Evolution of the alternative AQP2 gene: Acquisition of a novel protein-coding sequence in dolphins.

PubMed

Kishida, Takushi; Suzuki, Miwa; Takayama, Asuka

2018-01-01

Taxon-specific de novo protein-coding sequences are thought to be important for taxon-specific environmental adaptation. A recent study revealed that bottlenose dolphins acquired a novel isoform of aquaporin 2 generated by alternative splicing (alternative AQP2), which helps dolphins to live in hyperosmotic seawater. The AQP2 gene consists of four exons, but the alternative AQP2 gene lacks the fourth exon and instead has a longer third exon that includes the original third exon and a part of the original third intron. Here, we show that the latter half of the third exon of the alternative AQP2 arose from a non-protein-coding sequence. Intact ORF of this de novo sequence is shared not by all cetaceans, but only by delphinoids. However, this sequence is conservative in all modern cetaceans, implying that this de novo sequence potentially plays important roles for marine adaptation in cetaceans. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Gene discovery in Boophilus microplus, the cattle tick: the transcriptomes of ovaries, salivary glands, and hemocytes.

PubMed

Santos, Isabel K F de Miranda; Valenzuela, Jesus G; Ribeiro, José Marcos C; de Castro, Marilia; Costa, Juliana Nardelli; Costa, Ana Maria; da Silva, Edson Ramiro; Neto, Olavo Bilac Rego; Rocha, Clarisse; Daffre, Sirlei; Ferreira, Beatriz R; da Silva, João Santana; Szabó, Matias Pablo; Bechara, Gervasio Henrique

2004-10-01

The quest for new control strategies for ticks can profit from high throughput genomics. In order to identify genes that are involved in oogenesis and development, in defense, and in hematophagy, the transcriptomes of ovaries, hemocytes, and salivary glands from rapidly ingurgitating females, and of salivary glands from males of Boophilus microplus were PCR amplified, and the expressed sequence tags (EST) of random clones were mass sequenced. So far, more than 1,344 EST have been generated for these tissues, with approximately 30% novelty, depending on the the tissue studied. To date approximately 760 nucleotide sequences from B. microplus are deposited in the NCBI database. Mass sequencing of partial cDNAs of parasite genes can build up this scant database and rapidly generate a large quantity of useful information about potential targets for immunobiological or chemical control.

Effect of annealing on structural, electrical and optical properties of p-quaterphenyl thin films

NASA Astrophysics Data System (ADS)

Darwish, A. A. A.

2017-05-01

Thin films of p-quaterphenyl are deposited by an evaporation technique. IR spectra confirm that the thermal evaporation method is a decent one to acquire p-quaterphenyl films without dissociation. The X-ray diffraction studies demonstrate that the as-deposited and annealed films are polycrystalline with monoclinic structure. The electrical conductivity shows an activated behavior and indicating that p-quaterphenyl behaves as an organic semiconductor. The value of activation energy decreases by annealing, which explains due to the adjustment in the crystallite size. Optical properties of p-quaterphenyl films were performed to determine some optical constants. Dispersion of the refractive index is described utilizing the Wemple-DiDomenico model. In addition, the third order nonlinear susceptibility and the nonlinear refractive index are calculated. The analysis of the absorption coefficient for the as-deposited film showed an allowed direct optical band gap with a value of 2.35 eV, which decreased by annealing to 2.05 eV.

Compilation of DNA sequences of Escherichia coli (update 1991)

PubMed Central

Kröger, Manfred; Wahl, Ralf; Rice, Peter

1991-01-01

We have compiled the DNA sequence data for E.coli available from the GENBANK and EMBL data libraries and over a period of several years independently from the literature. This is the third listing replacing and increasing the former listing roughly by one fifth. However, in order to save space this printed version contains DNA sequence information only. The complete compilation is now available in machine readable form from the EMBL data library (ECD release 6). After deletion of all detected overlaps a total of 1 492 282 individual bp is found to be determined till the beginning of 1991. This corresponds to a total of 31.62% of the entire E.coli chromosome consisting of about 4,720 kbp. This number may actually be higher by some extra 2,5% derived from lysogenic bacteriophage lambda and various DNA sequences already received for statistical purposes only. PMID:2041799

Silurian sequence stratigraphy in the North American craton, Great Lakes area

USGS Publications Warehouse

Shaver, R.H.; ,

1996-01-01

A notable circumstance of late Early through Late Silurian sedimentation on the Great Lakes area craton is that at least two and possibly three cycles of third-order duration (if eustatically considered) are recognized in basin and shallow-platform settings alike. Both virtually pure and siliciclastic-rich carbonate rocks exist in parts of platform-situated sections in contrast to siliciclastic-rich to evaporite-dominated basin sections. Knowledge of the reef history, together with evidence of incidental periodic incursions of siliciclastic sediments, permitted understanding of a regional event or sequence stratigraphy more than 15 years ago before conventional biostratigraphic and physical stratigraphic evidence became adequate to corroborate. This midwestern US and Ontario Silurian record has become strategic for testing different schools of thought that champion either tectonism or eustasy to explain cyclical sequences.

