Canyon trough (including its onshore margin) and Hatteras basin (northern part). We propose stratotype sections for each alloformation and present a regional allostratigraphic reference section, which crosses these basins from the inner edge of the coastal plain to the inner edge of the abyssal plain. Selected supplementary reference sections on the coastal plain allow observation of the alloformations and their bounding unconformities in outcrop. Our analyses show that sediment supply and its initial dispersal on the middle segment of the U. S. Atlantic margin have been governed, in large part, by hinterland tectonism and subsequently have been modified by paleoclimate, sea-level changes, and oceanic current systems. Notable events in the Late Cretaceous to Holocene sedimentary evolution of this margin include (1) development of continental-rise depocenters in the northern part of the Hatteras basin during the Late Cretaceous; (2) the appear ance of a dual shelf-edge system, a marked decline in siliciclastic sediment accumulation rates, and widespread acceleration of carbonate production during high sea levels of the Paleogene; (3) rapid deposition and progradation of thick terrigenous delta complexes and development of abyssal depocenters during the middle Miocene to Quaternary interval; and (4) deep incision of the shelf edge by submarine canyons, especially during the Pleistocene. Massive downslope gravity flows have dominated both the depositional and erosional history of the middle segment of the U. S. Atlantic Continental Slope and Rise during most of the last 84 million years. The importance of periodic widespread erosion is recorded by well-documented unconformities, many of which can be traced from coastal-plain outcrops to coreholes on the continental slope and lower continental rise. These unconformities form the boundaries of the 12 allostratigraphic units we formally propose herein. Seven of the unconformities correlate with supercycle boundaries (sequence boundaries) that characterize the Exxon sequence-stratigraphy model.

Visualization of the internal globus pallidus: sequence and orientation for deep brain stimulation using a standard installation protocol at 3.0 Tesla.

PubMed

Nölte, Ingo S; Gerigk, Lars; Al-Zghloul, Mansour; Groden, Christoph; Kerl, Hans U

2012-03-01

Deep-brain stimulation (DBS) of the internal globus pallidus (GPi) has shown remarkable therapeutic benefits for treatment-resistant neurological disorders including dystonia and Parkinson's disease (PD). The success of the DBS is critically dependent on the reliable visualization of the GPi. The aim of the study was to evaluate promising 3.0 Tesla magnetic resonance imaging (MRI) methods for pre-stereotactic visualization of the GPi using a standard installation protocol. MRI at 3.0 T of nine healthy individuals and of one patient with PD was acquired (FLAIR, T1-MPRAGE, T2-SPACE, T2*-FLASH2D, susceptibility-weighted imaging mapping (SWI)). Image quality and visualization of the GPi for each sequence were assessed by two neuroradiologists independently using a 6-point scale. Axial, coronal, and sagittal planes of the T2*-FLASH2D images were compared. Inter-rater reliability, contrast-to-noise ratios (CNR) and signal-to-noise ratios (SNR) for the GPi were determined. For illustration, axial T2*-FLASH2D images were fused with a section schema of the Schaltenbrand-Wahren stereotactic atlas. The GPi was best and reliably visualized in axial and to a lesser degree on coronal T2*-FLASH2D images. No major artifacts in the GPi were observed in any of the sequences. SWI offered a significantly higher CNR for the GPi compared to standard T2-weighted imaging using the standard parameters. The fusion of the axial T2*-FLASH2D images and the atlas projected the GPi clearly in the boundaries of the section schema. Using a standard installation protocol at 3.0 T T2*-FLASH2D imaging (particularly axial view) provides optimal and reliable delineation of the GPi.

Characterization of the human gene (TBXAS1) encoding thromboxane synthase.

PubMed

Miyata, A; Yokoyama, C; Ihara, H; Bandoh, S; Takeda, O; Takahashi, E; Tanabe, T

1994-09-01

The gene encoding human thromboxane synthase (TBXAS1) was isolated from a human EMBL3 genomic library using human platelet thromboxane synthase cDNA as a probe. Nucleotide sequencing revealed that the human thromboxane synthase gene spans more than 75 kb and consists of 13 exons and 12 introns, of which the splice donor and acceptor sites conform to the GT/AG rule. The exon-intron boundaries of the thromboxane synthase gene were similar to those of the human cytochrome P450 nifedipine oxidase gene (CYP3A4) except for introns 9 and 10, although the primary sequences of these enzymes exhibited 35.8% identity each other. The 1.2-kb of the 5'-flanking region sequence contained potential binding sites for several transcription factors (AP-1, AP-2, GATA-1, CCAAT box, xenobiotic-response element, PEA-3, LF-A1, myb, basic transcription element and cAMP-response element). Primer-extension analysis indicated the multiple transcription-start sites, and the major start site was identified as an adenine residue located 142 bases upstream of the translation-initiation site. However, neither a typical TATA box nor a typical CAAT box is found within the 100-b upstream of the translation-initiation site. Southern-blot analysis revealed the presence of one copy of the thromboxane synthase gene per haploid genome. Furthermore, a fluorescence in situ hybridization study revealed that the human gene for thromboxane synthase is localized to band q33-q34 of the long arm of chromosome 7. A tissue-distribution study demonstrated that thromboxane synthase mRNA is widely expressed in human tissues and is particularly abundant in peripheral blood leukocyte, spleen, lung and liver. The low but significant levels of mRNA were observed in kidney, placenta and thymus.

Interpersonal boundaries in clinical nursing education: An exploratory Canadian qualitative study.

PubMed

Zieber, Mark P; Hagen, Brad

2009-11-01

Clinical nursing instructors and students spend considerable time together, and share clinical experiences that can be intense and emotionally charged. Yet despite clinical teaching being so commonplace, little is known about how clinical instructors experience relationships with their students, and how they negotiate interpersonal boundaries within these relationships. In-depth unstructured interviews were conducted with eight clinical nursing instructors in Western Canada, to explore how they defined and constructed interpersonal boundaries with their students during clinical nursing teaching rotations. The data analysis resulted in four major themes: "the fluidity of boundaries", "personal sharing and self-disclosure", "time dependent", and "the touchy topic of touch". All participants agreed that rigid boundaries were occasionally needed to prevent flagrant boundary violations, such as sexual relations with students. However, participants also stated that overall, the unique and complex nature of clinical teaching called for instructors to have fluid and flexible interpersonal boundaries with students. The nature of clinical nursing education may encourage instructors to form relationships with their students that are characterized by flexible and fluid interpersonal boundaries. Clinical nursing instructors may benefit from opportunities to dialogue with trusted colleagues about the unique nature of relationships and boundaries with students during clinical teaching.

Seamless contiguity method for parallel segmentation of remote sensing image

NASA Astrophysics Data System (ADS)

Wang, Geng; Wang, Guanghui; Yu, Mei; Cui, Chengling

2015-12-01

Seamless contiguity is the key technology for parallel segmentation of remote sensing data with large quantities. It can be effectively integrate fragments of the parallel processing into reasonable results for subsequent processes. There are numerous methods reported in the literature for seamless contiguity, such as establishing buffer, area boundary merging and data sewing. et. We proposed a new method which was also based on building buffers. The seamless contiguity processes we adopt are based on the principle: ensuring the accuracy of the boundary, ensuring the correctness of topology. Firstly, block number is computed based on data processing ability, unlike establishing buffer on both sides of block line, buffer is established just on the right side and underside of the line. Each block of data is segmented respectively and then gets the segmentation objects and their label value. Secondly, choose one block(called master block) and do stitching on the adjacent blocks(called slave block), process the rest of the block in sequence. Through the above processing, topological relationship and boundaries of master block are guaranteed. Thirdly, if the master block polygons boundaries intersect with buffer boundary and the slave blocks polygons boundaries intersect with block line, we adopt certain rules to merge and trade-offs them. Fourthly, check the topology and boundary in the buffer area. Finally, a set of experiments were conducted and prove the feasibility of this method. This novel seamless contiguity algorithm provides an applicable and practical solution for efficient segmentation of massive remote sensing image.

A systematic comparison between visual cues for boundary detection.

PubMed

Mély, David A; Kim, Junkyung; McGill, Mason; Guo, Yuliang; Serre, Thomas

2016-03-01

The detection of object boundaries is a critical first step for many visual processing tasks. Multiple cues (we consider luminance, color, motion and binocular disparity) available in the early visual system may signal object boundaries but little is known about their relative diagnosticity and how to optimally combine them for boundary detection. This study thus aims at understanding how early visual processes inform boundary detection in natural scenes. We collected color binocular video sequences of natural scenes to construct a video database. Each scene was annotated with two full sets of ground-truth contours (one set limited to object boundaries and another set which included all edges). We implemented an integrated computational model of early vision that spans all considered cues, and then assessed their diagnosticity by training machine learning classifiers on individual channels. Color and luminance were found to be most diagnostic while stereo and motion were least. Combining all cues yielded a significant improvement in accuracy beyond that of any cue in isolation. Furthermore, the accuracy of individual cues was found to be a poor predictor of their unique contribution for the combination. This result suggested a complex interaction between cues, which we further quantified using regularization techniques. Our systematic assessment of the accuracy of early vision models for boundary detection together with the resulting annotated video dataset should provide a useful benchmark towards the development of higher-level models of visual processing. Copyright © 2016 Elsevier Ltd. All rights reserved.

IDENTIFICATION OF THE LITHIUM DEPLETION BOUNDARY AND AGE OF THE SOUTHERN OPEN CLUSTER BLANCO 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cargile, P. A.; James, D. J.; Jeffries, R. D., E-mail: p.cargile@vanderbilt.ed

2010-12-20

We present results from a spectroscopic study of the very low mass members of the Southern open cluster Blanco 1 using the Gemini-N telescope. We obtained intermediate resolution (R {approx} 4400) GMOS spectra for 15 cluster candidate members with I {approx} 14-20 mag, and employed a series of membership criteria-proximity to the cluster's sequence in an I/I - K{sub s} color-magnitude diagram (CMD), kinematics agreeing with the cluster systemic motion, magnetic activity as a youth indicator-to classify 10 of these objects as probable cluster members. For these objects, we searched for the presence of the Li I 6708 A featuremore » to identify the lithium depletion boundary (LDB) in Blanco 1. The I/I - K{sub s} CMD shows a clear mass segregation in the Li distribution along the cluster sequence; namely, all higher mass stars are found to be Li poor, while lower mass stars are found to be Li rich. The division between Li-poor and Li-rich (i.e., the LDB) in Blanco 1 is found at I = 18.78 {+-} 0.24 and I - K{sub s} = 3.05 {+-} 0.10. Using current pre-main-sequence evolutionary models, we determine an LDB age of 132 {+-} 24 Myr. Comparing our derived LDB age to upper-main-sequence isochrone ages for Blanco 1, as well as for other open clusters with identified LDBs, we find good chronometric consistency when using stellar evolution models that incorporate a moderate degree of convective core overshoot.« less

Paleocene to Middle Miocene planktic foraminifera of the southwestern Salisbury Embayment, Virginia and Maryland: biostratigraphy, allostratigraphy, and sequence stratigraphy

USGS Publications Warehouse

Poag, C.W.; Commeau, J.A.

1995-01-01

The Paleocene to Middle Miocene sedimentary fill of the southwestern Salisbury Embayment contains a fragmental depositional record, interrupted by numerous local diastems and regional unconformities. Using planktic foraminiferal biostratigraphy, 15 unconformity-bounded depositional units have been identified, assigned to six formations and seven alloformations previously recognized in the embayment. The units correlate with second- and third-order sequences of the Exxon sequence stratigraphy model, and include transgressive and highstand systems tracts. Alloformation, formation, and sequence boundaries are marked by abrupt, scoured, burrowed, erosional surfaces, which display lag deposits, biostratigraphic gaps, and intense reworking of microfossils above and below the boundaries.Paleocene deposits represent the upper parts of upper Pleocene Biochronozones P4 and P5, and rest uncomformably  on Cretaceous sedimentary beds of various ages (Maastrichtian to Albian). Lower Eocene deposits represent parts of Biochronozones P6 and P9. Middle Eocene strata represent mainly parts of Biochronozones P11, P12, and P14. Upper Eocene sediments include parts of Biochronozones P15, P16, and P17. Oligocene deposits encompass parts of Biochronozones. N4b to N7 undifferentiated, P21a, and, perhaps, N4a. Lower Miocene deposits encompass parts of Biochronozones N4b to N7 undifferentiated. Middle Miocene strata represent mainly parts of Biochronorones N8, N9, and N10.Nine plates of scanning electron micrographs illustrate the principal planktic foraminifera used to establish the biostratigraphic framework. Two new informal formine of Praeterenuitella praegemma Li, 1987, are introduced.

cisprimertool: software to implement a comparative genomics strategy for the development of conserved intron scanning (CIS) markers.

PubMed

Jayashree, B; Jagadeesh, V T; Hoisington, D

2008-05-01

The availability of complete, annotated genomic sequence information in model organisms is a rich resource that can be extended to understudied orphan crops through comparative genomic approaches. We report here a software tool (cisprimertool) for the identification of conserved intron scanning regions using expressed sequence tag alignments to a completely sequenced model crop genome. The method used is based on earlier studies reporting the assessment of conserved intron scanning primers (called CISP) within relatively conserved exons located near exon-intron boundaries from onion, banana, sorghum and pearl millet alignments with rice. The tool is freely available to academic users at http://www.icrisat.org/gt-bt/CISPTool.htm. © 2007 ICRISAT.

Effect of boundary conditions and panel geometry on the response of laminated panels subjected to transverse pressure loads

NASA Technical Reports Server (NTRS)

Jegley, Dawn C.

1993-01-01

The behavior of thin laminated flat and curved panels subjected to transverse pressure and inplane loads is considered. The effects of panel geometry, boundary conditions and laminate stacking sequence on the response of panels subjected to transverse pressure loads up to 12.4 N/sq cm is presented. The response of thin laminated panels is evaluated analytically and selected results are compared with test data. A parametric study of the deformation and strain responses of panels with radius of curvature ranging from 20 to 305 cm is presented. The combination of inplane tensile and pressure loads is also considered.

Identification of Major Risk Sources for Surface Water Pollution by Risk Indexes (RI) in the Multi-Provincial Boundary Region of the Taihu Basin, China

PubMed Central

Yao, Hong; Li, Weixin; Qian, Xin

2015-01-01

Environmental safety in multi-district boundary regions has been one of the focuses in China and is mentioned many times in the Environmental Protection Act of 2014. Five types were categorized concerning the risk sources for surface water pollution in the multi-provincial boundary region of the Taihu basin: production enterprises, waste disposal sites, chemical storage sites, agricultural non-point sources and waterway transportations. Considering the hazard of risk sources, the purification property of environmental medium and the vulnerability of risk receptors, 52 specific attributes on the risk levels of each type of risk source were screened out. Continuous piecewise linear function model, expert consultation method and fuzzy integral model were used to calculate the integrated risk indexes (RI) to characterize the risk levels of pollution sources. In the studied area, 2716 pollution sources were characterized by RI values. There were 56 high-risk sources screened out as major risk sources, accounting for about 2% of the total. The numbers of sources with high-moderate, moderate, moderate-low and low pollution risk were 376, 1059, 101 and 1124, respectively, accounting for 14%, 38%, 5% and 41% of the total. The procedure proposed could be included in the integrated risk management systems of the multi-district boundary region of the Taihu basin. It could help decision makers to identify major risk sources in the risk prevention and reduction of surface water pollution. PMID:26308032

Identification of Major Risk Sources for Surface Water Pollution by Risk Indexes (RI) in the Multi-Provincial Boundary Region of the Taihu Basin, China.

PubMed

Yao, Hong; Li, Weixin; Qian, Xin

2015-08-21

Environmental safety in multi-district boundary regions has been one of the focuses in China and is mentioned many times in the Environmental Protection Act of 2014. Five types were categorized concerning the risk sources for surface water pollution in the multi-provincial boundary region of the Taihu basin: production enterprises, waste disposal sites, chemical storage sites, agricultural non-point sources and waterway transportations. Considering the hazard of risk sources, the purification property of environmental medium and the vulnerability of risk receptors, 52 specific attributes on the risk levels of each type of risk source were screened out. Continuous piecewise linear function model, expert consultation method and fuzzy integral model were used to calculate the integrated risk indexes (RI) to characterize the risk levels of pollution sources. In the studied area, 2716 pollution sources were characterized by RI values. There were 56 high-risk sources screened out as major risk sources, accounting for about 2% of the total. The numbers of sources with high-moderate, moderate, moderate-low and low pollution risk were 376, 1059, 101 and 1124, respectively, accounting for 14%, 38%, 5% and 41% of the total. The procedure proposed could be included in the integrated risk management systems of the multi-district boundary region of the Taihu basin. It could help decision makers to identify major risk sources in the risk prevention and reduction of surface water pollution.

Discovery and evolution of bunyavirids in arctic phantom midges and ancient bunyavirid-like sequences in insect genomes.

PubMed

Ballinger, Matthew J; Bruenn, Jeremy A; Hay, John; Czechowski, Donna; Taylor, Derek J

2014-08-01

Bunyaviridae is a large family of RNA viruses chiefly comprised of vertebrate and plant pathogens. We discovered novel bunyavirids that are approximately equally divergent from each of the five known genera. We characterized novel genome sequences for two bunyavirids, namely, Kigluaik phantom virus (KIGV), from tundra-native phantom midges (Chaoborus), and Nome phantom virus (NOMV), from tundra-invading phantom midges, and demonstrated that these bunyavirid-like sequences belong to an infectious virus by passaging KIGV in mosquito cell culture, although the infection does not seem to be well sustained beyond a few passages. Virus and host gene sequences from individuals collected on opposite ends of North America, a region spanning 4,000 km, support a long-term, vertically transmitted infection of KIGV in Chaoborus trivittatus. KIGV-like sequences ranging from single genes to full genomes are present in transcriptomes and genomes of insects belonging to six taxonomic orders, suggesting an ancient association of this clade with insect hosts. In Drosophila, endogenous virus genes have been coopted, forming an orthologous tandem gene family that has been maintained by selection during the radiation of the host genus. Our findings indicate that bunyavirid-host interactions in nonbloodsucking arthropods have been much more extensive than previously thought. Very little is known about the viral diversity in polar freshwater ponds, and perhaps less is known about the effects that climate-induced habitat changes in these regions will have on virus-host interactions in the coming years. Our results show that at the tundra-boreal boundary, a hidden viral landscape is being altered as infected boreal phantom midges colonize tundra ponds. Likewise, relatively little is known of the deeper evolutionary history of bunyavirids that has led to the stark lifestyle contrasts between some genera. The discovery of this novel bunyavirid group suggests that ancient and highly divergent bunyavirid lineages remain undetected in nature and may offer fresh insight into host reservoirs, potential sources of emerging disease, and major lifestyle shifts in the evolutionary history of viruses in the family Bunyaviridae. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Analysis of ancient-river systems by 3D seismic time-slice technique: A case study in northeast Malay Basin, offshore Terengganu, Malaysia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sulaiman, Noorzamzarina; Hamzah, Umar; Samsudin, Abdul Rahim

2014-09-03

Fluvial sandstones constitute one of the major clastic petroleum reservoir types in many sedimentary basins around the world. This study is based on the analysis of high-resolution, shallow (seabed to 500 m depth) 3D seismic data which generated three-dimensional (3D) time slices that provide exceptional imaging of the geometry, dimension and temporal and spatial distribution of fluvial channels. The study area is in the northeast of Malay Basin about 280 km to the east of Terengganu offshore. The Malay Basin comprises a thick (> 8 km), rift to post-rift Oligo-Miocene to Pliocene basin-fill. The youngest (Miocene to Pliocene), post-rift successionmore » is dominated by a thick (1–5 km), cyclic succession of coastal plain and coastal deposits, which accumulated in a humid-tropical climatic setting. This study focuses on the Pleistocene to Recent (500 m thick) succession, which comprises a range of seismic facies analysis of the two-dimensional (2D) seismic sections, mainly reflecting changes in fluvial channel style and river architecture. The succession has been divided into four seismic units (Unit S1-S4), bounded by basin-wide strata surfaces. Two types of boundaries have been identified: 1) a boundary that is defined by a regionally-extensive erosion surface at the base of a prominent incised valley (S3 and S4); 2) a sequence boundary that is defined by more weakly-incised, straight and low-sinuosity channels which is interpreted as low-stand alluvial bypass channel systems (S1 and S2). Each unit displays a predictable vertical change of the channel pattern and scale, with wide low-sinuosity channels at the base passing gradationally upwards into narrow high-sinuosity channels at the top. The wide variation in channel style and size is interpreted to be controlled mainly by the sea-level fluctuations on the widely flat Sunda land Platform.« less

Analysis of ancient-river systems by 3D seismic time-slice technique: A case study in northeast Malay Basin, offshore Terengganu, Malaysia

NASA Astrophysics Data System (ADS)

Sulaiman, Noorzamzarina; Hamzah, Umar; Samsudin, Abdul Rahim

2014-09-01

Fluvial sandstones constitute one of the major clastic petroleum reservoir types in many sedimentary basins around the world. This study is based on the analysis of high-resolution, shallow (seabed to 500 m depth) 3D seismic data which generated three-dimensional (3D) time slices that provide exceptional imaging of the geometry, dimension and temporal and spatial distribution of fluvial channels. The study area is in the northeast of Malay Basin about 280 km to the east of Terengganu offshore. The Malay Basin comprises a thick (> 8 km), rift to post-rift Oligo-Miocene to Pliocene basin-fill. The youngest (Miocene to Pliocene), post-rift succession is dominated by a thick (1-5 km), cyclic succession of coastal plain and coastal deposits, which accumulated in a humid-tropical climatic setting. This study focuses on the Pleistocene to Recent (500 m thick) succession, which comprises a range of seismic facies analysis of the two-dimensional (2D) seismic sections, mainly reflecting changes in fluvial channel style and river architecture. The succession has been divided into four seismic units (Unit S1-S4), bounded by basin-wide strata surfaces. Two types of boundaries have been identified: 1) a boundary that is defined by a regionally-extensive erosion surface at the base of a prominent incised valley (S3 and S4); 2) a sequence boundary that is defined by more weakly-incised, straight and low-sinuosity channels which is interpreted as low-stand alluvial bypass channel systems (S1 and S2). Each unit displays a predictable vertical change of the channel pattern and scale, with wide low-sinuosity channels at the base passing gradationally upwards into narrow high-sinuosity channels at the top. The wide variation in channel style and size is interpreted to be controlled mainly by the sea-level fluctuations on the widely flat Sunda land Platform.

Influence of trans-boundary air pollution from China on multi-day high PM10 episodes in Seoul, Korea

NASA Astrophysics Data System (ADS)

Oh, H. R.; Ho, C. H.; Kim, J.; Chen, D.; Lee, S.; Choi, Y. S.; Chang, L. S.; Song, C. K.

2014-12-01

Air quality problems have become a serious global issue as it causes over 3 million deaths per year all over the world. With generations of massive air pollutants in China, the effects of trans-boundary transports of air pollutants on human health have become a serious international concern in East Asia. However, only a limited number of studies are available for providing scientific evidences for quantifying the sources and transports of air pollutants over major countries in East Asia. Here, it is shown that particulate matters originated from China played major role in the occurrence of multi-day (≥ 4 days) severe air pollution episodes in Seoul, Korea, in which the concentration of particulate matter of diameters ≤ 10 μm exceeds 100 μg m-3. Observations show that these multi-day severe air quality episodes occur when a strong high-pressure system resides over the eastern China - Korea region. Such a weather condition confines air pollutants within the atmospheric boundary layer and spread them by slow westerlies within the boundary layer from China into the neighboring countries. Understanding such dynamical processes is a key for advancing the predictability of trans-boundary air pollutants and their health impacts in East Asia as well as developing international measures to improve air quality for the region.

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

USGS Publications Warehouse

Cunningham, Kevin J.; Robinson, Edward

2017-07-18

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

Mitochondrial sequences of Seriatopora corals show little agreement with morphology and reveal the duplication of a tRNA gene near the control region

NASA Astrophysics Data System (ADS)

Flot, J.-F.; Licuanan, W. Y.; Nakano, Y.; Payri, C.; Cruaud, C.; Tillier, S.

2008-12-01

The taxonomy of corals of the genus Seriatopora has not previously been studied using molecular sequence markers. As a first step toward a re-evaluation of species boundaries in this genus, mitochondrial sequence variability was analyzed in 51 samples collected from Okinawa, New Caledonia, and the Philippines. Four clusters of sequences were detected that showed little concordance with species currently recognized on a morphological basis. The most likely explanation is that the skeletal characters used for species identification are highly variable (polymorphic or phenotypically plastic); alternative explanations include introgression/hybridization, or deep coalescence and the retention of ancestral mitochondrial polymorphisms. In all individuals sequenced, two copies of trnW were found on either side of the atp8 gene near the putative D-loop, a novel mitochondrial gene arrangement that may have arisen from a duplication of the trnW-atp8 region followed by a deletion of one atp8.

Biostratigraphy of the Cretaceous/Tertiary boundary in the Sirwan Valley (Sulaimani Region, Kurdistan, NE Iraq)

NASA Astrophysics Data System (ADS)

Sharbazheri, Khalid Mahmood; Ghafor, Imad Mahmood; Muhammed, Qahtan Ahmad

2009-10-01

The Cretaceous/Tertiary (K/T) boundary sequence, which crops out in the studied area is located within the High Folded Zone, in the Sirwan Valley, northeastern Iraq. These units mainly consist of flysch and flysch-type successions of thick clastic beds of Tanjero/Kolosh Formations. A detailed lithostratigraphic study is achieved on the outcropping uppermost part of the Upper Cretaceous successions (upper part of Tanjero Formation) and the lowermost part of the Kolosh Formation. On the basis of the identified planktonic foraminiferal assemblages, five biozones are recorded from the uppermost part of Tanjero Formation and four biozones from the lower part of the Kolosh Formation (Lower Paleocene) in the Sirwan section. The biostratigraphic correlations based on planktonic foraminiferal zonations showed a comparison between the biostratigraphic zones established in this study and other equivalents of the commonly used planktonic zonal scheme around the Cretaceous/Tertiary boundary in and outside Iraq.

Implementation of the block-Krylov boundary flexibility method of component synthesis

NASA Technical Reports Server (NTRS)

Carney, Kelly S.; Abdallah, Ayman A.; Hucklebridge, Arthur A.

1993-01-01

A method of dynamic substructuring is presented which utilizes a set of static Ritz vectors as a replacement for normal eigenvectors in component mode synthesis. This set of Ritz vectors is generated in a recurrence relationship, which has the form of a block-Krylov subspace. The initial seed to the recurrence algorithm is based on the boundary flexibility vectors of the component. This algorithm is not load-dependent, is applicable to both fixed and free-interface boundary components, and results in a general component model appropriate for any type of dynamic analysis. This methodology was implemented in the MSC/NASTRAN normal modes solution sequence using DMAP. The accuracy is found to be comparable to that of component synthesis based upon normal modes. The block-Krylov recurrence algorithm is a series of static solutions and so requires significantly less computation than solving the normal eigenspace problem.

Helmholtz decomposition revisited: Vorticity generation and trailing edge condition. I - Incompressible flows

NASA Technical Reports Server (NTRS)

Morino, L.

1986-01-01

Using the decomposition for the infinite-space, the issue of the nonuniqueness of the Helmholtz decomposition for the problem of the three-dimensional unsteady incompressible flow around a body is considered. A representation for the velocity that is valid for both the fluid region and the region inside the boundary surface is employed, and the motion of the boundary is described as the limiting case of a sequence of impulsive accelerations. At each instant of velocity discontinuity, vorticity is shown to be generated by the boundary condition on the normal component of the velocity, for both inviscid and viscous flows. In viscous flows, the vorticity is shown to diffuse into the surroundings, and the no-slip conditions are automatically satisfied. A trailing edge condition must be satisfied for the solution to the Euler equations to be the limit of the solution of the Navier-Stokes equations.

The Kinematics of Turbulent Boundary Layer Structure

NASA Technical Reports Server (NTRS)

Robinson, Stephen Kern

1991-01-01

The long history of research into the internal structure of turbulent boundary layers has not provided a unified picture of the physics responsible for turbulence production and dissipation. The goals of the present research are to: (1) define the current state of boundary layer structure knowledge; and (2) utilize direct numerical simulation results to help close the unresolved issues identified in part A and to unify the fragmented knowledge of various coherent motions into a consistent kinematic model of boundary layer structure. The results of the current study show that all classes of coherent motion in the low Reynolds number turbulent boundary layer may be related to vortical structures, but that no single form of vortex is representative of the wide variety of vortical structures observed. In particular, ejection and sweep motions, as well as entrainment from the free-streem are shown to have strong spatial and temporal relationships with vortical structures. Disturbances of vortex size, location, and intensity show that quasi-streamwise vortices dominate the buffer region, while transverse vortices and vortical arches dominate the wake region. Both types of vortical structure are common in the log region. The interrelationships between the various structures and the population distributions of vortices are combined into a conceptual kinematic model for the boundary layer. Aspects of vortical structure dynamics are also postulated, based on time-sequence animations of the numerically simulated flow.

Synchronous Wildfire Activity Rise and Mire Deforestation at the Triassic–Jurassic Boundary

PubMed Central

Petersen, Henrik I.; Lindström, Sofie

2012-01-01

The end-Triassic mass extinction event (∼201.4 million years ago) caused major faunal and floral turnovers in both the marine and terrestrial realms. The biotic changes have been attributed to extreme greenhouse warming across the Triassic–Jurassic (T–J) boundary caused by massive release of carbon dioxide and/or methane related to extensive volcanism in the Central Atlantic Magmatic Province (CAMP), resulting in a more humid climate with increased storminess and lightning activity. Lightning strikes are considered the primary source of wildfires, producing charcoal, microscopically recognized as inertinite macerals. The presence of polycyclic aromatic hydrocarbons (PAHs) of pyrolytic origin and allochthonous charcoal in siliciclastic T–J boundary strata has suggested widespread wildfire activity at the time. We have investigated largely autochthonous coal and coaly beds across the T–J boundary in Sweden and Denmark. These beds consist of predominantly organic material from the in situ vegetation in the mires, and as the coaly beds represent a substantial period of time they are excellent environmental archives. We document a remarkable increase in inertinite content in the coal and coaly beds across the T–J boundary. We show estimated burning temperatures derived from inertinite reflectance measurements coupled with palynological data and conclude that pre-boundary late Rhaetian mire wildfires included high-temperature crown fires, whereas latest Rhaetian–Sinemurian mire wildfires were more frequent but dominated by lower temperature surface fires. Our results suggest a major change in the mire ecosystems across the T–J boundary from forested, conifer dominated mires to mires with a predominantly herbaceous and shrubby vegetation. Contrary to the overall regional vegetation for which onset of recovery commenced in the early Hettangian, the sensitive mire ecosystem remained affected during the Hettangian and did not start to recover until around the Hettangian–Sinemurian boundary. Decreasing inertinite content through the Lower Jurassic suggests that fire activity gradually resumed to considerable lower levels. PMID:23077574

Straight velocity boundaries in the lattice Boltzmann method

NASA Astrophysics Data System (ADS)

Latt, Jonas; Chopard, Bastien; Malaspinas, Orestis; Deville, Michel; Michler, Andreas

2008-05-01

Various ways of implementing boundary conditions for the numerical solution of the Navier-Stokes equations by a lattice Boltzmann method are discussed. Five commonly adopted approaches are reviewed, analyzed, and compared, including local and nonlocal methods. The discussion is restricted to velocity Dirichlet boundary conditions, and to straight on-lattice boundaries which are aligned with the horizontal and vertical lattice directions. The boundary conditions are first inspected analytically by applying systematically the results of a multiscale analysis to boundary nodes. This procedure makes it possible to compare boundary conditions on an equal footing, although they were originally derived from very different principles. It is concluded that all five boundary conditions exhibit second-order accuracy, consistent with the accuracy of the lattice Boltzmann method. The five methods are then compared numerically for accuracy and stability through benchmarks of two-dimensional and three-dimensional flows. None of the methods is found to be throughout superior to the others. Instead, the choice of a best boundary condition depends on the flow geometry, and on the desired trade-off between accuracy and stability. From the findings of the benchmarks, the boundary conditions can be classified into two major groups. The first group comprehends boundary conditions that preserve the information streaming from the bulk into boundary nodes and complete the missing information through closure relations. Boundary conditions in this group are found to be exceptionally accurate at low Reynolds number. Boundary conditions of the second group replace all variables on boundary nodes by new values. They exhibit generally much better numerical stability and are therefore dedicated for use in high Reynolds number flows.

Eulerian Formulation of Spatially Constrained Elastic Rods

NASA Astrophysics Data System (ADS)

Huynen, Alexandre

Slender elastic rods are ubiquitous in nature and technology. For a vast majority of applications, the rod deflection is restricted by an external constraint and a significant part of the elastic body is in contact with a stiff constraining surface. The research work presented in this doctoral dissertation formulates a computational model for the solution of elastic rods constrained inside or around frictionless tube-like surfaces. The segmentation strategy adopted to cope with this complex class of problems consists in sequencing the global problem into, comparatively simpler, elementary problems either in continuous contact with the constraint or contact-free between their extremities. Within the conventional Lagrangian formulation of elastic rods, this approach is however associated with two major drawbacks. First, the boundary conditions specifying the locations of the rod centerline at both extremities of each elementary problem lead to the establishment of isoperimetric constraints, i.e., integral constraints on the unknown length of the rod. Second, the assessment of the unilateral contact condition requires, in principle, the comparison of two curves parametrized by distinct curvilinear coordinates, viz. the rod centerline and the constraint axis. Both conspire to burden the computations associated with the method. To streamline the solution along the elementary problems and rationalize the assessment of the unilateral contact condition, the rod governing equations are reformulated within the Eulerian framework of the constraint. The methodical exploration of both types of elementary problems leads to specific formulations of the rod governing equations that stress the profound connection between the mechanics of the rod and the geometry of the constraint surface. The proposed Eulerian reformulation, which restates the rod local equilibrium in terms of the curvilinear coordinate associated with the constraint axis, describes the rod deformed configuration by means of either its relative position with respect to the constraint axis (contact-free segments) or its angular position on the constraint surface (continuous contacts.) This formulation circumvents both drawbacks that afflict the conventional Lagrangian approach associated with the segmentation strategy. As the a priori unknown domain, viz. the rod length, is substituted for the known constraint axis, the free boundary problem and the associated isoperimetric constraints are converted into a classical two-point boundary value problem. Additionally, the description of the rod deflection by means of its eccentricity with respect to the constraint axis trivializes the assessment of the unilateral contact condition. Along continuous contacts, this formulation expresses the strain variables, measuring the rod change of shape, in terms of the geometric invariants of the constraint surface, and emphasizes the influence of the constraint local geometry on the reaction pressure. Formalizing the segmentation strategy, a computational model that exploits the Eulerian formulation of the rod governing equations is devised. To solve the quasi-static deflection of elastic rods constrained inside or around a tube-like surface, this computational model identifies the number of contacts, their nature (either discrete or continuous), and the rod configuration at the connections that satisfies the unilateral contact condition and preserves the rod integrity along the sequence of elementary problems.

15 CFR 921.33 - Boundary changes, amendments to the management plan, and addition of multiple-site components.

Code of Federal Regulations, 2010 CFR

2010-01-01

... management plan, and addition of multiple-site components. 921.33 Section 921.33 Commerce and Foreign Trade... management plan, and addition of multiple-site components. (a) Changes in the boundary of a Reserve and major... management plan shall address goals and objectives for all components of the multi-site Reserve and the...

Geologic framework of the Alaska Peninsula, southwest Alaska, and the Alaska Peninsula terrane

USGS Publications Warehouse

Wilson, Frederic H.; Detterman, Robert L.; DuBois, Gregory D.

2015-01-01

The boundaries separating the Alaska Peninsula terrane from other terranes are commonly indistinct or poorly defined. A few boundaries have been defined at major faults, although the extensions of these faults are speculative through some areas. The west side of the Alaska Peninsula terrane is overlapped by Tertiary sedimentary and volcanic rocks and Quaternary deposits.

Crossing the Cultural Boundary from Home to Kindergarten in Hong Kong: A Case Study of a Child's Strategic Actions

ERIC Educational Resources Information Center

Lam, Mei Seung

2009-01-01

Transition from home to kindergarten is the first and major ecological transition in children's educational lives in Hong Kong. In this transition, children cross a cultural boundary from home to kindergarten and start to learn about "school" as a place to learn and about themselves as "pupils" in kindergarten. The conceptual…

Protected-Area Boundaries as Filters of Plant Invasions

PubMed Central

Foxcroft, Llewellyn C; JaroŠÍK, Vojtěch; Pyšek, Petr; Richardson, David M; Rouget, Mathieu

2011-01-01

Abstract Human land uses surrounding protected areas provide propagules for colonization of these areas by non-native species, and corridors between protected-area networks and drainage systems of rivers provide pathways for long-distance dispersal of non-native species. Nevertheless, the influence of protected-area boundaries on colonization of protected areas by invasive non-native species is unknown. We drew on a spatially explicit data set of more than 27,000 non-native plant presence records for South Africa's Kruger National Park to examine the role of boundaries in preventing colonization of protected areas by non-native species. The number of records of non-native invasive plants declined rapidly beyond 1500 m inside the park; thus, we believe that the park boundary limited the spread of non-native plants. The number of non-native invasive plants inside the park was a function of the amount of water runoff, density of major roads, and the presence of natural vegetation outside the park. Of the types of human-induced disturbance, only the density of major roads outside the protected area significantly increased the number of non-native plant records. Our findings suggest that the probability of incursion of invasive plants into protected areas can be quantified reliably. PMID:21166715

Linear and nonlinear stability of periodic orbits in annular billiards.

PubMed

Dettmann, Carl P; Fain, Vitaly

2017-04-01

An annular billiard is a dynamical system in which a particle moves freely in a disk except for elastic collisions with the boundary and also a circular scatterer in the interior of the disk. We investigate the stability properties of some periodic orbits in annular billiards in which the scatterer is touching or close to the boundary. We analytically show that there exist linearly stable periodic orbits of an arbitrary period for scatterers with decreasing radii that are located near the boundary of the disk. As the position of the scatterer moves away from a symmetry line of a periodic orbit, the stability of periodic orbits changes from elliptic to hyperbolic, corresponding to a saddle-center bifurcation. When the scatterer is tangent to the boundary, the periodic orbit is parabolic. We prove that slightly changing the reflection angle of the orbit in the tangential situation leads to the existence of Kolmogorov-Arnold-Moser islands. Thus, we show that there exists a decreasing to zero sequence of open intervals of scatterer radii, along which the billiard table is not ergodic.

Görtler instability of the axisymmetric boundary layer along a cone

NASA Astrophysics Data System (ADS)

ITOH, Nobutake

2014-10-01

Exact partial differential equations are derived to describe Görtler instability, caused by a weakly concave wall, of axisymmetric boundary layers with similar velocity profiles that are decomposed into a sequence of ordinary differential systems on the assumption that the solution can be expanded into inverse powers of local Reynolds number. The leading terms of the series solution are determined by solving a non-parallel version of Görtler’s eigenvalue problem and lead to a neutral stability curve and finite values of critical Görtler number and wave number for stationary and longitudinal vortices. Higher-order terms of the series solution indicate Reynolds-number dependence of Görtler instability and a limited validity of Görtler’s approximation based on the leading terms only. The present formulation is simply applicable to two-dimensional boundary layers of similar profiles, and critical Görtler number and wave number of the Blasius boundary layer on a flat plate are given by G2c = 1.23 and β2c = 0.288, respectively, if the momentum thickness is chosen as the reference length.

Linear and nonlinear stability of periodic orbits in annular billiards

NASA Astrophysics Data System (ADS)

Dettmann, Carl P.; Fain, Vitaly

2017-04-01

An annular billiard is a dynamical system in which a particle moves freely in a disk except for elastic collisions with the boundary and also a circular scatterer in the interior of the disk. We investigate the stability properties of some periodic orbits in annular billiards in which the scatterer is touching or close to the boundary. We analytically show that there exist linearly stable periodic orbits of an arbitrary period for scatterers with decreasing radii that are located near the boundary of the disk. As the position of the scatterer moves away from a symmetry line of a periodic orbit, the stability of periodic orbits changes from elliptic to hyperbolic, corresponding to a saddle-center bifurcation. When the scatterer is tangent to the boundary, the periodic orbit is parabolic. We prove that slightly changing the reflection angle of the orbit in the tangential situation leads to the existence of Kolmogorov-Arnold-Moser islands. Thus, we show that there exists a decreasing to zero sequence of open intervals of scatterer radii, along which the billiard table is not ergodic.