A Benchmark Study on Error Assessment and Quality Control of CCS Reads Derived from the PacBio RS

PubMed Central

Jiao, Xiaoli; Zheng, Xin; Ma, Liang; Kutty, Geetha; Gogineni, Emile; Sun, Qiang; Sherman, Brad T.; Hu, Xiaojun; Jones, Kristine; Raley, Castle; Tran, Bao; Munroe, David J.; Stephens, Robert; Liang, Dun; Imamichi, Tomozumi; Kovacs, Joseph A.; Lempicki, Richard A.; Huang, Da Wei

2013-01-01

PacBio RS, a newly emerging third-generation DNA sequencing platform, is based on a real-time, single-molecule, nano-nitch sequencing technology that can generate very long reads (up to 20-kb) in contrast to the shorter reads produced by the first and second generation sequencing technologies. As a new platform, it is important to assess the sequencing error rate, as well as the quality control (QC) parameters associated with the PacBio sequence data. In this study, a mixture of 10 prior known, closely related DNA amplicons were sequenced using the PacBio RS sequencing platform. After aligning Circular Consensus Sequence (CCS) reads derived from the above sequencing experiment to the known reference sequences, we found that the median error rate was 2.5% without read QC, and improved to 1.3% with an SVM based multi-parameter QC method. In addition, a De Novo assembly was used as a downstream application to evaluate the effects of different QC approaches. This benchmark study indicates that even though CCS reads are post error-corrected it is still necessary to perform appropriate QC on CCS reads in order to produce successful downstream bioinformatics analytical results. PMID:24179701

A Benchmark Study on Error Assessment and Quality Control of CCS Reads Derived from the PacBio RS.

PubMed

Jiao, Xiaoli; Zheng, Xin; Ma, Liang; Kutty, Geetha; Gogineni, Emile; Sun, Qiang; Sherman, Brad T; Hu, Xiaojun; Jones, Kristine; Raley, Castle; Tran, Bao; Munroe, David J; Stephens, Robert; Liang, Dun; Imamichi, Tomozumi; Kovacs, Joseph A; Lempicki, Richard A; Huang, Da Wei

2013-07-31

PacBio RS, a newly emerging third-generation DNA sequencing platform, is based on a real-time, single-molecule, nano-nitch sequencing technology that can generate very long reads (up to 20-kb) in contrast to the shorter reads produced by the first and second generation sequencing technologies. As a new platform, it is important to assess the sequencing error rate, as well as the quality control (QC) parameters associated with the PacBio sequence data. In this study, a mixture of 10 prior known, closely related DNA amplicons were sequenced using the PacBio RS sequencing platform. After aligning Circular Consensus Sequence (CCS) reads derived from the above sequencing experiment to the known reference sequences, we found that the median error rate was 2.5% without read QC, and improved to 1.3% with an SVM based multi-parameter QC method. In addition, a De Novo assembly was used as a downstream application to evaluate the effects of different QC approaches. This benchmark study indicates that even though CCS reads are post error-corrected it is still necessary to perform appropriate QC on CCS reads in order to produce successful downstream bioinformatics analytical results.

Classical seismic sequence stratigraphic interpretation of intraslope basin fill: Deepwater Nigeria

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

Duncan, E.A.