Investigation of the effect of finite pulse errors on the BABA pulse sequence using the Floquet-Magnus expansion approach

NASA Astrophysics Data System (ADS)

Mananga, Eugene S.; Reid, Alicia E.

2013-01-01

This paper presents a study of finite pulse widths for the BABA pulse sequence using the Floquet-Magnus expansion (FME) approach. In the FME scheme, the first order ? is identical to its counterparts in average Hamiltonian theory (AHT) and Floquet theory (FT). However, the timing part in the FME approach is introduced via the ? function not present in other schemes. This function provides an easy way for evaluating the spin evolution during the time in between' through the Magnus expansion of the operator connected to the timing part of the evolution. The evaluation of ? is particularly useful for the analysis of the non-stroboscopic evolution. Here, the importance of the boundary conditions, which provide a natural choice of ? , is ignored. This work uses the ? function to compare the efficiency of the BABA pulse sequence with ? and the BABA pulse sequence with finite pulses. Calculations of ? and ? are presented.

Redesigning Channel-Forming Peptides: Amino Acid Substitutions that Enhance Rates of Supramolecular Self-Assembly and Raise Ion Transport Activity

PubMed Central

Shank, Lalida P.; Broughman, James R.; Takeguchi, Wade; Cook, Gabriel; Robbins, Ashley S.; Hahn, Lindsey; Radke, Gary; Iwamoto, Takeo; Schultz, Bruce D.; Tomich, John M.

2006-01-01

Three series of 22-residue peptides derived from the transmembrane M2 segment of the glycine receptor α1-subunit (M2GlyR) have been designed, synthesized, and tested to determine the plasticity of a channel-forming sequence and to define whether channel pores with enhanced conductive properties could be created. Sixteen sequences were examined for aqueous solubility, solution-association tendency, secondary structure, and half-maximal concentration for supramolecular assembly, channel activity, and ion transport properties across epithelial monolayers. All peptides interact strongly with membranes: associating with, inserting across, and assembling to form homooligomeric bundles when in micromolar concentrations. Single and double amino acid replacements involving arginine and/or aromatic amino acids within the final five C-terminal residues of the peptide cause dramatic effects on the concentration dependence, yielding a range of K1/2 values from 36 ± 5 to 390 ± 220 μM for transport activity. New water/lipid interfacial boundaries were established for the transmembrane segment using charged or aromatic amino acids, thus limiting the peptides' ability to move perpendicularly to the plane of the bilayer. Formation of discrete water/lipid interfacial boundaries appears to be necessary for efficient supramolecular assembly and high anion transport activity. A peptide sequence is identified that may show efficacy in channel replacement therapy for channelopathies such as cystic fibrosis. PMID:16387776

Connecting Pre-Service Teachers with Contemporary Mathematics Practices: Selecting and Sequencing Students' Work Samples

ERIC Educational Resources Information Center

Livy, Sharyn; Muir, Tracey; Downton, Ann

2017-01-01

One of the challenges facing teacher educators is providing our pre-service teachers (PSTs) with authentic experiences that cross the boundaries between Initial Teacher Education (ITE) and the classroom. An additional challenge facing the mathematics teacher educator, is addressing and deepening PSTs' mathematical content knowledge (MCK), which…

Using Kites to Illustrate Some Features of Boundary Layer Winds.

ERIC Educational Resources Information Center

Tuller, Stanton E.

1983-01-01

Kites allow teachers to illustrate wind patterns by calling on past experience and by present demonstration. Features of the wind illustrated by kites--the effect of surface friction on wind speed, change of wind direction with elevation, gust and lull sequence, and atmospheric stability and turbulence type--are discussed. (SR)

Statistical Segmentation of Tone Sequences Activates the Left Inferior Frontal Cortex: A Near-Infrared Spectroscopy Study

ERIC Educational Resources Information Center

Abla, Dilshat; Okanoya, Kazuo

2008-01-01

Word segmentation, that is, discovering the boundaries between words that are embedded in a continuous speech stream, is an important faculty for language learners; humans solve this task partly by calculating transitional probabilities between sounds. Behavioral and ERP studies suggest that detection of sequential probabilities (statistical…

Sedimentary facies and depositional history of the Swan Islands, Honduras

NASA Astrophysics Data System (ADS)

Ivey, Marvin L.; Breyer, John A.; Britton, Joseph C.

1980-10-01

Swan Island is a Honduran possession in the western Caribbean, located on the southeastern side of the Cayman Trench. Two sedimentary assemblages are found on the island: an older bedded sequence of mid-Tertiary age (Aquitanian or Burdigalian) and a younger sedimentary sequence of Late Pleistocene age. The older sequence is composed of a series of calcarenites, calcilutites, and siliciclastic mudstones; capping these are cliff-forming reefal carbonates of the younger sequence. The rocks of the older bedded sequence accumulated in deep water. Sedimentation consisted of a constant rain of pyroclastic debris interrupted by the episodic introduction of upslope carbonate material by turbidity currents. Uplift and deformation of this sequence was initiated sometime after the Early Miocene. By the Late Pleistocene, uplift had brought the rocks into water depths conducive to coral growth. Pleistocene sedimentation on the island was controlled by the interaction between tectonic uplift and eustatic sea-level changes. The primary controlling force on the tectonic history of the island is its proximity to the boundary between the North American and Caribbean plates.

Expansion of inverted repeat does not decrease substitution rates in Pelargonium plastid genomes.

PubMed

Weng, Mao-Lun; Ruhlman, Tracey A; Jansen, Robert K

2017-04-01

For species with minor inverted repeat (IR) boundary changes in the plastid genome (plastome), nucleotide substitution rates were previously shown to be lower in the IR than the single copy regions (SC). However, the impact of large-scale IR expansion/contraction on plastid nucleotide substitution rates among closely related species remains unclear. We included plastomes from 22 Pelargonium species, including eight newly sequenced genomes, and used both pairwise and model-based comparisons to investigate the impact of the IR on sequence evolution in plastids. Ten types of plastome organization with different inversions or IR boundary changes were identified in Pelargonium. Inclusion in the IR was not sufficient to explain the variation of nucleotide substitution rates. Instead, the rate heterogeneity in Pelargonium plastomes was a mixture of locus-specific, lineage-specific and IR-dependent effects. Our study of Pelargonium plastomes that vary in IR length and gene content demonstrates that the evolutionary consequences of retaining these repeats are more complicated than previously suggested. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Deciphering the Transitional Tectonics of the Southern Alaska Margin Through Gulf Sedimentology and Geophysics: IODP Expedition 341

NASA Astrophysics Data System (ADS)

Reece, R.; Gulick, S. P. S.; Jaeger, J. M.

2014-12-01

Southern Alaska is a complex amalgam of tectonic environments, centered on the subduction/collision of the Yakutat Block with North America. Along the Aleutians in the west, the Pacific Plate subducts normally beneath North America, with a gradually shallowing subduction angle towards the Yakutat Terrane to the east. The western region of the Yakutat Block undergoes nearly flat-slab subduction beneath North America, whereas it transitions to collision in the northeast, which is the primary driver for the growth of the Chugach-St. Elias orogen. Farther to the east, the collisional system transitions to a transform boundary with the Fairweather-Queen Charlotte fault system. The collisional system contributes to farfield tectonic effects in many regions, including northern Alaska and the Pacific Plate, but also combines with glaciation to drive sedimentation in the Gulf of Alaska. Glaciation has periodically increased in the St. Elias Range since the Miocene, but began dominating erosion and spurred enhanced exhumation since the intensification of Northern Hemisphere glaciation, at ~2.5 Ma. Results from IODP Expedition 341 show the first appearance of ice-rafted debris and a doubling of Gulf sedimentation at site U1417 at this age, and a major increase in sedimentation at ~1 Ma at sites U1417 and U1418. Glacigenic sediment flux into the Gulf of Alaska represents the majority of accumulation in the deepwater Surveyor Fan, and was the impetus for formation of the Surveyor Channel system. Climate events correlate to three major differentiable sequences across the Surveyor Fan that have been previously mapped using seismic reflection profiles. The change in morphology observed throughout the sequences allows us to characterize the influence that a glaciated orogen can have in shaping margin processes and the sediment pathways from source to sink. IODP Expedition 341 results allow us to now apply this method at higher resolution time scales (i.e., 100 kyr). We will explore changes in fan geomorphology observed in seismic reflection data to decipher changes in southern Alaska tectonics and climate, and to show the effect of those changes on deepwater sedimentary systems.

Sequence-Dependent Diastereospecific and Diastereodivergent Crosslinking of DNA by Decarbamoylmitomycin C.

PubMed

Aguilar, William; Paz, Manuel M; Vargas, Anayatzinc; Clement, Cristina C; Cheng, Shu-Yuan; Champeil, Elise

2018-04-20

Mitomycin C (MC), a potent antitumor drug, and decarbamoylmitomycin C (DMC), a derivative lacking the carbamoyl group, form highly cytotoxic DNA interstrand crosslinks. The major interstrand crosslink formed by DMC is the C1'' epimer of the major crosslink formed by MC. The molecular basis for the stereochemical configuration exhibited by DMC was investigated using biomimetic synthesis. The formation of DNA-DNA crosslinks by DMC is diastereospecific and diastereodivergent: Only the 1''S-diastereomer of the initially formed monoadduct can form crosslinks at GpC sequences, and only the 1''R-diastereomer of the monoadduct can form crosslinks at CpG sequences. We also show that CpG and GpC sequences react with divergent diastereoselectivity in the first alkylation step: 1"S stereochemistry is favored at GpC sequences and 1''R stereochemistry is favored at CpG sequences. Therefore, the first alkylation step results, at each sequence, in the selective formation of the diastereomer able to generate an interstrand DNA-DNA crosslink after the "second arm" alkylation. Examination of the known DNA adduct pattern obtained after treatment of cancer cell cultures with DMC indicates that the GpC sequence is the major target for the formation of DNA-DNA crosslinks in vivo by this drug. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

High Diversity of Myocyanophage in Various Aquatic Environments Revealed by High-Throughput Sequencing of Major Capsid Protein Gene With a New Set of Primers.

PubMed

Hou, Weiguo; Wang, Shang; Briggs, Brandon R; Li, Gaoyuan; Xie, Wei; Dong, Hailiang

2018-01-01

Myocyanophages, a group of viruses infecting cyanobacteria, are abundant and play important roles in elemental cycling. Here we investigated the particle-associated viral communities retained on 0.2 μm filters and in sediment samples (representing ancient cyanophage communities) from four ocean and three lake locations, using high-throughput sequencing and a newly designed primer pair targeting a gene fragment (∼145-bp in length) encoding the cyanophage gp23 major capsid protein (MCP). Diverse viral communities were detected in all samples. The fragments of 142-, 145-, and 148-bp in length were most abundant in the amplicons, and most sequences (>92%) belonged to cyanophages. Additionally, different sequencing depths resulted in different diversity estimates of the viral community. Operational taxonomic units obtained from deep sequencing of the MCP gene covered the majority of those obtained from shallow sequencing, suggesting that deep sequencing exhibited a more complete picture of cyanophage community than shallow sequencing. Our results also revealed a wide geographic distribution of marine myocyanophages, i.e., higher dissimilarities of the myocyanophage communities corresponded with the larger distances between the sampling sites. Collectively, this study suggests that the newly designed primer pair can be effectively used to study the community and diversity of myocyanophage from different environments, and the high-throughput sequencing represents a good method to understand viral diversity.

High Diversity of Myocyanophage in Various Aquatic Environments Revealed by High-Throughput Sequencing of Major Capsid Protein Gene With a New Set of Primers

PubMed Central

Hou, Weiguo; Wang, Shang; Briggs, Brandon R.; Li, Gaoyuan; Xie, Wei; Dong, Hailiang

2018-01-01

Myocyanophages, a group of viruses infecting cyanobacteria, are abundant and play important roles in elemental cycling. Here we investigated the particle-associated viral communities retained on 0.2 μm filters and in sediment samples (representing ancient cyanophage communities) from four ocean and three lake locations, using high-throughput sequencing and a newly designed primer pair targeting a gene fragment (∼145-bp in length) encoding the cyanophage gp23 major capsid protein (MCP). Diverse viral communities were detected in all samples. The fragments of 142-, 145-, and 148-bp in length were most abundant in the amplicons, and most sequences (>92%) belonged to cyanophages. Additionally, different sequencing depths resulted in different diversity estimates of the viral community. Operational taxonomic units obtained from deep sequencing of the MCP gene covered the majority of those obtained from shallow sequencing, suggesting that deep sequencing exhibited a more complete picture of cyanophage community than shallow sequencing. Our results also revealed a wide geographic distribution of marine myocyanophages, i.e., higher dissimilarities of the myocyanophage communities corresponded with the larger distances between the sampling sites. Collectively, this study suggests that the newly designed primer pair can be effectively used to study the community and diversity of myocyanophage from different environments, and the high-throughput sequencing represents a good method to understand viral diversity.

Glacial survival east and west of the 'Mekong-Salween Divide' in the Himalaya-Hengduan Mountains region as revealed by AFLPs and cpDNA sequence variation in Sinopodophyllum hexandrum (Berberidaceae).

PubMed

Li, Yong; Zhai, Sheng-Nan; Qiu, Ying-Xiong; Guo, Yan-Ping; Ge, Xue-Jun; Comes, Hans Peter

2011-05-01

Molecular phylogeographic studies have recently begun to elucidate how plant species from the Qinghai-Tibetan Plateau (QTP) and adjacent regions responded to the Quaternary climatic oscillations. In this regard, however, far less attention has been paid to the southern and south-eastern declivities of the QTP, i.e. the Himalaya-Hengduan Mountains (HHM) region. Here, we report a survey of amplified fragment length polymorphisms (AFLPs) and chloroplast DNA (cpDNA) sequence variation in the HHM endemic Sinopodophyllum hexandrum, a highly selfing alpine perennial herb with mainly gravity-dispersed berries (105 individuals, 19 localities). We specifically aimed to test a vicariant evolutionary hypothesis across the 'Mekong-Salween Divide', a known biogeographic and phytogeographic boundary of north-to-south trending river valleys separating the East Himalayas and Hengduan Mts. Both cpDNA and AFLPs identified two divergent phylogroups largely congruent with these mountain ranges. There was no genetic depauperation in the more strongly glaciated East Himalayas (AFLPs: H(E)=0.031; cpDNA: h(S)=0.133) compared to the mainly ice-free Hengduan Mts. (AFLPs: H(E)=0.037; cpDNA: h(S)=0.082), while population differentiation was consistently higher in the former region (AFLPs: Φ(ST)=0.522 vs. 0.312; cpDNA: Φ(ST)=0.785 vs. 0.417). Our results suggest that East Himalayan and Hengduan populations of S. hexandrum were once fragmented, persisted in situ during glacials in both areas, and have not merged again, except for a major instance of inter-lineage chloroplast capture identified at the MSD boundary. Our coalescent time estimate for all cpDNA haplotypes (c. 0.37-0.48 mya), together with paleogeological evidence, strongly rejects paleo-drainage formation as a mechanism underlying allopatric fragmentation, whereas mountain glaciers following the ridges of the MSD during glacials (and possible interglacials) could have been responsible. This study thus indicates an important role for mountain glaciers in driving (incipient) allopatric speciation across the MSD in the HHM region by causing vicariant lineage divergence and acting as barriers to post-divergence gene flow. Copyright © 2011 Elsevier Inc. All rights reserved.

Oceanic broad multifault transform plate boundaries

NASA Astrophysics Data System (ADS)

Ligi, Marco; Bonatti, Enrico; Gasperini, Luca; Poliakov, Alexei N. B.

2002-01-01

Oceanic transform plate boundaries consist of a single, narrow (a few kilometers wide) strike-slip seismic zone offsetting two mid-ocean ridge segments. However, we define here a new class of oceanic transform boundaries, with broad complex multifault zones of deformation, similar to some continental strike-slip systems. Examples are the 750-km- long, 120-km-wide Andrew Bain transform on the Southwest Indian Ridge, and the Romanche transform, where the Mid-Atlantic Ridge is offset by a lens-shaped, ˜900-km- long, ˜100-km-wide sliver of deformed lithosphere bound by two major transform valleys. One of the valleys is seismically highly active and constitutes the present-day principal transform boundary. However, strike-slip seismic events also occur in the second valley and elsewhere in the deformed zone. Some of these events may be triggered by earthquakes from the principal boundary. Numerical modeling predicts the development of wide multiple transform boundaries when the age offset is above a threshold value of ˜30 m.y., i.e., in extra-long (>500 km) slow-slip transforms. Multiple boundaries develop so that strike-slip ruptures avoid very thick and strong lithosphere.

Classification with an edge: Improving semantic image segmentation with boundary detection

NASA Astrophysics Data System (ADS)

Marmanis, D.; Schindler, K.; Wegner, J. D.; Galliani, S.; Datcu, M.; Stilla, U.

2018-01-01

We present an end-to-end trainable deep convolutional neural network (DCNN) for semantic segmentation with built-in awareness of semantically meaningful boundaries. Semantic segmentation is a fundamental remote sensing task, and most state-of-the-art methods rely on DCNNs as their workhorse. A major reason for their success is that deep networks learn to accumulate contextual information over very large receptive fields. However, this success comes at a cost, since the associated loss of effective spatial resolution washes out high-frequency details and leads to blurry object boundaries. Here, we propose to counter this effect by combining semantic segmentation with semantically informed edge detection, thus making class boundaries explicit in the model. First, we construct a comparatively simple, memory-efficient model by adding boundary detection to the SEGNET encoder-decoder architecture. Second, we also include boundary detection in FCN-type models and set up a high-end classifier ensemble. We show that boundary detection significantly improves semantic segmentation with CNNs in an end-to-end training scheme. Our best model achieves >90% overall accuracy on the ISPRS Vaihingen benchmark.

Aspects of Turbulent / Non-Turbulent Interfaces

NASA Technical Reports Server (NTRS)

Bisset, D. K.; Hunt, J. C. R.; Rogers, M. M.; Koen, Dennis (Technical Monitor)

1999-01-01

A distinct boundary between turbulent and non-turbulent regions in a fluid of otherwise constant properties is found in many laboratory and engineering turbulent flows, including jets, mixing layers, boundary layers and wakes. Generally, the flow has mean shear in at least one direction within t he turbulent zone, but the non-turbulent zones have no shear (adjacent laminar shear is a different case, e.g. transition in a boundary layer). There may be purely passive differences between the turbulent and non-turbulent zones, e.g. small variations in temperature or scalar concentration, for which turbulent mixing is an important issue. The boundary has several major characteristics of interest for the present study. Firstly, the boundary advances into the non-turbulent fluid, or in other words, nonturbulent fluid is entrained. Secondly, the change in turbulence properties across the boundary is remarkably abrupt; strong turbulent motions come close to the nonturbulent fluid, promoting entrainment. Thirdly, the boundary is irregular with a continually changing convoluted shape, which produces statistical intermittency. Its shape is contorted at all scales of the turbulent motion.

Simulations of Dynamics and Transport during the September 2002 Antarctic Major Warming

NASA Technical Reports Server (NTRS)

Manney, Gloria L.; Sabutis, Joseph L.; Allen, Douglas R.; Lahoz, Willian A.; Scaife, Adam A.; Randall, Cora E.; Pawson, Steven; Naujokat, Barbara; Swinbank, Richard

2005-01-01

A mechanistic model simulation initialized on 14 September 2002, forced by 100-hPa geopotential heights from Met Office analyses, reproduced the dynamical features of the 2002 Antarctic major warming. The vortex split on approx.25 September; recovery after the warming, westward and equatorward tilting vortices, and strong baroclinic zones in temperature associated with a dipole pattern of upward and downward vertical velocities were all captured in the simulation. Model results and analyses show a pattern of strong upward wave propagation throughout the warming, with zonal wind deceleration throughout the stratosphere at high latitudes before the vortex split, continuing in the middle and upper stratosphere and spreading to lower latitudes after the split. Three-dimensional Eliassen-Palm fluxes show the largest upward and poleward wave propagation in the 0(deg)-90(deg)E sector prior to the vortex split (coincident with the location of strongest cyclogenesis at the model's lower boundary), with an additional region of strong upward propagation developing near 180(deg)-270(deg)E. These characteristics are similar to those of Arctic wave-2 major warmings, except that during this warming, the vortex did not split below approx.600 K. The effects of poleward transport and mixing dominate modeled trace gas evolution through most of the mid- to high-latitude stratosphere, with a core region in the lower-stratospheric vortex where enhanced descent dominates and the vortex remains isolated. Strongly tilted vortices led to low-latitude air overlying vortex air, resulting in highly unusual trace gas profiles. Simulations driven with several meteorological datasets reproduced the major warming, but in others, stronger latitudinal gradients at high latitudes at the model boundary resulted in simulations without a complete vortex split in the midstratosphere. Numerous tests indicate very high sensitivity to the boundary fields, especially the wave-2 amplitude. Major warmings occurred for initial fields with stronger winds and larger vortices, but not smaller vortices, consistent with the initiation of wind-deceleration by upward-propagating waves near the poleward edge of the region where wave 2 can propagate above the jet core. Thus, given the observed 100-hPa boundary forcing, stratospheric preconditioning is not needed to reproduce a major warming similar to that observed. The anomalously strong forcing in the lower stratosphere can be viewed as the primary direct cause of the major warming.

Online Dectection and Modeling of Safety Boundaries for Aerospace Application Using Bayesian Statistics

NASA Technical Reports Server (NTRS)

He, Yuning

2015-01-01

The behavior of complex aerospace systems is governed by numerous parameters. For safety analysis it is important to understand how the system behaves with respect to these parameter values. In particular, understanding the boundaries between safe and unsafe regions is of major importance. In this paper, we describe a hierarchical Bayesian statistical modeling approach for the online detection and characterization of such boundaries. Our method for classification with active learning uses a particle filter-based model and a boundary-aware metric for best performance. From a library of candidate shapes incorporated with domain expert knowledge, the location and parameters of the boundaries are estimated using advanced Bayesian modeling techniques. The results of our boundary analysis are then provided in a form understandable by the domain expert. We illustrate our approach using a simulation model of a NASA neuro-adaptive flight control system, as well as a system for the detection of separation violations in the terminal airspace.

Cyclostratigraphic calibration of the Famennian stage (Late Devonian, Illinois Basin, USA)

NASA Astrophysics Data System (ADS)

Pas, Damien; Hinnov, Linda; Day, James E. (Jed); Kodama, Kenneth; Sinnesael, Matthias; Liu, Wei

2018-04-01

The Late Devonian biosphere was affected by two of the most severe biodiversity crises in Earth's history, the Kellwasser and Hangenberg events near the Frasnian-Famennian (F-F) and the Devonian-Carboniferous (D-C) boundaries, respectively. Current hypotheses for the causes of the Late Devonian extinctions are focused on climate changes and associated ocean anoxia. Testing these hypotheses has been impeded by a lack of sufficient temporal resolution in paleobiological, tectonic and climate proxy records. While there have been recent advances in astronomical calibration that have improved the accuracy of the Frasnian time scale and part of the Famennian, the time duration of the entire Famennian Stage remains poorly constrained. During the Late Devonian, a complete Late Frasnian-Early Carboniferous succession of deep-shelf deposits accumulated in the epieric sea in Illinois Basin of the central North-American mid-continent. A record of this sequence is captured in three overlapping cores (H-30, Sullivan and H-32). The H-30 core section spans the F-F boundary; the Sullivan section spans almost all of the Famennian and the H-32 section sampled spans the interval of the Upper Famennian and the D-C boundary. To have the best chance of capturing Milankovitch cycles, 2000 rock samples were collected at minimum 5-cm-interval across the entire sequence. Magnetic susceptibility (MS) was measured on each sample and the preservation of climatic information into the MS signal was verified through geochemical analyses and low-temperature magnetic susceptibility acquisition. To estimate the duration of the Famennian Stage, we applied multiple spectral techniques and tuned the MS signal using the highly stable 405 kyr cycle for Sullivan and the obliquity cycle for the H-30 and H-32 cores. Based on the correlation between the cores we constructed a Famennian floating astronomical time scale, which indicates a duration of 13.5 ± 0.5 myr. An uncertainty of 0.5 myr was estimated for the uncertainties arising from the errors in the stratigraphic position of the F-F and D-C boundaries, and the 405 kyr cycle counting. Interpolated from the high-resolution U-Pb radiometric ages available for the Devonian-Carboniferous boundary we recalibrated the Frasnian-Famennian boundary numerical age to 372.4 ± 0.9 Ma.

Operational Dynamic Configuration Analysis

NASA Technical Reports Server (NTRS)

Lai, Chok Fung; Zelinski, Shannon

2010-01-01

Sectors may combine or split within areas of specialization in response to changing traffic patterns. This method of managing capacity and controller workload could be made more flexible by dynamically modifying sector boundaries. Much work has been done on methods for dynamically creating new sector boundaries [1-5]. Many assessments of dynamic configuration methods assume the current day baseline configuration remains fixed [6-7]. A challenging question is how to select a dynamic configuration baseline to assess potential benefits of proposed dynamic configuration concepts. Bloem used operational sector reconfigurations as a baseline [8]. The main difficulty is that operational reconfiguration data is noisy. Reconfigurations often occur frequently to accommodate staff training or breaks, or to complete a more complicated reconfiguration through a rapid sequence of simpler reconfigurations. Gupta quantified a few aspects of airspace boundary changes from this data [9]. Most of these metrics are unique to sector combining operations and not applicable to more flexible dynamic configuration concepts. To better understand what sort of reconfigurations are acceptable or beneficial, more configuration change metrics should be developed and their distribution in current practice should be computed. This paper proposes a method to select a simple sequence of configurations among operational configurations to serve as a dynamic configuration baseline for future dynamic configuration concept assessments. New configuration change metrics are applied to the operational data to establish current day thresholds for these metrics. These thresholds are then corroborated, refined, or dismissed based on airspace practitioner feedback. The dynamic configuration baseline selection method uses a k-means clustering algorithm to select the sequence of configurations and trigger times from a given day of operational sector combination data. The clustering algorithm selects a simplified schedule containing k configurations based on stability score of the sector combinations among the raw operational configurations. In addition, the number of the selected configurations is determined based on balance between accuracy and assessment complexity.

Evidence of displacement-driven maturation along the San Cristobal Trough transform plate boundary

NASA Astrophysics Data System (ADS)

Neely, James S.; Furlong, Kevin P.

2018-03-01

The San Cristobal Trough (SCT), formed by the tearing of the Australia plate as it subducts under the Pacific plate near the Solomon Islands, provides an opportunity to study the transform boundary development process. Recent seismicity (2013-2016) along the 280 km long SCT, known as a Subduction-Transform Edge Propagator (STEP) fault, highlights the tearing process and ongoing development of the plate boundary. The region's earthquakes reveal two key characteristics. First, earthquakes at the western terminus of the SCT, which we interpret to indicate the Australia plate tearing, display disparate fault geometries. These events demonstrate that plate tearing is accommodated via multiple intersecting planes rather than a single through-going fault. Second, the SCT hosts sequences of Mw ∼7 strike-slip earthquakes that migrate westward through a rapid succession of events. Sequences in 1993 and 2015 both began along the eastern SCT and propagated west, but neither progression ruptured into or nucleated a large earthquake within the region near the tear. Utilizing b-value and Coulomb Failure Stress analyses, we examine these along-strike variations in the SCT's seismicity. b-Values are highest along the youngest, western end of the SCT and decrease with increasing distance from the tear. This trend may reflect increasing strain localization with increasing displacement. Coulomb Failure Stress analyses indicate that the stress conditions were conducive to continued western propagation of the 1993 and 2015 sequences suggesting that the unruptured western SCT may have fault geometries or properties that inhibit continued rupture. Our results indicate a displacement-driven fault maturation process. The multi-plane Australia plate tearing likely creates a western SCT with diffuse strain accommodated along a network of disorganized faults. After ∼90 km of cumulative displacement (∼900,000 yr of plate motion), strain localizes and faults align, allowing the SCT to host large earthquakes.

Probing storm-time near-Earth magnetotail dynamics using 30 keV proton isotropic boundaries as tracers of precipitating and trapped populations

NASA Astrophysics Data System (ADS)

Ganushkina, N. Y.; Dubyagin, S.; Liemohn, M. W.

2017-12-01

The isotropic boundaries of the energetic protons, which can be routinely observed by low-altitude satellites, have been used as a tool to probe remotely the nightside magnetic configuration in the near-Earth region. The validity of this method is based on the assumption that the isotropic boundary is formed by the particle scattering on the curved field lines in the magnetotail current sheet. However recent results revealed that the wave-particle interaction process often can be responsible for the isotropic boundary formation especially during active times. Using numerous observations of the 30 keV proton isotropic boundaries and conjugated measurements of the magnetic field in the equatorial magnetosphere we demonstrate that isotropic boundary location can be used as a proxy of the magnetotail stretching even during magnetic storms. The results imply that the scattering on the curved field lines still plays major role as a mechanism of the isotropic boundary formation during storm-time. We found that the wave-particle interaction could lead to isotropic boundary formation in 15% of events. In addition, we discuss the morphology of the storm-time energetic proton precipitations.

Genetic diversity of Haemonchus contortus isolated from sympatric wild blue sheep (Pseudois nayaur) and sheep in Helan Mountains, China.

PubMed

Shen, Dong-Dong; Wang, Ji-Fei; Zhang, Dan-Yu; Peng, Zhi-Wei; Yang, Tian-Yun; Wang, Zhao-Ding; Bowman, Dwight D; Hou, Zhi-Jun; Liu, Zhen-Sheng

2017-09-19

Haemonchus contortus is known among parasitic nematodes as one of the major veterinary pathogens of small ruminants and results in great economic losses worldwide. Human activities, such as the sympatric grazing of wild with domestic animals, may place susceptible wildlife hosts at risk of increased prevalence and infection intensity with this common small ruminant parasite. Studies on phylogenetic factors of H. contortus should assist in defining the amount of the impact of anthropogenic factors on the extent of sharing of agents such as this nematode between domestic animals and wildlife. H. contortus specimens (n = 57) were isolated from wild blue sheep (Pseudois nayaur) inhabiting Helan Mountains (HM), China and additional H. contortus specimens (n = 20) were isolated from domestic sheep that were grazed near the natural habitat of the blue sheep. Complete ITS2 (second internal transcribed spacer) sequences and partial sequences of the nad4 (nicotinamide dehydrogenase subunit 4 gene) gene were amplified to determine the sequence variations and population genetic diversities between these two populations. Also, 142 nad4 haplotype sequences of H. contortus from seven other geographical regions of China were retrieved from database to further examine the H. contortus population structure. Sequence analysis revealed 10 genotypes (ITS2) and 73 haplotypes (nad4) among the 77 specimens, with nucleotide diversities of 0.007 and 0.021, respectively, similar to previous studies in other countries, such as Pakistan, Malaysia and Yemen. Phylogenetic analyses (BI, MP, NJ) of nad4 sequences showed that there were no noticeable boundaries among H. contortus populations from different geographical origin and population genetic analyses revealed that most of the variation (94.21%) occurred within H. contortus populations. All phylogenetic analyses indicated that there was little genetic differentiation but a high degree of gene flow among the H. contortus populations among wild blue sheep and domestic ruminants in China. The current work is the first genetic characterization of H. contortus isolated from wild blue sheep in the Helan Mountains region. The results revealed a low genetic differentiation and high degree of gene flow between the H. contortus populations from sympatric wild blue sheep and domestic sheep, indicating regular cross-infection between the sympatrically reared ruminants.

Northern Cascadia Subduction Zone Earthquake Records from Onshore and Offshore Core Data

NASA Astrophysics Data System (ADS)

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

2016-12-01

We are investigating the paleoseismic record at Bull Run Lake, at the latitude of Portland, Oregon, central Cascadia margin. Bull Run is a landslide dammed lake in a cirque basin on the western flanks of Mt. Hood, 65 km east of Portland, and is the City of Portland's primary water supply. We collected full coverage high-resolution multibeam and backscatter data, high resolution CHIRP sub-bottom profiles, and seven sediment cores which contain a correlative turbidite sequence of post Mazama beds. The continuity of the turbidite record shows little or no relationship to the minor stream inlets, suggesting the disturbance beds are not likely to be storm related. CT and physical property data were used to separate major visible beds and background sedimentation, which also contain thin laminae. The XRF element Compton scattering may show grading due to mineralogical variation and a change in wave profile, commonly found at bed boundaries. We have identified 27 post -Mazama event beds and 5 ashes in the lake, and constructed an OxCal age model anchored by radiocarbon ages, the Mazama ash, and the twin Timberline ash beds. The radiocarbon ages, age model results, as well as electron microprobe (EMP) data clearly identify the Mazama ash at the base of our cores. Two closely-spaced ash beds in our cores likely correlate to the Timberline eruptive period at 1.5ka. The number, timing and sequence of the event beds, and physical property log correlation, as well as key bed characteristics, closely matches offshore turbidite sequences off northern Oregon. For example, key regional bed T11, observed as a thick two-pulse bed in all offshore cores, also anchors the Bull Run sequence. One difference is that the twin Timberline ash occupies the stratigraphic position of regional offshore paleoseismic bed T4, which is also a two pulse event at this latitude. The cores also contain many faint laminae that may contain a storm record, however, the identification of small beds is complicated by the low sedimentation rate and low resolution of the Bull Run cores. The watershed and lake may also contain evidence of crustal faulting, though the event sequence appears to be primarily that of the Cascadia subduction zone earthquake sequence. See also Goldfinger et al. for investigation of slope stability and ground motions at Bull Run and other Cascadia lakes.

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

PubMed

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

2016-08-01

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

Cenomanian-Turonian biostratigraphy of the Jardas Al Abid area, Al Jabal Al Akhdar, northeast Libya

NASA Astrophysics Data System (ADS)

El Qot, Gamal M.; Abdulsamad, Esam O.

2016-09-01

The Upper Cenomanian-Turonian succession exposed at Jardas al'Abid area consists mainly of carbonates with siliciclastic intercalations. This succession is subdivided lithostratigraphically into: Qasr al'Abid (Late Cenomanian) and Al Baniyah (Late Cenomanian-Coniacian) formations. This sequence is relatively rich in macrofossil assemblages especially bivalves, gastropods, and echinoids with rare ammonites. Based on the first occurrence (FO) and last occurrence (LO) of some index species of these macrofossil groups, an integrated biostratigraphic framework has been constructed. The studied Cenomanian-Turonian sequence is subdivided biostratigraphically into three ammonite biozones; Pseudaspidoceras pseudonodosoides Total Range Zone, Choffaticeras segne Total Range Zone, and Coilopoceras requienianum Total Range Zone. Based on the rest of macrofossil assemblages other than the ammonites, eight biozones were recognized; Mecaster batnensis Total Range Zone, Ceratostreon flabellatum-Neithea dutrugei Acme Zone, Costagyra olisiponensis Acme Zone, Pycnodonte (Phygraea) vesicularis vesiculosa Acme Zone, Mytiloides labiatus Total Range Zone = Mecaster turonensis Acme Zone, Rachiosoma rectilineatum-Curvostrea rouvillei-Tylostoma (T.) globosum Assemblage Zone, Radiolites sp.-Apricardia? matheroni Total Range Zone, and Nerinea requieniana Total Range Zone. Most of the proposed biozones are recorded for the first time from Libya. The integration among these biozones as well as local and inter-regional correlation of the biozones have been discussed. The stage boundaries of the studied stratigraphic intervals are discussed, where the Cenomanian/Turonian boundary is delineated at the last occurrence (LO) of Pseudaspidoceras pseudonodosoides (Choffat), while the Turonian/Coniacian boundary is delineated arbitrary being agree with the LO of the Turonian fauna.

Anomalous Buckling Characteristics of Laminated Metal-Matrix Composite Plates with Central Square Holes

NASA Technical Reports Server (NTRS)

Ko, William L.

1998-01-01

Compressive buckling analysis was performed on metal-matrix composite (MMC) plates with central square holes. The MMC plates have varying aspect ratios and hole sizes and are supported under different boundary conditions. The finite-element structural analysis method was used to study the effects of plate boundary conditions, plate aspect ratio, hole size, and the composite stacking sequence on the compressive buckling strengths of the perforated MMC plates. Studies show that by increasing the hole sizes, compressive buckling strengths of the perforated MMC plates could be considerably increased under certain boundary conditions and aspect ratios ("anomalous" buckling behavior); and that the plate buckling mode could be symmetrical or antisymmetrical, depending on the plate boundary conditions, aspect ratio, and the hole size. For same-sized plates with same-sized holes, the compressive buckling strengths of the perforated MMC plates with [90/0/0/90]2 lamination could be as much as 10 percent higher or lower than those of the [45/- 45/- 45/45]2 laminations, depending on the plate boundary conditions, plate aspect ratios, and the hole size. Clamping the plate edges induces far stronger "anomalous" buckling behavior (enhancing compressive buckling strengths at increasing hole sizes) of the perforated MMC plates than simply supporting the plate edges.

Faunal and erosional events in the Eastern Tethyan Sea across the K/T boundary

NASA Technical Reports Server (NTRS)

Keller, G.; Benjamini, C.

1988-01-01

A regional pattern of three closely spaced erosional events at and above the K/T boundary was determined from six Cretaceous/Tertiary boundary sections in the Negev of Israel. The sections were collected from locations throughout the central and northern Negev. All sections are lithologically similar. The Maastrichtian consists of a sequence of limestone beds intercalated with thin marly beds. In some sections, the last limestone bed is followed by 1 to 2 m of calcareous marls grading upwards into several meters of grey shale. In other sections the limestone bed is followed directly by grey shale with the contact containing particles of limestone and marl. A 5 to 20 cm thick dark grey organic-rich clay layer is present about 1.5 to 2.5 m above the base of the grey shale. The grey shale grades upwards into increasingly carbonate rich marls. No unconformities are apparent in field outcrops. During field collection the dark grey clay layer was believed to represent the K/T boundary clay. Microfossil analysis however identified the boundary at the base of the grey shale. The black shale represents a low productivity anoxic event similar to, but younger than, the K/T boundary clay in other K/T boundary sections. High resolution planktic foraminiferal and carbonate analysis of these sections (at 5 to 10 cm intervals) yield surprising results. The K/T boundary is marked by an erosional event which removed part or all of the uppermost Maastrichtian marls above the last limestone bed. Percent carbonate data for four Negev sections are illustrated and show the regional similarities in carbonate sedimentation. Faunal and carbonate data from the Negev sections thus show three closely spaced short erosional events at the K/T boundary and within the first 50,000 to 100,000 years of the Danian. These K/T boundary erosional events may represent global climatic or paleoceanographic events.

Highlights of the Didymellaceae: A polyphasic approach to characterise Phoma and related pleosporalean genera

PubMed Central

Aveskamp, M.M.; de Gruyter, J.; Woudenberg, J.H.C.; Verkley, G.J.M.; Crous, P.W.

2010-01-01

Fungal taxonomists routinely encounter problems when dealing with asexual fungal species due to poly- and paraphyletic generic phylogenies, and unclear species boundaries. These problems are aptly illustrated in the genus Phoma. This phytopathologically significant fungal genus is currently subdivided into nine sections which are mainly based on a single or just a few morphological characters. However, this subdivision is ambiguous as several of the section-specific characters can occur within a single species. In addition, many teleomorph genera have been linked to Phoma, three of which are recognised here. In this study it is attempted to delineate generic boundaries, and to come to a generic circumscription which is more correct from an evolutionary point of view by means of multilocus sequence typing. Therefore, multiple analyses were conducted utilising sequences obtained from 28S nrDNA (Large Subunit - LSU), 18S nrDNA (Small Subunit - SSU), the Internal Transcribed Spacer regions 1 & 2 and 5.8S nrDNA (ITS), and part of the β-tubulin (TUB) gene region. A total of 324 strains were included in the analyses of which most belonged to Phoma taxa, whilst 54 to related pleosporalean fungi. In total, 206 taxa were investigated, of which 159 are known to have affinities to Phoma. The phylogenetic analysis revealed that the current Boeremaean subdivision is incorrect from an evolutionary point of view, revealing the genus to be highly polyphyletic. Phoma species are retrieved in six distinct clades within the Pleosporales, and appear to reside in different families. The majority of the species, however, including the generic type, clustered in a recently established family, Didymellaceae. In the second part of this study, the phylogenetic variation of the species and varieties in this clade was further assessed. Next to the genus Didymella, which is considered to be the sole teleomorph of Phoma s. str., we also retrieved taxa belonging to the teleomorph genera Leptosphaerulina and Macroventuria in this clade. Based on the sequence data obtained, the Didymellaceae segregate into at least 18 distinct clusters, of which many can be associated with several specific taxonomic characters. Four of these clusters were defined well enough by means of phylogeny and morphology, so that the associated taxa could be transferred to separate genera. Aditionally, this study addresses the taxonomic description of eight species and two varieties that are novel to science, and the recombination of 61 additional taxa. PMID:20502538

Boundary scavenging in the Pacific Ocean - A comparison of Be-10 and Pa-231

NASA Technical Reports Server (NTRS)

Anderson, R. F.; Lao, Y.; Broecker, W. S.; Trumbore, S. E.; Hofmann, H. J.