Detailed interpretation of seismic facies patterns performed within the workstation environment provides an observation based methodology for constructing depositional models of turbidite and other reservoir bearing systems expected in deepwater Nigeria. The increased fidelity of the workstation allows greater detail and accuracy to be imposed onto depositional model construction by vastly improving the discrimination of depositional from structural seismic reflection geometries. In deepwater Nigeria interslope basins, depositional cyclicity is clearly indicated by vertical seismic facies successions in the same way as can be recognized in bed thickness trends from outcrop or well log data. The recognition of the seismic faciesmore » successions appears to break the stratigraphy into at least fourth and fifth order scale sequences. Highly {open_quotes}zoomed{close_quotes} instantaneous phase displays enhance the reflection character so that near outcrop scale (resolution less than 50 mters) interpretations of depositional facies can be made. Common seismic facies and geologic interpretation include: (1) low angle erosional surfaces as channel scour or mass wasting detachment; (2) low relief mounds, often in compensation cycle overlapping stacks reflecting compacted channelbelt fill; (3) unidirectional, low angle clinoform sets suggesting laterial accretion within a channel belt or possible contourite mounds; (4) abrupt, shingled blocks illustrating tilted fault blocks of small scale intraformation slumping; and (5) high reflection amplitude and continuous, parallel reflections of pelagic and hemipelagic condensed sections. There are other subtle seismic facies resolvable given the incraesed fidelity of the workstation interpretation. Mapping and translation of these geometries into more robust stratigraphic predictions should have positive impact on exploration and development success.« less

Observation of Discrete-Time-Crystal Signatures in an Ordered Dipolar Many-Body System

NASA Astrophysics Data System (ADS)

Rovny, Jared; Blum, Robert L.; Barrett, Sean E.

2018-05-01

A discrete time crystal (DTC) is a robust phase of driven systems that breaks the discrete time translation symmetry of the driving Hamiltonian. Recent experiments have observed DTC signatures in two distinct systems. Here we show nuclear magnetic resonance observations of DTC signatures in a third, strikingly different system: an ordered spatial crystal. We use a novel DTC echo experiment to probe the coherence of the driven system. Finally, we show that interactions during the pulse of the DTC sequence contribute to the decay of the signal, complicating attempts to measure the intrinsic lifetime of the DTC.

Observation of Discrete-Time-Crystal Signatures in an Ordered Dipolar Many-Body System.

PubMed

Rovny, Jared; Blum, Robert L; Barrett, Sean E

2018-05-04

A discrete time crystal (DTC) is a robust phase of driven systems that breaks the discrete time translation symmetry of the driving Hamiltonian. Recent experiments have observed DTC signatures in two distinct systems. Here we show nuclear magnetic resonance observations of DTC signatures in a third, strikingly different system: an ordered spatial crystal. We use a novel DTC echo experiment to probe the coherence of the driven system. Finally, we show that interactions during the pulse of the DTC sequence contribute to the decay of the signal, complicating attempts to measure the intrinsic lifetime of the DTC.

Miocene depositional history, sequences and chronostratigraphy of the ANDRILL AND-2A drillcore, Victoria Land Basin, Antarctica

NASA Astrophysics Data System (ADS)

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

2009-12-01

ANDRILL’s Southern McMurdo Sound Project (SMS) completed the AND-2A drillhole (77°45.488 S; 165°16.613 E) from a floating sea-ice platform (~8.5 meters thick), over ~380 meters of water, reaching a total depth of 1138.54 mbsf, and obtaining an excellent quality core with 98% recovery through the cored interval. This sedimentary archive comprises an expanded early and middle Miocene section deposited in a high-accommodation continental margin location, proximal to glacial ice influence from the West Antarctic Ice Sheet, East Antarctic Ice Sheet, and local ice in the Transantarctic Mountains. Stratigraphic sequences and facies interpretations reveal a cyclical history of environmental variation influenced by climate, glacial advance/retreat cycles, and water depth variation. A well-developed chronostratigraphic framework developed through integrated diatom biostratigraphy, magneto-stratigraphy, Sr isotope geochemistry, and radiometric dating of volcanic materials, allows for the comparison of events recognized in this drillcore with events identified in distal proxy records from deep-sea stable isotope studies, and in sea-level reconstructions based on continental shelf sequence stratigraphy. The AND-2A drillcore recovered a 600 m-thick stratigraphic interval documenting the Antarctic coastal environment during the warm middle Miocene climatic optimum (17.5 to 14.5 Ma). A disconformity separating the middle and upper Miocene intervals in the AND-2A drillcore represents a substantial climate step into cold, glacial conditions of the late Miocene. Lower and middle Miocene shallow marine sediments were deposited in the subsiding Victoria Land Basin, during a period of relatively steady thermal subsidence, on the coastal plain and continental shelf seaward of the rising Transantarctic Mountains. More than 60 sequences recognized in the AND-2A drillcore represent repeating lithological changes in glacimarine, terrigenous, volcanic and biogenic sediments, deposited during a dynamic climate regime, and likely reflecting Milankovitch forcing. Fossils preserved in these strata suggest non-polar climate conditions similar to southern Patagonia and southwestern New Zealand today, influenced by high sediment discharge from river run-off, and high coastal turbidity. The AND-2A drillcore represents the third high-quality drillcore in Southern Victoria Land to record early Miocene paleoenvironmental changes (the other two records are preserved in the CRP-1 and CRP-2 drillcores), so that the timing and magnitude of glacial and eustatic variations can be examined at several sites along the Southern Victoria Land margin.