1990-01-01

Measurements of U, Th, Pa-231, and Be-10 concentrations were conducted in Holocene sediments from several sites representing open-ocean and ocean-margin environments in the Pacific Ocean. The results show that boundary scavenging plays a major role in the removal of Be-10 from the Pacific. Deposition of Be-10 is more than an order of magnitude greater at margin sites than at deep central Pacific sites, while Pa-231 is 4- to 5-fold greater at margin sites. The factors controling boundary scavenging of Pa and Be are discussed.

Higher-order continuation for the determination of robot workspace boundaries

NASA Astrophysics Data System (ADS)

Hentz, Gauthier; Charpentier, Isabelle; Renaud, Pierre

2016-02-01

In the medical and surgical fields, robotics may be of great interest for safer and more accurate procedures. Space constraints for a robotic assistant are however strict. Therefore, roboticists study non-conventional mechanisms with advantageous size/workspace ratios. The determination of mechanism workspace, and primarily its boundaries, is thus of major importance. This Note builds on boundary equation definition, continuation and automatic differentiation to propose a general, accurate, fast and automated method for the determination of mechanism workspace. The method is illustrated with a planar RRR mechanism and a three-dimensional Orthoglide parallel mechanism.

First principles determination of dislocation properties.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamilton, John C.

2003-12-01

This report details the work accomplished on first principles determination of dislocation properties. It contains an introduction and three chapters detailing three major accomplishments. First, we have used first principle calculations to determine the shear strength of an aluminum twin boundary. We find it to be remarkably small ({approx}17 mJ/m{sup 2}). This unexpected result is explained and will likely pertain for many other grain boundaries. Second, we have proven that the conventional explanation for finite grain boundary facets is wrong for a particular aluminum grain boundary. Instead of finite facets being stabilized by grain boundary stress, we find them tomore » originate from kinetic effects. Finally we report on a new application of the Frenkel-Kontorova model to understand reconstructions of (100) type surfaces. In addition to the commonly accepted formation of rectangular dislocation arrays, we find numerous other possible solutions to the model including hexagonal reconstructions and a clock-rotated structure.« less

Boundary conditions for the Middle Miocene Climate Transition (MMCT v1.0)

NASA Astrophysics Data System (ADS)

Frigola, Amanda; Prange, Matthias; Schulz, Michael

2018-04-01

The Middle Miocene Climate Transition was characterized by major Antarctic ice sheet expansion and global cooling during the interval ˜ 15-13 Ma. Here we present two sets of boundary conditions for global general circulation models characterizing the periods before (Middle Miocene Climatic Optimum; MMCO) and after (Middle Miocene Glaciation; MMG) the transition. These boundary conditions include Middle Miocene global topography, bathymetry, and vegetation. Additionally, Antarctic ice volume and geometry, sea level, and atmospheric CO2 concentration estimates for the MMCO and the MMG are reviewed. The MMCO and MMG boundary conditions have been successfully applied to the Community Climate System Model version 3 (CCSM3) to provide evidence of their suitability for global climate modeling. The boundary-condition files are available for use as input in a wide variety of global climate models and constitute a valuable tool for modeling studies with a focus on the Middle Miocene.

Defect and grain boundary scattering in tungsten: A combined theoretical and experimental study

NASA Astrophysics Data System (ADS)

Lanzillo, Nicholas A.; Dixit, Hemant; Milosevic, Erik; Niu, Chengyu; Carr, Adra V.; Oldiges, Phil; Raymond, Mark V.; Cho, Jin; Standaert, Theodorus E.; Kamineni, Vimal K.

2018-04-01

Several major electron scattering mechanisms in tungsten (W) are evaluated using a combination of first-principles density functional theory, a Non-Equilibrium Green's Function formalism, and thin film Kelvin 4-point sheet resistance measurements. The impact of grain boundary scattering is found to be roughly an order of magnitude larger than the impact of defect scattering. Ab initio simulations predict average grain boundary reflection coefficients for a number of twin grain boundaries to lie in the range r = 0.47 to r = 0.62, while experimental data can be fit to the empirical Mayadas-Schatzkes model with a comparable but slightly larger value of r = 0.69. The experimental and simulation data for grain boundary resistivity as a function of grain size show excellent agreement. These results provide crucial insights for understanding the impact of scaling of W-based contacts between active devices and back-end-of-line interconnects in next-generation semiconductor technology.

Coordinated Parameterization Development and Large-Eddy Simulation for Marine and Arctic Cloud-Topped Boundary Layers

NASA Technical Reports Server (NTRS)

Bretherton, Christopher S.

2002-01-01

The goal of this project was to compare observations of marine and arctic boundary layers with: (1) parameterization systems used in climate and weather forecast models; and (2) two and three dimensional eddy resolving (LES) models for turbulent fluid flow. Based on this comparison, we hoped to better understand, predict, and parameterize the boundary layer structure and cloud amount, type, and thickness as functions of large scale conditions that are predicted by global climate models. The principal achievements of the project were as follows: (1) Development of a novel boundary layer parameterization for large-scale models that better represents the physical processes in marine boundary layer clouds; and (2) Comparison of column output from the ECMWF global forecast model with observations from the SHEBA experiment. Overall the forecast model did predict most of the major precipitation events and synoptic variability observed over the year of observation of the SHEBA ice camp.

Magnetopause structure from satellite observations

NASA Technical Reports Server (NTRS)

Sonnerup, B. U. O.

1979-01-01

Observations on magnetopause structure are reported. Major topics covered include: classical reconnection, transport mechanisms, magnetospheric boundary layers, tearing modes, and Jupiter's magnetopause.

Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs.

PubMed

Yang, Jun-Bo; Li, De-Zhu; Li, Hong-Tao

2014-09-01

Chloroplast genomes supply indispensable information that helps improve the phylogenetic resolution and even as organelle-scale barcodes. Next-generation sequencing technologies have helped promote sequencing of complete chloroplast genomes, but compared with the number of angiosperms, relatively few chloroplast genomes have been sequenced. There are two major reasons for the paucity of completely sequenced chloroplast genomes: (i) massive amounts of fresh leaves are needed for chloroplast sequencing and (ii) there are considerable gaps in the sequenced chloroplast genomes of many plants because of the difficulty of isolating high-quality chloroplast DNA, preventing complete chloroplast genomes from being assembled. To overcome these obstacles, all known angiosperm chloroplast genomes available to date were analysed, and then we designed nine universal primer pairs corresponding to the highly conserved regions. Using these primers, angiosperm whole chloroplast genomes can be amplified using long-range PCR and sequenced using next-generation sequencing methods. The primers showed high universality, which was tested using 24 species representing major clades of angiosperms. To validate the functionality of the primers, eight species representing major groups of angiosperms, that is, early-diverging angiosperms, magnoliids, monocots, Saxifragales, fabids, malvids and asterids, were sequenced and assembled their complete chloroplast genomes. In our trials, only 100 mg of fresh leaves was used. The results show that the universal primer set provided an easy, effective and feasible approach for sequencing whole chloroplast genomes in angiosperms. The designed universal primer pairs provide a possibility to accelerate genome-scale data acquisition and will therefore magnify the phylogenetic resolution and species identification in angiosperms. © 2014 John Wiley & Sons Ltd.

Desert bird associations with broad-scale boundary length: Applications in avian conservation

USGS Publications Warehouse

Gutzwiller, K.J.; Barrow, W.C.

2008-01-01

1. Current understanding regarding the effects of boundaries on bird communities has originated largely from studies of forest-non-forest boundaries in mesic systems. To assess whether broad-scale boundary length can affect bird community structure in deserts, and to identify patterns and predictors of species' associations useful in avian conservation, we studied relations between birds and boundary-length variables in Chihuahuan Desert landscapes. Operationally, a boundary was the border between two adjoining land covers, and broad-scale boundary length was the total length of such borders in a large area. 2. Within 2-km radius areas, we measured six boundary-length variables. We analysed bird-boundary relations for 26 species, tested for assemblage-level patterns in species' associations with boundary-length variables, and assessed whether body size, dispersal ability and cowbird-host status were correlates of these associations. 3. The abundances or occurrences of a significant majority of species were associated with boundary-length variables, and similar numbers of species were related positively and negatively to boundary-length variables. 4. Disproportionately small numbers of species were correlated with total boundary length, land-cover boundary length and shrubland-grassland boundary length (variables responsible for large proportions of boundary length). Disproportionately large numbers of species were correlated with roadside boundary length and riparian vegetation-grassland boundary length (variables responsible for small proportions of boundary length). Roadside boundary length was associated (positively and negatively) with the most species. 5. Species' associations with boundary-length variables were not correlated with body size, dispersal ability or cowbird-host status. 6. Synthesis and applications. For the species we studied, conservationists can use the regressions we report as working models to anticipate influences of boundary-length changes on bird abundance and occurrence, and to assess avifaunal composition for areas under consideration for protection. Boundary-length variables associated with a disproportionate or large number of species can be used as foci for landscape management. Assessing the underlying causes of bird-boundary relations may improve the prediction accuracy of associated models. We therefore advocate local- and broad-scale manipulative experiments involving the boundary types with which species were correlated, as indicated by the regressions. ?? 2008 The Authors.

After the blowdown: a resource assessment of the Boundary Waters Canoe Area Wilderness, 1999-2003

Treesearch

W. Keith Moser; Mark H. Hansen; Mark D. Nelson; Susan J. Crocker; Charles H. Perry; Bethany Schulz; Christopher W. Woodall

2007-01-01

The Boundary Waters Canoe Area Wilderness (BWCAW) was struck by a major windstorm on July 4, 1999. Estimated volume in blowdown areas was up to 29 percent less than in non-blowdown areas. Mean down woody fuel loadings were twice as high in blowdown areas than in non-blowdown areas. Overstory species diversity declined in blowdown areas, but understory diversity,...

Special Area Coding Community College District Boundaries on the Los Angeles County DIME File.

ERIC Educational Resources Information Center

Kinney, Paul W.; And Others

This report documents the development of three major products: (1) a Los Angeles County Dual Independent Map Encoding (DIME) File to which community college district boundaries have been special area coded; (2) a book-like listing of all house number ranges and street names and the college district and census tract they are found in; and (3) a…

Diabetes educator role boundaries in Australia: a documentary analysis.

PubMed

King, Olivia; Nancarrow, Susan; Grace, Sandra; Borthwick, Alan

2017-01-01

Diabetes educators provide self-management education for people living with diabetes to promote optimal health and wellbeing. Their national association is the Australian Diabetes Educators Association (ADEA), established in 1981. In Australia the diabetes educator workforce is a diverse, interdisciplinary entity, with nurses, podiatrists, dietitians and several other health professional groups recognised by ADEA as providers of diabetes education. Historically nurses have filled the diabetes educator role and anecdotally, nurses are perceived to have wider scope of practice when undertaking the diabetes educator role than the other professions eligible to practise diabetes education. The nature of the interprofessional role boundaries and differing scopes of practice of diabetes educators of various primary disciplines are poorly understood. Informed by a documentary analysis, this historical review explores the interprofessional evolution of the diabetes educator workforce in Australia and describes the major drivers shaping the role boundaries of diabetes educators from 1981 until 2017. This documentary analysis was undertaken in the form of a literature review. STARLITE framework guided the searches for grey and peer reviewed literature. A timeline featuring the key events and changes in the diabetes educator workforce was developed. The timeline was analysed and emerging themes were identified as the major drivers of change within this faction of the health workforce. This historical review illustrates that there have been drivers at the macro, meso and micro levels which reflect and are reflected by the interprofessional role boundaries in the diabetes educator workforce. The most influential drivers of the interprofessional evolution of the diabetes educator workforce occurred at the macro level and can be broadly categorised according to three major influences: the advent of non-medical prescribing; the expansion of the Medicare Benefits Schedule to include rebates for allied health services; and the competency movement. This analysis illustrates the gradual movement of the diabetes educator workforce from a nursing dominant entity, with an emphasis on interprofessional role boundaries, to an interdisciplinary body, in which role flexibility is encouraged. There is however, recent evidence of role boundary delineation at the meso and micro levels.

Poleward displacement of coastal upwelling-favorable winds through the 21st century

NASA Astrophysics Data System (ADS)

Rykaczewski, R. R.; Dunne, J. P.; Sydeman, W. J.; Garcia-Reyes, M.; Black, B.; Bograd, S. J.

2016-02-01

Coastal upwelling is a critical factor influencing the biological production, acidification, and deoxygenation of the ocean's major eastern boundary current ecosystems. A leading conceptual hypothesis projects that the winds that induce coastal upwelling will intensify in response to increased land-sea temperature differences associated with anthropogenic global warming. We examine this hypothesis using an ensemble of coupled, ocean-atmosphere models and find limited evidence for intensification of upwelling-favorable winds or atmospheric pressure gradients in response to increasing land-sea temperature differences. However, our analyses reveal consistent latitudinal and seasonal dependencies of projected changes in wind intensity associated with poleward migration of major atmospheric high-pressure cells. Summertime winds near poleward boundaries of climatological upwelling zones are projected to intensify, while winds near equatorward boundaries are projected to weaken. Developing a better understanding of future changes in upwelling winds is essential to identifying portions of the oceans susceptible to increased hypoxia, ocean acidification, and eutrophication under climate change.

Parcellation in Left Lateral Parietal Cortex Is Similar in Adults and Children

PubMed Central

Nelson, Steven M.; Cohen, Alexander L.; Power, Jonathan D.; Coalson, Rebecca S.; Miezin, Francis M.; Vogel, Alecia C.; Dubis, Joseph W.; Church, Jessica A.; Petersen, Steven E.; Schlaggar, Bradley L.

2012-01-01

A key question in developmental neuroscience involves understanding how and when the cerebral cortex is partitioned into distinct functional areas. The present study used functional connectivity MRI mapping and graph theory to identify putative cortical areas and generate a parcellation scheme of left lateral parietal cortex (LLPC) in 7 to 10-year-old children and adults. Results indicated that a majority of putative LLPC areas could be matched across groups (mean distance between matched areas across age: 3.15 mm). Furthermore, the boundaries of children's putative LLPC areas respected the boundaries generated from the adults' parcellation scheme for a majority of children's areas (13/15). Consistent with prior research, matched LLPC areas showed age-related differences in functional connectivity strength with other brain regions. These results suggest that LLPC cortical parcellation and functional connectivity mature along different developmental trajectories, with adult-like boundaries between LLPC areas established in school-age children prior to adult-like functional connectivity. PMID:21810781

Identification of two novel pathogenic compound heterozygous MYO7A mutations in Usher syndrome by whole exome sequencing.

PubMed

Jia, Ying; Li, Xiaoge; Yang, Dong; Xu, Yi; Guo, Ying; Li, Xin

2018-01-01

The current study aims to identify the pathogenic sites in a core pedigree of Usher syndrome (USH). A core pedigree of USH was analyzed by whole exome sequencing (WES). Mutations were verified by polymerase chain reaction (PCR) amplification and Sanger sequencing. Two pathogenic variations (c.849+2T>C and c.5994G>A) in MYO7A were successfully identified and individually separated from parents. One variant (c.849+2T>C) was nonsense mutation, causing the protein terminated in advance, and the other one (c.5994G>A) located near the boundary of exon could cause aberrant splicing. This study provides a meaningful exploration for identification of clinical core genetic pedigrees. Copyright © 2017 Elsevier B.V. All rights reserved.

Adapted ECC ozonesonde for long-duration flights aboard boundary-layer pressurised balloons

NASA Astrophysics Data System (ADS)

Gheusi, François; Durand, Pierre; Verdier, Nicolas; Dulac, François; Attié, Jean-Luc; Commun, Philippe; Barret, Brice; Basdevant, Claude; Clenet, Antoine; Derrien, Solène; Doerenbecher, Alexis; El Amraoui, Laaziz; Fontaine, Alain; Hache, Emeric; Jambert, Corinne; Jaumouillé, Elodie; Meyerfeld, Yves; Roblou, Laurent; Tocquer, Flore

2016-12-01

Since the 1970s, the French space agency CNES has developed boundary-layer pressurised balloons (BLPBs) with the capability to transport lightweight scientific payloads at isopycnic level and offer a quasi-Lagrangian sampling of the lower atmosphere over very long distances and durations (up to several weeks).

Electrochemical concentration cell (ECC) ozonesondes are widely used under small sounding balloons. However, their autonomy is limited to a few hours owing to power consumption and electrolyte evaporation. An adaptation of the ECC sonde has been developed specifically for long-duration BLPB flights. Compared to conventional ECC sondes, the main feature is the possibility of programming periodic measurement sequences (with possible remote control during the flight). To increase the ozonesonde autonomy, the strategy has been adopted of short measurement sequences (2-3 min) regularly spaced in time (e.g. every 15 min). The rest of the time, the sonde pump is turned off. Results of preliminary ground-based tests are first presented. In particular, the sonde was able to provide correct ozone concentrations against a reference UV-absorption ozone analyser every 15 min for 4 days. Then we illustrate results from 16 BLBP flights launched over the western Mediterranean during three summer field campaigns of the ChArMEx project (http://charmex.lsce.ipsl.fr): TRAQA in 2012, and ADRIMED and SAFMED in 2013. BLPB drifting altitudes were in the range 0.25-3.2 km. The longest flight lasted more than 32 h and covered more than 1000 km. Satisfactory data were obtained when compared to independent ozone measurements close in space and time. The quasi-Lagrangian measurements allowed a first look at ozone diurnal evolution in the marine boundary layer as well as in the lower free troposphere. During some flight segments, there was indication of photochemical ozone production in the marine boundary layer or even in the free troposphere, at rates ranging from 1 to 2 ppbv h -1, which is slower than previously found in the boundary layer over land in the same region.

Automatic 3D motion estimation of left ventricle from C-arm rotational angiocardiography using a prior motion model and learning based boundary detector.

PubMed

Chen, Mingqing; Zheng, Yefeng; Wang, Yang; Mueller, Kerstin; Lauritsch, Guenter

2013-01-01

Compared to pre-operative imaging modalities, it is more convenient to estimate the current cardiac physiological status from C-arm angiocardiography since C-arm is a widely used intra-operative imaging modality to guide many cardiac interventions. The 3D shape and motion of the left ventricle (LV) estimated from rotational angiocardiography provide important cardiac function measurements, e.g., ejection fraction and myocardium motion dyssynchrony. However, automatic estimation of the 3D LV motion is difficult since all anatomical structures overlap on the 2D X-ray projections and the nearby confounding strong image boundaries (e.g., pericardium) often cause ambiguities to LV endocardium boundary detection. In this paper, a new framework is proposed to overcome the aforementioned difficulties: (1) A new learning-based boundary detector is developed by training a boosting boundary classifier combined with the principal component analysis of a local image patch; (2) The prior LV motion model is learned from a set of dynamic cardiac computed tomography (CT) sequences to provide a good initial estimate of the 3D LV shape of different cardiac phases; (3) The 3D motion trajectory is learned for each mesh point; (4) All these components are integrated into a multi-surface graph optimization method to extract the globally coherent motion. The method is tested on seven patient scans, showing significant improvement on the ambiguous boundary cases with a detection accuracy of 2.87 +/- 1.00 mm on LV endocardium boundary delineation in the 2D projections.

From fields to objects: A review of geographic boundary analysis

NASA Astrophysics Data System (ADS)

Jacquez, G. M.; Maruca, S.; Fortin, M.-J.

Geographic boundary analysis is a relatively new approach unfamiliar to many spatial analysts. It is best viewed as a technique for defining objects - geographic boundaries - on spatial fields, and for evaluating the statistical significance of characteristics of those boundary objects. This is accomplished using null spatial models representative of the spatial processes expected in the absence of boundary-generating phenomena. Close ties to the object-field dialectic eminently suit boundary analysis to GIS data. The majority of existing spatial methods are field-based in that they describe, estimate, or predict how attributes (variables defining the field) vary through geographic space. Such methods are appropriate for field representations but not object representations. As the object-field paradigm gains currency in geographic information science, appropriate techniques for the statistical analysis of objects are required. The methods reviewed in this paper are a promising foundation. Geographic boundary analysis is clearly a valuable addition to the spatial statistical toolbox. This paper presents the philosophy of, and motivations for geographic boundary analysis. It defines commonly used statistics for quantifying boundaries and their characteristics, as well as simulation procedures for evaluating their significance. We review applications of these techniques, with the objective of making this promising approach accessible to the GIS-spatial analysis community. We also describe the implementation of these methods within geographic boundary analysis software: GEM.

Horizontal gravity gradient - An aid to the definition of crustal structure in North America

NASA Technical Reports Server (NTRS)

Sharpton, V. L.; Grieve, R. A. F.; Thomas, M. D.; Halpenny, J. F.

1987-01-01

A map of the magnitude of the horizontal Bouguer gravity gradient over the North American continent is used to delineate lateral discontinuities in upper crustal density and/or thickness associated with such processes as suturing and rifting. The usefulness of gradient trends in mapping major structural boundaries, which are sometimes poorly exposed or completely buried, is demonstrated by examples such as the buried southward extension of the Grenville Front and buried boundaries of the Superior Province. Gradient trends also draw attention to poorly known structures, which may have major tectonic significance, and to a continent-wide structural fabric, which may provide a record of the tectonic growth of the North American continent.

Characterization of reniform nematode genome through shotgun sequencing

USDA-ARS?s Scientific Manuscript database

The reniform nematode (RN), a major agricultural pest particularly on cotton in the United States(U.S.), is among the major plant parasitic nematodes for which limited genomic information exists. In this study, over 380 Mb of sequence data were generated from four pooled adult female RN and assembl...

Opinion: Clarifying Two Controversies about Information Mapping's Method.

ERIC Educational Resources Information Center

Horn, Robert E.

1992-01-01

Describes Information Mapping, a methodology for the analysis, organization, sequencing, and presentation of information and explains three major parts of the method: (1) content analysis, (2) project life-cycle synthesis and integration of the content analysis, and (3) sequencing and formatting. Major criticisms of the methodology are addressed.…

Lithostratigraphic and biostratigraphic evidence for brief and synchronous Early Mesozoic basalt eruption over the Maghreb (Northwest Africa)

NASA Astrophysics Data System (ADS)

Et-Touhami, M.; Et-Touhami, M.; Olsen, P. E.; Puffer, J.

2001-05-01

Previously very sparse biostratigraphic data suggested that the Early Mesozoic tholeiitic effusive and intrusive magmatism in the various basins of the Maghreb occurred over a long time (Ladinian-Hettangian). However, a detailed comparison of the stratigraphy underlying, interbedded with, and overlying the basalts in these basins shows not only remarkable similarities with each other, but also with sequences in the latest Triassic and earliest Jurassic of eastern North America. There, the sequences have been shown to be cyclical, controlled by Milankovitch-type climate cycles; the same seems to be true in at least part of the Maghreb. Thus, the Moroccan basins have cyclical sequences surrounding and interbedded with one or two basaltic units. In the Argana and Khemisset basins the Tr-J boundary is identified by palynology to be below the lowest basalt, and the remarkably close lithological similarity between the pre-basalt sequence in the other Moroccan basins and to the North American basins - especially the Fundy basin - suggests a tight correlation in time. Likewise, the strata above the lowest basalt in Morocco show a similar pattern to what is seen above the lowest basalt formation in eastern North America, as do the overlying sequences. Furthermore, geochemistry on basalts in the Argana, Bou Fekrane, Khemisset, and Iouawen basins indicate they are high-Ti quartz-normative tholeiites as are the Orange Mountain Basalt (Fundy basin) and the North Mountain Basalt (Newark basin). The remarkable lithostratigraphic similarity across the Maghreb of these strata suggest contemporaneous and synchronous eruption over a time span of less than 200 ky, based on Milankovitch calibration, and within a ~20 ky interval after the Triassic-Jurassic boundary. Differences with previous interpretations of the biostratigraphy can be rationalized as a result of: 1, an over-reliance on comparisons with northern European palynology; 2, over-interpretation of poorly preserved fossils; and 3, rarity of early Jurassic non-marine ostracode assemblages.

Multigene assessment of the species boundaries and sexual status of the basidiomycetous yeasts Cryptococcus flavescens and C. terrestris (Tremellales).

PubMed

Yurkov, Andrey; Guerreiro, Marco A; Sharma, Lav; Carvalho, Cláudia; Fonseca, Álvaro

2015-01-01

Cryptococcus flavescens and C. terrestris are phenotypically indistinguishable sister species that belong to the order Tremellales (Tremellomycetes, Basidiomycota) and which may be mistaken for C. laurentii based on phenotype. Phylogenetic separation between C. flavescens and C. terrestris was based on rDNA sequence analyses, but very little is known on their intraspecific genetic variability or propensity for sexual reproduction. We studied 59 strains from different substrates and geographic locations, and used a multilocus sequencing (MLS) approach complemented with the sequencing of mating type (MAT) genes to assess genetic variation and reexamine the boundaries of the two species, as well as their sexual status. The following five loci were chosen for MLS: the rDNA ITS-LSU region, the rDNA IGS1 spacer, and fragments of the genes encoding the largest subunit of RNA polymerase II (RPB1), the translation elongation factor 1 alpha (TEF1) and the p21-activated protein kinase (STE20). Phylogenetic network analyses confirmed the genetic separation of the two species and revealed two additional cryptic species, for which the names Cryptococcus baii and C. ruineniae are proposed. Further analyses of the data revealed a high degree of genetic heterogeneity within C. flavescens as well as evidence for recombination between lineages detected for this species. Strains of C. terrestris displayed higher levels of similarity in all analysed genes and appear to make up a single recombining group. The two MAT genes (STE3 and SXI1/SXI2) sequenced for C. flavescens strains confirmed the potential for sexual reproduction and suggest the presence of a tetrapolar mating system with a biallelic pheromone/receptor locus and a multiallelic HD locus. In C. terrestris we could only sequence STE3, which revealed a biallelic P/R locus. In spite of the strong evidence for sexual recombination in the two species, attempts at mating compatible strains of both species on culture media were unsuccessful.

Observations of Displacement-driven Maturation along a Subduction-Transform Edge Propagator Fault

NASA Astrophysics Data System (ADS)

Neely, J. S.; Furlong, K. P.

2016-12-01

The Solomon Islands-Vanuatu composite subduction zone represents a tectonically complex region along the Pacific-Australia plate boundary in the southwest Pacific Ocean. Here the Australia plate subducts under the Pacific plate in two parts - the Solomon Trench and the Vanuatu Trench - with the two segments separated by a transform fault produced by a tear in the approaching Australia plate. As a result of the Australia plate tearing, the two subducting sections are offset by the 280 km long San Cristobal Trough (SCT) transform fault, which acts as a Subduction-Transform Edge Propagator (STEP) fault. The formation of this transform fault provides an opportunity to study the evolution of a newly created transform plate boundary. As distance from the tear increases, both the magnitude and frequency of earthquakes along the transform increase reflecting the coalescence of fault segments into a through-going structure. Over the past few decades, there have been several instances of larger magnitude earthquakes migrating westward along the STEP through a rapid succession of events. A recent May 2015 sequence of MW 6.8, MW 6.9, and MW 6.8 earthquakes followed this pattern, with an east to west migration over three days. However, neither this 2015 sequence, nor a previous 1993 progression, ruptured into or nucleated a large earthquake within the region near the tear. SCT sequence termination outside the region of the newly formed fault occurs even though Coulomb Failure Stress analyses reveal that the tear end of the SCT is positively loaded for failure by the earthquake sequence. Changing seismicity patterns along the SCT are also mapped by b-value variations that correspond to the rupture patterns of these propagating sequences. These seismicity pattern changes along the SCT reveal a fault maturation process with strain localization driven by cumulative slip corresponding to approximately 80-100 km of displacement.

A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional herbal medicinal genus

PubMed Central

Yao, Gang

2017-01-01

The herbal medicinal genus Aconitum L., belonging to the Ranunculaceae family, represents the earliest diverging lineage within the eudicots. It currently comprises of two subgenera, A. subgenus Lycoctonum and A. subg. Aconitum. The complete chloroplast (cp) genome sequences were characterized in three species: A. angustius, A. finetianum, and A. sinomontanum in subg. Lycoctonum and compared to other Aconitum species to clarify their phylogenetic relationship and provide molecular information for utilization of Aconitum species particularly in Eastern Asia. The length of the chloroplast genome sequences were 156,109 bp in A. angustius, 155,625 bp in A. finetianum and 157,215 bp in A. sinomontanum, with each species possessing 126 genes with 84 protein coding genes (PCGs). While genomic rearrangements were absent, structural variation was detected in the LSC/IR/SSC boundaries. Five pseudogenes were identified, among which Ψrps19 and Ψycf1 were in the LSC/IR/SSC boundaries, Ψrps16 and ΨinfA in the LSC region, and Ψycf15 in the IRb region. The nucleotide variability (Pi) of Aconitum was estimated to be 0.00549, with comparably higher variations in the LSC and SSC than the IR regions. Eight intergenic regions were revealed to be highly variable and a total of 58–62 simple sequence repeats (SSRs) were detected in all three species. More than 80% of SSRs were present in the LSC region. Altogether, 64.41% and 46.81% of SSRs are mononucleotides in subg. Lycoctonum and subg. Aconitum, respectively, while a higher percentage of di-, tri-, tetra-, and penta- SSRs were present in subg. Aconitum. Most species of subg. Aconitum in Eastern Asia were first used for phylogenetic analyses. The availability of the complete cp genome sequences of these species in subg. Lycoctonum will benefit future phylogenetic analyses and aid in germplasm utilization in Aconitum species. PMID:29134154

Multigene Assessment of the Species Boundaries and Sexual Status of the Basidiomycetous Yeasts Cryptococcus flavescens and C. terrestris (Tremellales)

PubMed Central

Sharma, Lav; Carvalho, Cláudia; Fonseca, Álvaro

2015-01-01

Cryptococcus flavescens and C. terrestris are phenotypically indistinguishable sister species that belong to the order Tremellales (Tremellomycetes, Basidiomycota) and which may be mistaken for C. laurentii based on phenotype. Phylogenetic separation between C. flavescens and C. terrestris was based on rDNA sequence analyses, but very little is known on their intraspecific genetic variability or propensity for sexual reproduction. We studied 59 strains from different substrates and geographic locations, and used a multilocus sequencing (MLS) approach complemented with the sequencing of mating type (MAT) genes to assess genetic variation and reexamine the boundaries of the two species, as well as their sexual status. The following five loci were chosen for MLS: the rDNA ITS-LSU region, the rDNA IGS1 spacer, and fragments of the genes encoding the largest subunit of RNA polymerase II (RPB1), the translation elongation factor 1 alpha (TEF1) and the p21-activated protein kinase (STE20). Phylogenetic network analyses confirmed the genetic separation of the two species and revealed two additional cryptic species, for which the names Cryptococcus baii and C. ruineniae are proposed. Further analyses of the data revealed a high degree of genetic heterogeneity within C. flavescens as well as evidence for recombination between lineages detected for this species. Strains of C. terrestris displayed higher levels of similarity in all analysed genes and appear to make up a single recombining group. The two MAT genes (STE3 and SXI1/SXI2) sequenced for C. flavescens strains confirmed the potential for sexual reproduction and suggest the presence of a tetrapolar mating system with a biallelic pheromone/receptor locus and a multiallelic HD locus. In C. terrestris we could only sequence STE3, which revealed a biallelic P/R locus. In spite of the strong evidence for sexual recombination in the two species, attempts at mating compatible strains of both species on culture media were unsuccessful. PMID:25811603

A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional herbal medicinal genus.

PubMed

Kong, Hanghui; Liu, Wanzhen; Yao, Gang; Gong, Wei

2017-01-01

The herbal medicinal genus Aconitum L., belonging to the Ranunculaceae family, represents the earliest diverging lineage within the eudicots. It currently comprises of two subgenera, A . subgenus Lycoctonum and A . subg. Aconitum . The complete chloroplast (cp) genome sequences were characterized in three species: A. angustius , A. finetianum , and A. sinomontanum in subg. Lycoctonum and compared to other Aconitum species to clarify their phylogenetic relationship and provide molecular information for utilization of Aconitum species particularly in Eastern Asia. The length of the chloroplast genome sequences were 156,109 bp in A. angustius , 155,625 bp in A. finetianum and 157,215 bp in A. sinomontanum , with each species possessing 126 genes with 84 protein coding genes (PCGs). While genomic rearrangements were absent, structural variation was detected in the LSC/IR/SSC boundaries. Five pseudogenes were identified, among which Ψ rps 19 and Ψ ycf 1 were in the LSC/IR/SSC boundaries, Ψ rps 16 and Ψ inf A in the LSC region, and Ψ ycf 15 in the IRb region. The nucleotide variability ( Pi ) of Aconitum was estimated to be 0.00549, with comparably higher variations in the LSC and SSC than the IR regions. Eight intergenic regions were revealed to be highly variable and a total of 58-62 simple sequence repeats (SSRs) were detected in all three species. More than 80% of SSRs were present in the LSC region. Altogether, 64.41% and 46.81% of SSRs are mononucleotides in subg. Lycoctonum and subg. Aconitum , respectively, while a higher percentage of di-, tri-, tetra-, and penta- SSRs were present in subg. Aconitum . Most species of subg. Aconitum in Eastern Asia were first used for phylogenetic analyses. The availability of the complete cp genome sequences of these species in subg. Lycoctonum will benefit future phylogenetic analyses and aid in germplasm utilization in Aconitum species.

Rifting Process and Geomorphic Development of the Okinawa Tough, Southwest Japan

NASA Astrophysics Data System (ADS)

Sato, T.; Arai, K.; Inoue, T.; Matsumoto, D.

2012-12-01

The Ryukyu Island Arc extends from Kyushu to Taiwan, a distance of 1,200 km, along the Ryukyu Trench where the Philippine Sea Plate is subducting beneath the Eurasian Plate. The Okinawa Trough, a back arc basin has formed behind the Ryukyu Island Arc in late Pliocene to early Pleistocene. The research cruises of GH11 (from 14 July to 15 August, 2011) and GH12 (from 20 to 30 July, 2012) were carried out around the Okinawa Trough. More than 3,600 miles multi channel high-resolution seismic profiles were acquired during these cruises by the GI-gun (Generator 250 cu inch and Injector 105 cu. inch) systems with 16ch digital streamer cable. As a result, two unconformities and three depositional sequence divided by the unconformities are recognized in the trough. The lower and the midlle sequence are tilted and blocked by many normal faults, on the other hand the upper one is not tilted and shows the pattern of onlap fill. From this result, the upper sequence started to deposit after start of the rifting. Additionally, internal reflection of the upper sequence shows the cyclic activities of the rifting. The position of the rifting axis was revealed based on dip of the normal faults. As a result, rifting axis shows echelon arrangement and the displacement of the faults are varied with the segment of the arrangement. The location of the segment boundaries is correlated with geometrical boundary of the adjacent slope. Steep slope with incised valley is distributed in southwestern part where the displacement of the normal fault is large, on the other hand, gentle slope without incised valley is distributed in northeastern part where the displacement is small. This difference of the displacement strongly controls the geometry of the adjacent slope.

An implicit boundary integral method for computing electric potential of macromolecules in solvent

NASA Astrophysics Data System (ADS)

Zhong, Yimin; Ren, Kui; Tsai, Richard

2018-04-01

A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equation that arises in mathematical models for the electrostatics of molecules in solvent. The proposed method uses an implicit boundary integral formulation to derive a linear system defined on Cartesian nodes in a narrowband surrounding the closed surface that separates the molecule and the solvent. The needed implicit surface is constructed from the given atomic description of the molecules, by a sequence of standard level set algorithms. A fast multipole method is applied to accelerate the solution of the linear system. A few numerical studies involving some standard test cases are presented and compared to other existing results.

Biostratigraphic, chronostratigraphic, and stratigraphic sequence analysis of Lower Tertiary marine sediments of Alabama for indicators of sea-level change

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, P.R.; Baum, G.R.

1991-03-01

Early Eocene to late Oligocene marine sedimentary units in southwestern Alabama were sampled at closely spaced intervals to derive a precise time-stratigraphic framework and to determine the paleoecological and mineralogical responses to fluctuations in sea level. Paleontologic control consisted of planktonic, smaller and larger benthonic foraminifera, calcareous nannofossils, dinoflagellates, and megafossils. Paleomagnetic reversals were delineated in two boreholes which, when supplemented by strontium isotope dates and the biostratigraphic control, provided a robust in situ chronostratigraphy for the Gulf Coast lower Tertiary. Paleoecologic trends in regression and transgression can be clearly correlated across major regional facies changes. Using the chronostratigraphy developedmore » here, the second-, third-, and fourth-orders of Vail's global sea-level cycles can be recognized and demonstrate the influence of sea-level change on sedimentation. Stratigraphic systems tracts (SSTs) and bounding surfaces in outcrop were determined by lithologic variations and paleoecologic trends, and additionally by gamma logs in the cores. The lower sequence boundary occurs at a contact where an older, relatively fine-grained, deep-water, fossiliferous unit was abruptly succeeded by a coarse-grained, shallow-water, poorly fossiliferous unit. The transgressive surface occurs at the base of a fining- and deepening-upwards unit that was commonly glauconitic and very fossiliferous. Transgression culminated with a pulse of planktonic microfossils in a bed having reduced clastic sedimentation; on the log the surface of maximum starvation was marked by a gamma spike.« less

Phytogeography of Najas gracillima (Hydrocharitaceae) in North America and its cryptic introduction to California.

PubMed

Les, Donald H; Peredo, Elena L; Benoit, Lori K; Tippery, Nicholas P; King, Ursula M; Sheldon, Sallie P

2013-09-01

The discontinuous North American distribution of Najas gracillima has not been explained satisfactorily. Influences of extirpation, nonindigenous introduction, and postglacial migration on its distribution were evaluated using field, fossil, morphological, and molecular data. Najas is a major waterfowl food, and appropriate conservation measures rely on accurate characterization of populations as indigenous or imperiled. • Seed lengths of N. gracillima from native Korean populations, a nonindigenous Italian population, and North American populations were compared using digital image analysis. DNA sequence analyses from these regions provided nine nrITS genotypes and eight cpDNA haplotypes. • Najas gracillima seeds from Eurasia and California are shorter than those from eastern North America. Nuclear and chloroplast DNA sequences of N. gracillima from Korea and Italy were identical to California material but differed from native eastern North American plants. Eastern North American specimens of N. gracillima at localities above the last glacial maximum boundary were identical or similar genetically to material from the northeastern United States and Atlantic Coastal Plain and Piedmont but divergent from plants of the Interior Highlands-Mississippi Embayment region. • In California, N. gracillima is nonindigenous and introduced from Asia. In eastern North America, populations that colonized deglaciated areas were derived primarily from refugia in the Atlantic Coastal Plain and Piedmont. Genetic data indicate initial postglacial migration to northeastern North America, with subsequent westward dispersal into the Upper Great Lakes. These results differentiate potentially invasive California populations from seriously imperiled indigenous eastern North American populations.

Fault source modeling of October 28, 2008 earthquake sequence in Baluchistan, Pakistan, on the basis of ALOS/PALSAR InSAR data

NASA Astrophysics Data System (ADS)

Usman, M.; Furuya, M.

2014-12-01

The Quetta Syntaxis in the western Baluchistan, Pakistan, serves as a junction for different thrust faults. As this area also lays close to the left lateral strike slip Chaman fault, which is supposed to be marking the boundary between Indian and Eurasian plate, thus the resulting seismological behavior of this regime becomes much more complex. In the region of Quetta Syntaxis, below the fold and thrust belt of Suleiman and Kirthar ranges and on 28 October 2008, there stroke an earthquake of magnitude 6.4 (Mw) which was followed by a doublet on the very next day. In association with these major events, there have been four more shocks, one foreshock and three aftershocks that have moment magnitude greater than 5. On the basis of seismological, GPS and ENVISAT/ASAR InSAR data many researchers tried to explain the source of this sequence. The latest source modeling results, on the basis of ENVISAT/ASAR data has provided an insight about the complexity of tectonics in the study area. However, in comparison to ALOS/PALSAR InSAR data, ENVISAT/ASAR has lacked signals near the epicentral area because of the low coherence. Probably, it has led to different interpretations by different researchers even on the basis of same satellite data. By using ALOS/PALSAR data, we have suggested a four faults model, two left laterals and two right laterals, which also retains the most desirable features of previous models.

Ecological and Genetic Divergences with Gene Flow of Two Sister Species (Leucomeris decora and Nouelia insignis) Driving by Climatic Transition in Southwest China.

PubMed

Zhao, Yujuan; Yin, Genshen; Pan, Yuezhi; Gong, Xun

2018-01-01

Understanding of the processes of divergence and speciation is a major task for biodiversity researches and may offer clearer insight into mechanisms generating biological diversity. Here, we employ an integrative approach to explore genetic and ecological differentiation of Leucomeris decora and Nouelia insignis distributed allopatrically along the two sides of the biogeographic boundary 'Tanaka Line' in Southwest China. We addressed these questions using ten low-copy nuclear genes and nine plastid DNA regions sequenced among individuals sampled from 28 populations across their geographic ranges in China. Phylogenetic, coalescent-based population genetic analyses, approximate Bayesian computation (ABC) framework and ecological niche models (ENMs) were conducted. We identified a closer phylogenetic relationship in maternal lineage of L. decora with N. insignis than that between L . decora and congeneric Leucomeris spectabilis . A deep divergence between the two species was observed and occurred at the boundary between later Pliocene and early Pleistocene. However, the evidence of significant chloroplast DNA gene flow was also detected between the marginal populations of L. decora and N. insignis . Niche models and statistical analyses showed significant ecological differentiation, and two nuclear loci among the ten nuclear genes may be under divergent selection. These integrative results imply that the role of climatic shift from Pliocene to Pleistocene may be the prominent factor for the divergence of L . decora and N . insignis , and population expansion after divergence may have given rise to chloroplast DNA introgression. The divergence was maintained by differential selection despite in the face of gene flow.

Segmentation of British Sign Language (BSL): mind the gap!

PubMed

Orfanidou, Eleni; McQueen, James M; Adam, Robert; Morgan, Gary

2015-01-01

This study asks how users of British Sign Language (BSL) recognize individual signs in connected sign sequences. We examined whether this is achieved through modality-specific or modality-general segmentation procedures. A modality-specific feature of signed languages is that, during continuous signing, there are salient transitions between sign locations. We used the sign-spotting task to ask if and how BSL signers use these transitions in segmentation. A total of 96 real BSL signs were preceded by nonsense signs which were produced in either the target location or another location (with a small or large transition). Half of the transitions were within the same major body area (e.g., head) and half were across body areas (e.g., chest to hand). Deaf adult BSL users (a group of natives and early learners, and a group of late learners) spotted target signs best when there was a minimal transition and worst when there was a large transition. When location changes were present, both groups performed better when transitions were to a different body area than when they were within the same area. These findings suggest that transitions do not provide explicit sign-boundary cues in a modality-specific fashion. Instead, we argue that smaller transitions help recognition in a modality-general way by limiting lexical search to signs within location neighbourhoods, and that transitions across body areas also aid segmentation in a modality-general way, by providing a phonotactic cue to a sign boundary. We propose that sign segmentation is based on modality-general procedures which are core language-processing mechanisms.

The earthquake cycle in the San Francisco Bay region: A.D. 1600–2012

USGS Publications Warehouse

Schwartz, David P.; Lienkaemper, James J.; Hecker, Suzanne; Kelson, Keith I.; Fumal, Thomas E.; Baldwin, John N.; Seitz, Gordon G.; Niemi, Tina

2014-01-01

Stress changes produced by the 1906 San Francisco earthquake had a profound effect on the seismicity of the San Francisco Bay region (SFBR), dramatically reducing it in the twentieth century. Whether the SFBR is still within or has emerged from this seismic quiescence is an issue of debate with implications for earthquake mechanics and seismic hazards. Historically, the SFBR has not experienced one complete earthquake cycle (i.e., the accumulation of stress, its release primarily as coseismic slip during surface‐faulting earthquakes, its re‐accumulation in the interval following, and its subsequent rerelease). The historical record of earthquake occurrence in the SFBR appears to be complete at about M 5.5 back to 1850 (Bakun, 1999). For large events, the record may be complete back to 1776, which represents about half a cycle. Paleoseismic data provide a more complete view of the most recent pre‐1906 SFBR earthquake cycle, extending it back to about 1600. Using these, we have developed estimates of magnitude and seismic moment for alternative sequences of surface‐faulting paleoearthquakes occurring between 1600 and 1776 on the region’s major faults. From these we calculate seismic moment and moment release rates for different time intervals between 1600 and 2012. These show the variability in moment release and suggest that, in the SFBR regional plate boundary, stress can be released on a single fault in great earthquakes such as that in 1906 and in multiple ruptures distributed on the regional plate boundary fault system on a decadal time scale.

On the relation between carbon star spectral types and colors

NASA Technical Reports Server (NTRS)

Honeycutt, R. K.; Fay, T. D., Jr.; Warren, W. H., Jr.

1974-01-01

Observations of 32 carbon stars are listed in a table, taking into account the spectral classes given by Yamashita (1966) and Richer (1971). The relations between spectral type and color for carbon stars appear consistent with the differences between Yamashita's and Richer's types if carbon star groups I-III lie on a decreasing boundary temperature sequence.

Near-optimal energy transitions for energy-state trajectories of hypersonic aircraft

NASA Technical Reports Server (NTRS)

Ardema, M. D.; Bowles, J. V.; Terjesen, E. J.; Whittaker, T.

1992-01-01

A problem of the instantaneous energy transition that occurs in energy-state approximation is considered. The transitions are modeled as a sequence of two load-factor bounded paths (either climb-dive or dive-climb). The boundary-layer equations associated with the energy-state dynamic model are analyzed to determine the precise location of the transition.

Major histocompatibility complex variation in the endangered Przewalski's horse.

PubMed Central

Hedrick, P W; Parker, K M; Miller, E L; Miller, P S

1999-01-01

The major histocompatibility complex (MHC) is a fundamental part of the vertebrate immune system, and the high variability in many MHC genes is thought to play an essential role in recognition of parasites. The Przewalski's horse is extinct in the wild and all the living individuals descend from 13 founders, most of whom were captured around the turn of the century. One of the primary genetic concerns in endangered species is whether they have ample adaptive variation to respond to novel selective factors. In examining 14 Przewalski's horses that are broadly representative of the living animals, we found six different class II DRB major histocompatibility sequences. The sequences showed extensive nonsynonymous variation, concentrated in the putative antigen-binding sites, and little synonymous variation. Individuals had from two to four sequences as determined by single-stranded conformation polymorphism (SSCP) analysis. On the basis of the SSCP data, phylogenetic analysis of the nucleotide sequences, and segregation in a family group, we conclude that four of these sequences are from one gene (although one sequence codes for a nonfunctional allele because it contains a stop codon) and two other sequences are from another gene. The position of the stop codon is at the same amino-acid position as in a closely related sequence from the domestic horse. Because other organisms have extensive variation at homologous loci, the Przewalski's horse may have quite low variation in this important adaptive region. PMID:10430594

Epitope mapping and evaluation of specificity of T-helper sites in four major antigenic peptides of chicken riboflavin carrier protein in outbred rats.

PubMed

Subramanian, Sarada; Andal, S; Karande, Anjali A; Radhakantha Adiga, P

2003-11-07

This paper reviews our studies on synthetic peptides spanning the major antigenic determinants of the chicken riboflavin carrier protein (RCP; 219 AA). These determinants are composed of residues 4-24 (YGC), 64-83 (CED), 130-147 (GEN), and 200-219 (HAC) and function as minivaccines in terms of eliciting anti-peptide antibodies which recognize the native protein and are particularly promising contraceptive vaccine candidates. We have used 15-residue synthetic peptides to define short sequences involved in interaction with antibody and with T-cells. We have mapped the boundaries of T-cell epitopes of these peptides in outbred rats by immunizing the animals with each peptide and assaying the popliteal lymph node cell proliferation against a series of overlapping synthetic 15-mers covering the entire length of the individual peptides. The peptides YGC, GEN, and HAC harboured a single T-cell epitope each whereas the peptide CED exhibited bimodal response possessing two epitopes, one at N-terminus and the other at the C-terminus. These studies provide insight into the way in which an immunogen is viewed by the immune system. In addition, preferential T-cell helper function for B cells recognizing unique determinants on the same molecule was demonstrated. This information helps in exploiting synthetic peptides in the construction of designer immunogens which have potential as candidate vaccines.

Fungal communities in soils along a vegetative ecotone.

PubMed

Karst, Justine; Piculell, Bridget; Brigham, Christy; Booth, Michael; Hoeksema, Jason D

2013-01-01

We investigated the community composition and diversity of soil fungi along a sharp vegetative ecotone between coastal sage scrub (CSS) and nonnative annual grassland habitat at two sites in coastal California. USA- We pooled soil samples across 29 m transects on either side of the ecotone at each of the two sites, and. using clone libraries of fungal ribosomal DNA, we identified 280 operational taxonomic units (OTUs) from a total 40 g soil. We combined information from partial LSU and ITS sequences and found that the majority of OTUs belonged to the phylum Ascomycota, followed by Basidiomycota. Within the Ascomycota. a quarter of OTUs were Sordariomycetes. 17% were Leotiomycet.es, 16% were Dothideomycetes and the remaining OTUs were distributed among the classes Eurotiomycetes, Pezizomycetes, Lecanoromycetes, Orbiliomycetes and Arthoniomycetes. Within the Basidiomycota. all OTUs but one belonged to the subphylum Agaricomycotina. We also sampled plant communities at the same sites to offer a point of comparison for patterns in richness of fungal communities. Fungal communities had higher alpha and beta diversity than plant communities; fungal communities were approximately 20 times as rich as plant communities and the majority of OTUs were found in single soil samples. Soils harbored a unique mycoflora that did not reveal vegetative boundaries or site differences. High alpha and beta diversity and possible sampling artifacts necessitate extensive sampling to reveal differentiation in these fungal communities.

Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution

PubMed Central

Huang, Chien-Hsun; Sun, Renran; Hu, Yi; Zeng, Liping; Zhang, Ning; Cai, Liming; Zhang, Qiang; Koch, Marcus A.; Al-Shehbaz, Ihsan; Edger, Patrick P.; Pires, J. Chris; Tan, Dun-Yan; Zhong, Yang; Ma, Hong

2016-01-01

Brassicaceae is one of the most diverse and economically valuable angiosperm families with widely cultivated vegetable crops and scientifically important model plants, such as Arabidopsis thaliana. The evolutionary history, ecological, morphological, and genetic diversity, and abundant resources and knowledge of Brassicaceae make it an excellent model family for evolutionary studies. Recent phylogenetic analyses of the family revealed three major lineages (I, II, and III), but relationships among and within these lineages remain largely unclear. Here, we present a highly supported phylogeny with six major clades using nuclear markers from newly sequenced transcriptomes of 32 Brassicaceae species and large data sets from additional taxa for a total of 55 species spanning 29 out of 51 tribes. Clade A consisting of Lineage I and Macropodium nivale is sister to combined Clade B (with Lineage II and others) and a new Clade C. The ABC clade is sister to Clade D with species previously weakly associated with Lineage II and Clade E (Lineage III) is sister to the ABCD clade. Clade F (the tribe Aethionemeae) is sister to the remainder of the entire family. Molecular clock estimation reveals an early radiation of major clades near or shortly after the Eocene–Oligocene boundary and subsequent nested divergences of several tribes of the previously polytomous Expanded Lineage II. Reconstruction of ancestral morphological states during the Brassicaceae evolution indicates prevalent parallel (convergent) evolution of several traits over deep times across the entire family. These results form a foundation for future evolutionary analyses of structures and functions across Brassicaceae. PMID:26516094

Diversity of virus-host systems in hypersaline Lake Retba, Senegal.

PubMed

Sime-Ngando, Télesphore; Lucas, Soizick; Robin, Agnès; Tucker, Kimberly Pause; Colombet, Jonathan; Bettarel, Yvan; Desmond, Elie; Gribaldo, Simonetta; Forterre, Patrick; Breitbart, Mya; Prangishvili, David

2011-08-01

Remarkable morphological diversity of virus-like particles was observed by transmission electron microscopy in a hypersaline water sample from Lake Retba, Senegal. The majority of particles morphologically resembled hyperthermophilic archaeal DNA viruses isolated from extreme geothermal environments. Some hypersaline viral morphotypes have not been previously observed in nature, and less than 1% of observed particles had a head-and-tail morphology, which is typical for bacterial DNA viruses. Culture-independent analysis of the microbial diversity in the sample suggested the dominance of extremely halophilic archaea. Few of the 16S sequences corresponded to known archeal genera (Haloquadratum, Halorubrum and Natronomonas), whereas the majority represented novel archaeal clades. Three sequences corresponded to a new basal lineage of the haloarchaea. Bacteria belonged to four major phyla, consistent with the known diversity in saline environments. Metagenomic sequencing of DNA from the purified virus-like particles revealed very few similarities to the NCBI non-redundant database at either the nucleotide or amino acid level. Some of the identifiable virus sequences were most similar to previously described haloarchaeal viruses, but no sequence similarities were found to archaeal viruses from extreme geothermal environments. A large proportion of the sequences had similarity to previously sequenced viral metagenomes from solar salterns. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

Alaskan seismic gap only partially filled by 28 February 1979 earthquake

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lahr, J.C.; Stephens, C.D.; Hasegawa, H.S.

1980-03-21

The Saint Elias, Alaska, earthquake (magnitude 7.7) of 28 February 1979 is the first major earthquake since 1900 to occur along the complex Pacific-North American plate boundary between Yakutat Bay and Prince William Sound. This event involved complex rupture on a shallow, low-angle, north-dipping fault beneath the Chugach and Saint Elias Mountains. The plate boundary between Yakutat Bay and Prince William Sound had been identified as a seismic gap, an area devoid of major earthquakes during the last few decades, and was thought to be a likely site for a future major earthquake. Since the Saint Elias earthquake fills onlymore » the eastern quarter of the gap, the remainder of the gap to the west is a prime area for the study of precursory and coseismic phenomena associated with large earthquakes. 1 figure, 1 table.« less

Stratigraphy and structural evolution of southern Mare Serenitatis - A reinterpretation based on Apollo Lunar Sounder Experiment data

NASA Technical Reports Server (NTRS)

Sharpton, V. L.; Head, J. W., III

1983-01-01

Two subsurface reflecting horizons have been detected by the Apollo Lunar Sounder Experiment (ALSE) in the southern Mare Serenitatis which appear to be regolith layers more than 2 m thick, and are correlated with major stratigraphic boundaries in the southeastern Mare Serenitatis. The present stratigraphic boundaries in the southeastern Mare Serenitatis. The present analysis implies that the lower horizon represents the interface between the earliest mare unit and the modified Serenitatis basin material below. The depth of volcanic fill within Serenitatis is highly variable, with an average thickness of mare basalts under the ALSE ground track of 1.6 km. Comparisons with the Orientale basin topography suggests that a major increaae in load thickness could occur a few km basinward of the innermost extent of the traverse. The history of volcanic infilling of Mare Serenitatis was characterized by three major episodes of volcanism.

A STELLAR-MASS-DEPENDENT DROP IN PLANET OCCURRENCE RATES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mulders, Gijs D.; Pascucci, Ilaria; Apai, Dániel

2015-01-10

The Kepler spacecraft has discovered a large number of planets with up to one-year periods and down to terrestrial sizes. While the majority of the target stars are main-sequence dwarfs of spectral type F, G, and K, Kepler covers stars with effective temperatures as low as 2500 K, which corresponds to M stars. These cooler stars allow characterization of small planets near the habitable zone, yet it is not clear if this population is representative of that around FGK stars. In this paper, we calculate the occurrence of planets around stars of different spectral types as a function of planetmore » radius and distance from the star and show that they are significantly different from each other. We further identify two trends. First, the occurrence of Earth- to Neptune-sized planets (1-4 R {sub ⊕}) is successively higher toward later spectral types at all orbital periods probed by Kepler; planets around M stars occur twice as frequently as around G stars, and thrice as frequently as around F stars. Second, a drop in planet occurrence is evident at all spectral types inward of a ∼10 day orbital period, with a plateau further out. By assigning to each spectral type a median stellar mass, we show that the distance from the star where this drop occurs is stellar mass dependent, and scales with semi-major axis as the cube root of stellar mass. By comparing different mechanisms of planet formation, trapping, and destruction, we find that this scaling best matches the location of the pre-main-sequence co-rotation radius, indicating efficient trapping of migrating planets or planetary building blocks close to the star. These results demonstrate the stellar-mass dependence of the planet population, both in terms of occurrence rate and of orbital distribution. The prominent stellar-mass dependence of the inner boundary of the planet population shows that the formation or migration of planets is sensitive to the stellar parameters.« less

The Cretaceous-Paleogene boundary unit in the Gulf of Mexico: Large-scale oceanic basin response to the Chicxulub impact

NASA Astrophysics Data System (ADS)

Sanford, J. C.; Gulick, S. P.; Snedden, J.

2013-12-01

The prevailing theory for the Cretaceous-Paleogene (K-Pg) extinction event cites the Chicxulub asteroid impact on the Yucatán Peninsula as the catalyst for the global climatologic and ecologic crisis. This theory has been corroborated by a multitude of K-Pg boundary deposits observed globally in both boreholes and outcrops. The change in character of these deposits with proximity to the crater, from a millimeter-scale clay layer to a hectometer-scale carbonate sequence, supports a causal link between the boundary unit and the asteroid impact. Due to its passive marine setting and proximity to the Chicxulub crater, the Gulf of Mexico is the premier locale in which to study the near-field geologic effect of a massive bolide impact. Until recently, investigation of the K-Pg boundary deposit within the Gulf has been largely confined to outcrops and boreholes on the periphery of the basin due to the difficulty of observation of the boundary unit in the deep water. However, hydrocarbon exploration in the past decade has yielded significant borehole and seismic data that can be used to better understand the deep-water response to the impact and to gain a comprehensive regional understanding impact-related processes in the Gulf. Based on roughly 100 offshore and 300 onshore Cretaceous well penetrations, the K-Pg boundary is interpreted to range from a strictly erosional surface in shallow-water and coastal regimes to a mass transport deposit up to ~400 meters thick. Depth-converted seismic data throughout the Gulf corroborate such thicknesses and reveal that the deposit is virtually ubiquitous throughout the deep water. For the first time, the K-Pg boundary deposit has been tied from the central Gulf to the Chicxulub crater, further establishing a causative link between the two. Biostratigraphic data in wells confirm the age of the deposit and document the presence of the 'K-Pg boundary cocktail.' Seismic data reveals areas of extensive debris flows and slump deposits on the lower slope of the Florida Platform, providing further evidence of massive sediment redistribution. Log character of the boundary deposit varies significantly, suggesting changes in both depositional style (e.g, mass flow deposit, collapsed platform block, etc.) and sediment source (e.g., Yucatán Platform, Florida Platform, Texas coast, etc.). Reinvestigation of the classic K-Pg boundary deposits in DSDP Leg 77 cores reveals evidence of several sequences of debris flows and/or turbidites with possibly unique sediment sources, furthering our understanding of small-scale sedimentary processes of impact-related deposition. Generally, evidence supports the theory that the Chicxulub impact was a source of extreme allogenic energy that drastically altered the Gulf Mexico at the start of the Cenozoic. Seismogenic ground roll and multiple episodes of tsunami, erosion, platform collapse, and remobilized sediment effectively overwhelmed and resurfaced the basin's existing depositional systems within a matter of weeks to months. Such processes resulted in the nearly ubiquitous and often extremely thick K-Pg boundary unit in the Gulf. These results yield insight into the near-field effects of a massive bolide impact in a passive marine setting and the ability of such an impact to instantaneously restructure an oceanic basin and its depositional systems.

Telomere healing following DNA polymerase arrest-induced breakages is likely the main mechanism generating chromosome 4p terminal deletions.

PubMed

Hannes, Femke; Van Houdt, Jeroen; Quarrell, Oliver W; Poot, Martin; Hochstenbach, Ron; Fryns, Jean-Pierre; Vermeesch, Joris R

2010-12-01

Constitutional developmental disorders are frequently caused by terminal chromosomal deletions. The mechanisms and/or architectural features that might underlie those chromosome breakages remain largely unexplored. Because telomeres are the vital DNA protein complexes stabilizing linear chromosomes against chromosome degradation, fusion, and incomplete replication, those terminal-deleted chromosomes acquired new telomeres either by telomere healing or by telomere capture. To unravel the mechanisms leading to chromosomal breakage and healing, we sequenced nine chromosome 4p terminal deletion boundaries. A computational analysis of the breakpoint flanking region, including 12 previously published pure terminal breakage sites, was performed in order to identify architectural features that might be involved in this process. All terminal 4p truncations were likely stabilized by telomerase-mediated telomere healing. In the majority of breakpoints multiple genetic elements have a potential to induce secondary structures and an enrichment in replication stalling site motifs were identified. These findings suggest DNA replication stalling-induced chromosome breakage during early development is the first mechanistic step leading toward terminal deletion syndromes. © 2010 Wiley-Liss, Inc.

Surficial geology of the Cane Creek basin, Lauderdale County, Tennessee

USGS Publications Warehouse

Miller, J.H.

1991-01-01

The surficial geology of the Cane Creek basin, in Lauderdale County, West Tennessee, was studied from 1985-88. Peoria Loess is the parent material from which soils in the Cane Creek drainage basin were derived. In general, a brown silt grades into a gray silt from 5 to I7 feet below ground surface. This color change probably represents depth to water table prior to the channelization of Cane Creek. Only at river mile 11.9 does rock outcrop near the main channel. Lower reaches of major tributaries have surficial geology similar to the main channel. In upper reaches of Hyde Creek and Fain Spring Creek, the sequence from the St&ace is sand and gravels, red-brown sandstone, sand and clay layers, and then, an orange sand layer. Coarse-grained deposits are found most often along the northern boundary of the basin and only occasionally in areas to the west and south of the main channel. Depth to sand or gravel ranges from about 0 to 158 feet in the uplands, and generally deeper than 40 feet near the main channel.

Toward full exploitation of coherent and incoherent information in Sentinel-1 TOPS data for retrieving surface displacement: Application to the 2016 Kumamoto (Japan) earthquake

NASA Astrophysics Data System (ADS)

Jiang, Houjun; Feng, Guangcai; Wang, Teng; Bürgmann, Roland

2017-02-01

Sentinel-1's continuous observation program over all major plate boundary regions makes it well suited for earthquake studies. However, decorrelation due to large displacement gradients and limited azimuth resolution of the Terrain Observation by Progressive Scan (TOPS) data challenge acquiring measurements in the near field of many earthquake ruptures and prevent measurements of displacements in the along-track direction. Here we propose to fully exploit the coherent and incoherent information of TOPS data by using standard interferometric synthetic aperture radar (InSAR), split-bandwidth interferometry in range and azimuth, swath/burst-overlap interferometry, and amplitude cross correlation to map displacements in both the line-of-sight and the along-track directions. Application to the 2016 Kumamoto earthquake sequence reveals the coseismic displacements from the far field to the near field. By adding near-field constraints, the derived slip model reveals more shallow slip than obtained when only using far-field data from InSAR, highlighting the importance of exploiting all coherent and incoherent information in TOPS data.

Structural Analysis of Corneal Nano-nipple Arrays in Nymphalidae Butterflies

NASA Astrophysics Data System (ADS)

Lee, Ken Chun-Yi

This study is concerned with the two-dimensional arrangement of corneal nano-nipples on the eyes of two Nymphalid butterflies. While the nano-nipples are predominantly in close-packed ordered arrangements, there are coordination defects known as 5-7 defects that disrupt the local translational symmetry and generate a number of secondary defects. Most often 5-7 defects align in rows to separate nipple domains with different orientations much like grain boundaries in crystalline materials. Surprisingly, the majority of 5-7 defect rows are special low-sigma; boundaries that occur infrequently in random crystalline materials. Such prevalence of low-sigma; boundaries suggests that they may serve specific purposes. Based on the superlattices associated with the observed low-sigma; boundaries, it is tentatively suggested that they could lead to diffraction effects for infrared light.

Statistical learning of an auditory sequence and reorganization of acquired knowledge: A time course of word segmentation and ordering.

PubMed

Daikoku, Tatsuya; Yatomi, Yutaka; Yumoto, Masato

2017-01-27

Previous neural studies have supported the hypothesis that statistical learning mechanisms are used broadly across different domains such as language and music. However, these studies have only investigated a single aspect of statistical learning at a time, such as recognizing word boundaries or learning word order patterns. In this study, we neutrally investigated how the two levels of statistical learning for recognizing word boundaries and word ordering could be reflected in neuromagnetic responses and how acquired statistical knowledge is reorganised when the syntactic rules are revised. Neuromagnetic responses to the Japanese-vowel sequence (a, e, i, o, and u), presented every .45s, were recorded from 14 right-handed Japanese participants. The vowel order was constrained by a Markov stochastic model such that five nonsense words (aue, eao, iea, oiu, and uoi) were chained with an either-or rule: the probability of the forthcoming word was statistically defined (80% for one word; 20% for the other word) by the most recent two words. All of the word transition probabilities (80% and 20%) were switched in the middle of the sequence. In the first and second quarters of the sequence, the neuromagnetic responses to the words that appeared with higher transitional probability were significantly reduced compared with those that appeared with a lower transitional probability. After switching the word transition probabilities, the response reduction was replicated in the last quarter of the sequence. The responses to the final vowels in the words were significantly reduced compared with those to the initial vowels in the last quarter of the sequence. The results suggest that both within-word and between-word statistical learning are reflected in neural responses. The present study supports the hypothesis that listeners learn larger structures such as phrases first, and they subsequently extract smaller structures, such as words, from the learned phrases. The present study provides the first neurophysiological evidence that the correction of statistical knowledge requires more time than the acquisition of new statistical knowledge. Copyright © 2016 Elsevier Ltd. All rights reserved.

Food supply and bioenergy production within the global cropland planetary boundary.

PubMed

Henry, R C; Engström, K; Olin, S; Alexander, P; Arneth, A; Rounsevell, M D A

2018-01-01

Supplying food for the anticipated global population of over 9 billion in 2050 under changing climate conditions is one of the major challenges of the 21st century. Agricultural expansion and intensification contributes to global environmental change and risks the long-term sustainability of the planet. It has been proposed that no more than 15% of the global ice-free land surface should be converted to cropland. Bioenergy production for land-based climate mitigation places additional pressure on limited land resources. Here we test normative targets of food supply and bioenergy production within the cropland planetary boundary using a global land-use model. The results suggest supplying the global population with adequate food is possible without cropland expansion exceeding the planetary boundary. Yet this requires an increase in food production, especially in developing countries, as well as a decrease in global crop yield gaps. However, under current assumptions of future food requirements, it was not possible to also produce significant amounts of first generation bioenergy without cropland expansion. These results suggest that meeting food and bioenergy demands within the planetary boundaries would need a shift away from current trends, for example, requiring major change in the demand-side of the food system or advancing biotechnologies.

Food supply and bioenergy production within the global cropland planetary boundary

PubMed Central

Olin, S.; Alexander, P.; Arneth, A.; Rounsevell, M. D. A.

2018-01-01

Supplying food for the anticipated global population of over 9 billion in 2050 under changing climate conditions is one of the major challenges of the 21st century. Agricultural expansion and intensification contributes to global environmental change and risks the long-term sustainability of the planet. It has been proposed that no more than 15% of the global ice-free land surface should be converted to cropland. Bioenergy production for land-based climate mitigation places additional pressure on limited land resources. Here we test normative targets of food supply and bioenergy production within the cropland planetary boundary using a global land-use model. The results suggest supplying the global population with adequate food is possible without cropland expansion exceeding the planetary boundary. Yet this requires an increase in food production, especially in developing countries, as well as a decrease in global crop yield gaps. However, under current assumptions of future food requirements, it was not possible to also produce significant amounts of first generation bioenergy without cropland expansion. These results suggest that meeting food and bioenergy demands within the planetary boundaries would need a shift away from current trends, for example, requiring major change in the demand-side of the food system or advancing biotechnologies. PMID:29566091

Shared Resources

Treesearch

David B. Butts

1987-01-01

Wildfires do not respect property boundaries. Whole geographic regions are typically impacted by major wildfire outbreaks. Various fire related resources can be shared to solve such crises; whether they are shared, and how they are shared depends to a great extent upon the rapport among the agencies involved. Major progress has been achieved over the past decade...

Earthquake-driven fluid flow rates inferred from borehole temperature measurements within the Japan Trench plate boundary fault zone

NASA Astrophysics Data System (ADS)

Fulton, P. M.; Brodsky, E. E.

2016-12-01

Using borehole sub-seafloor temperature measurements, we have recently identified signatures suggestive of earthquake-driven fluid pulses within the Japan Trench plate boundary fault zone during a major aftershock sequence. Here we use numerical models to show that these signatures are consistent with time-varying fluid flow rates out of permeable zones within the formation into the borehole annulus. In addition, we also identify an apparent time-varying sensitivity of whether suspected fluid pulses occur in response to earthquakes of a given magnitude and distance. The results suggest a damage and healing process and therefore provides a mechanism to allow for a disproportionate amount of heat and chemical transport in the short time frame after an earthquake. Our observations come from an observatory installed across the main plate boundary fault as part of IODP's Japan Trench Fast Drilling Project (JFAST) following the March 2011 Mw 9.0 Tohoku-oki earthquake. It operated from July 2012 - April 2013 during which a Mw 7.3 earthquake and numerous aftershocks occurred. High-resolution temperature time series data reveal spatially correlated transients in response to earthquakes with distinct patterns interpreted to reflect advection by transient pulses of fluid flow from permeable zones into the borehole annulus. Typical transients involve perturbations over 12 m with increases of 10 mK that build over 0.1 days at shallower depths and decreases at deeper depths. They are consistently centered around 792.5 m below seafloor (mbsf) where a secondary fault and permeable zone have been independently identified within the damage zone above the main plate boundary fault at 820 mbsf . Model simulations suggest transient flow rates of up to 10-3m/s from the formation that quickly decrease. Comparison of characteristics of earthquakes identified in nearby ocean bottom pressure measurements suggest there is not a clear relationship between fluid pulses and static strain. There does appear to be a time-varying sensitivity likely from dynamic stresses suggestive of a damage process followed by healing over 1 month time. The transient redistribution of fluid pressures and fluid flow within fault zones inferred here is a potential mechanism for earthquake triggering and episodic heat and chemical transport.

Phase transitions in MgSiO3 at high pressures and temperatures

NASA Astrophysics Data System (ADS)

Ono, S.

2017-12-01

As olivine, pyroxene and garnet are major minerals in the upper mantle, understanding the dynamics and evolution of the mantle requires knowledge of MgSiO3, which is an end-member of pyroxene. Therefore, phase relations in MgSiO3 have been repeatedly investigated by a number of authors. However, the transition sequence of the MgSiO3 mineral remains as yet unconfirmed. The discrepancy among researchers is likely due to the accuracy of phase boundary determinations related with the stability field of two phases, wadsleyite + stishovite or ringwoodite + stishovite.High-pressure experiments were carried out using multi-anvil high-pressure apparatus installed at the synchrotron facilities of KEK and SPring-8 in Japan. Experimental details were described elsewhere [e.g., 1,2]. A mixture of the powdered MgSiO3 and gold was used. Experimental pressures were determined from the unit cell volumes of gold. All recovered samples were investigated by an electron microprobe analyzer to identify the stable phase in each experimental run.Experimental runs were performed at pressures between 15 and 21 GPa. Two types of recovered samples, single (MgSiO3) and two phases (Mg2SiO4 + SiO2), were confirmed. The single phase was high-pressure clinoenstatite or akimotoite, and two phases were wadsleyite + stishovite or ringwoodite + stishovite. According to experimental data, two reaction boundaries were determined. The reaction boundary between high-pressure clinoenstatite and wadsleyite + stishovite has a positive dP/dT gradient, 0.0064 GPa/K [3]. In contrast, the reaction boundary between ringwoodite + stishovite and akimotoite has a negative dP/dT gradient, -0.0012 GPa/K [4]. This study indicates that the stability field of wadsleyite + stishovite expands to a low temperature region corresponding to the P-T path in the subducted slab. Moreover, a triple point of wadsleyite + stishovite-ringwoodite + stishovite-akimotoite is located at a temperature slightly lower than the geotherm. These experimental results can reconcile the inconsistency recorded between previous studies regarding the phase relation in MgSiO3.[1] Ono et al., Phys. Chem. Minerals, 40, 811-816 (2013)[2] Ono et al., Phys. Earth Planet. Inter., 264, 1-6 (2017)[3] Ono et al., (under review)[4] Ono et al., Phys. Chem. Minerals, 44, 425-430 (2017)

Boundaries and e-health implementation in health and social care.

PubMed

King, Gerry; O'Donnell, Catherine; Boddy, David; Smith, Fiona; Heaney, David; Mair, Frances S

2012-09-07

The major problem facing health and social care systems globally today is the growing challenge of an elderly population with complex health and social care needs. A longstanding challenge to the provision of high quality, effectively coordinated care for those with complex needs has been the historical separation of health and social care. Access to timely and accurate data about patients and their treatments has the potential to deliver better care at less cost. To explore the way in which structural, professional and geographical boundaries have affected e-health implementation in health and social care, through an empirical study of the implementation of an electronic version of Single Shared Assessment (SSA) in Scotland, using three retrospective, qualitative case studies in three different health board locations. Progress in effectively sharing electronic data had been slow and uneven. One cause was the presence of established structural boundaries, which lead to competing priorities, incompatible IT systems and infrastructure, and poor cooperation. A second cause was the presence of established professional boundaries, which affect staffs' understanding and acceptance of data sharing and their information requirements. Geographical boundaries featured but less prominently and contrasting perspectives were found with regard to issues such as co-location of health and social care professionals. To provide holistic care to those with complex health and social care needs, it is essential that we develop integrated approaches to care delivery. Successful integration needs practices such as good project management and governance, ensuring system interoperability, leadership, good training and support, together with clear efforts to improve working relations across professional boundaries and communication of a clear project vision. This study shows that while technological developments make integration possible, long-standing boundaries constitute substantial risks to IT implementations across the health and social care interface which those initiating major changes would do well to consider before committing to the investment.

Dynamically hot galaxies. I - Structural properties

NASA Technical Reports Server (NTRS)

Bender, Ralf; Burstein, David; Faber, S. M.

1992-01-01

Results are reported from an analysis of the structural properties of dynamically hot galaxies which combines central velocity dispersion, effective surface brightness, and effective radius into a new 3-space (k), in which the axes are parameters that are physically meaningful. Hot galaxies are found to divide into groups in k-space that closely parallel conventional morphological classifications, namely, luminous ellipticals, compacts, bulges, bright dwarfs, and dwarf spheroidals. A major sequence is defined by luminous ellipticals, bulges, and most compacts, which together constitute a smooth continuum in k-space. Several properties vary smoothly with mass along this continuum, including bulge-to-disk ratio, radio properties, rotation, degree of velocity anisotropy, and 'unrelaxed'. A second major sequence is comprised of dwarf ellipticals and dwarf spheroidals. It is suggested that mass loss is a major factor in hot dwarf galaxies, but the dwarf sequence cannot be simply a mass-loss sequence, as it has the wrong direction in k-space.

Identification of presumed ancestral DNA sequences of phaseolin in Phaseolus vulgaris.

PubMed Central

Kami, J; Velásquez, V B; Debouck, D G; Gepts, P

1995-01-01

Common bean (Phaseolus vulgaris) consists of two major geographic gene pools, one distributed in Mexico, Central America, and Colombia and the other in the southern Andes (southern Peru, Bolivia, and Argentina). Amplification and sequencing of members of the multigene family coding for phaseolin, the major seed storage protein of the common bean, provide evidence for accumulation of tandem direct repeats in both introns and exons during evolution of the multigene family in this species. The presumed ancestral phaseolin sequences, without tandem repeats, were found in recently discovered but nearly extinct wild common bean populations of Ecuador and northern Peru that are intermediate between the two major gene pools of the species based on geographical and molecular arguments. Our results illustrate the usefulness of tandem direct repeats in establishing the polarity of DNA sequence divergence and therefore in proposing phylogenies. Images Fig. 1 Fig. 3 PMID:7862642

Ecosystems response and restitution time across the K/Pg boundary transition at high-latitudes, Southern Hemisphere, New Zealand - a palynological approach

NASA Astrophysics Data System (ADS)

Willumsen, Pi; Vajda, Vivi

2010-05-01

Several major groups of biota/fauna disappeared globally across the Cretaceous-Paleogene boundary (K/Pg boundary) and several other important groups suffered considerable, but not complete, species-level extinction. For marine phytoplankton - a major driver of ocean productivity - darkness and suppression of photosynthesis, in the aftermath of the asteroid impact, was likely a major killing mechanism. Thus, in the marine realm there is a separation in extinction rate between strongly affected groups with calcareous shells and groups that had organic cysts or siliceous tests. Detailed regional records of the long-term post-K/Pg boundary therefore still need to be undertaken to enhance the understanding of how each of the major microfossil groups recovered to elucidate recovery in different ecosystem types following this unique event. Throughout the New Zealand region, widespread deposition of siliceous sediments occurred during the Late Cretaceous to early Paleocene indicating the existence of a south Pacific upwelling regime (Hollis 1993, 1995; Strong et al. 1995). Silica concentration in the oceans increased after the K/Pg event and remained high for 1-2 millions years during the early Paleogene, reflecting high bio-siliceous productivity in the aftermath of the K/Pg boundary event (Hollis et al. 1995, 2003). The geological archives of New Zealand includes outcrops from several basins which provide a unique possibility for examining ecosystem response and restitution time from latest Cretaceous to early Paleogene in a suite of depositional environments spanning from terrestrial to bathyal (Willumsen 2000, Vajda et al. 2001, Vajda and Raine 2003). High-resolution palynological comparative studies of organic-walled microfossils such as dinoflagellate assemblages (dinocysts), spores and pollen are currently carried out on New Zealand sediments. The recovery period in the marine realm is much extended compared with the much shorter recovery time reflected by the terrestrial record e.g. "Fern-spike" interval (Vajda et al. 2001; Vajda and Raine 2003; Vajda and McLoughlin 2004). Interestingly, the dinocyst Trithyrodinium evittii has first occurrence immediately above the K/Pg boundary horizon in the southwest Pacific (Helby et al., 1987; Wilson 1987, 1988; Williams et al. 2004; Willumsen 2000, 2006). This dinocyst pattern is interpreted to reflect an invasion of this species into the southwest Pacific, in the aftermath of the Chicxulub impact. In the New Zealand sections, two earliest Paleocene intervals with dominance of T. evittii are separated by an acme interval of Paleoperidinium pyrophorum (Willumsen 2000, 2006; Willumsen et al., 2004a; 2004b). The sudden acme of P. pyrophorum ca. 0.5 Ma after the K/Pg boundary event is interpreted to reflect a regional cold water pulse taking place after a period with relatively warmer sea-surface e.g. T. evittii dominated dinocyst assemblages. A second period with warm-surface water is observed c. 0.8-1.5 Ma after the event. The end of the main marine recovery period is marked by a gradual arrival of new suite of dinocyst species and oligotrophic conditions. The timing of these early Paleocene events in New Zealand aligns well with D'Hondt et al. (1998, 2005) who propose that the marine ecosystem was radically altered due to the K/Pg boundary event and that the post-K/Pg boundary is divided into several recovery steps before the open-ocean ecosystem was fully recovered c. 3 Ma after the event.

The bacteria and bacteriophages from a Mesquite Flats site of the Death Valley desert.

PubMed

Prestel, Eric; Regeard, Christophe; Salamitou, Sylvie; Neveu, Julie; Dubow, Michael S

2013-06-01

Arid zones cover over 30 % of the Earth's continental surface. In order to better understand the role of microbes in this type of harsh environment, we isolated and characterized the bacteriophages from samples of the surface sand of the Mesquite Flats region via electron microscopy and DNA sequencing of a select number of cloned phage DNAs. An electron microscopic analysis of the recovered virus-like particles revealed at least 11 apparently different morphotypes sharing structural characteristics of the Caudoviridae family of tailed phages. We found that 36 % of the sequences contained no significant identity (e-value >10(-3)) with sequences in the databases. Pilot sequencing of cloned 16S rRNA genes identified Bacteroidetes and Proteobacteria as the major bacterial groups present in this severe environment. The majority of the 16S rDNA sequences from the total (uncultured) bacterial population displayed ≤96 % identity to 16S rRNA genes in the database, suggesting an unexplored bacterial population likely adapted to a desert environment. In addition, we also isolated and identified 38 cultivable bacterial strains, the majority of which belonged to the genus Bacillus. Mitomycin-C treatment of the cultivable bacteria demonstrated that the vast majority (84 %) contained at least one SOS-inducible prophage.