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.

Late Pleistocene sediments and fossils near the mouth of Mad River, Humboldt County, California: Facies analysis, sequence development, and possible age correlation

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

Harvey, E.W.

Study of late Pleistocene-age sediments near the mouth of the Mad River revealed a sequence of nearshore marine and shallow bay deposits. This sequence, bounded by unconformities, is informally named the Mouth of Mad unit. The Mouth of mad unit can be divided into four distinct depositional facies at the study site. The lowest facies are the Nearshore Sand and Estuarine Mud, which lie unconformably on a paleosol. The sand facies grades upward into a high-energy, interbedded Nearshore Sand and Gravel facies containing storm and rip-channel deposits. Above the sand and gravel is a Strand-Plain Sand facies. This sand ismore » overlain by a laterally variable sequence of shell-rich Bay facies. The bay deposits can be further divided into five subfacies: (1) a Bioturbated Sand; (2) a Lower Tidal Flat Mud; (3) a Mixed Sand and Mud; (4) an oyster-rich Bay Mud; and (5) an Upper Tidal Flat Mud. The bay sequence is overlain unconformably by younger late Pleistocene-age marine terrace deposits. The depositional environments represented by these facies progress from a shoreline estuary to nearshore deposits, above storm wave base, and slowly back to shoreline and finally shallow bay conditions. The Mouth of Mad unit represents a transgressive-regressive sequence, involving the development of a protective spit. The uppermost mud within the Mouth of Mad unit has been dated, using thermoluminescence age estimation, at 176 [+-] 33 ka, placing it in the late Pleistocene. The Mouth of Mad unit appears to be younger than the fossiliferous deposits at Elk Head, Crannell Junction, Trinidad Head, Moonstone Beach, and the Falor Formation near Maple Creek, and possibly time equivalent with gravel deposits exposed at the western end of School Road in McKinleyville.« less

Tuning the third-order nonlinear optical properties of In:ZnO thin films by 8 MeV electron beam irradiation

NASA Astrophysics Data System (ADS)

Shettigar, Nayana; Pramodini, S.; Kityk, I. V.; Abd-Lefdil, M.; Eljald, E. M.; Regragui, M.; Antony, Albin; Rao, Ashok; Sanjeev, Ganesh; Ajeyakashi, K. C.; Poornesh, P.

2017-11-01

We report the third-order nonlinear optical properties of electron beam treated Indium doped ZnO (Zn1-xInxO (x = 0.03) thin films at different dose rate. Zn1-xInxO (x = 0.03) thin films prepared by spray pyrolysis deposition technique were irradiated using 8 MeV electron beam at dose rates ranging from 1 kGy to 4 kGy. X-ray diffraction patterns were obtained to examine the structural changes, The transformation from sphalerite to wurtzite structure of ZnO was observed which indicates occurrence of structural changes due to irradiation. Morphology of irradiated thin films examined using atomic force microscopy (AFM) technique indicates the surface roughness varying with irradiation dose rate. The switching over from Saturable Absorption (SA) to Reverse Saturable Absorption (RSA) behaviour was noted when the irradiation dose rate was increased from 1 kGy to 4 kGy. The significant changes observed in the third-order nonlinear optical susceptibility χ(3) of the Zn1-xInxO (x = 0.03) thin films is attributed mainly due to electron beam irradiation. The study indicates that nonlinear optical parameters can be controlled by electron beam irradiation by choosing appropriate dose rate which is very much essential for device applications. Hence Zn1-xInxO (x = 0.03) materialize as a promising material for use in nonlinear optical device applications.

Mechano-optic logic gate controlled by third-order nonlinear optical properties in a rotating ZnO:Au thin film

NASA Astrophysics Data System (ADS)

Carrillo-Delgado, C.; García-Gil, C. I.; Trejo-Valdez, M.; Torres-Torres, C.; García-Merino, J. A.; Martínez-Gutiérrez, H.; Khomenko, A. V.; Torres-Martínez, R.

2016-01-01

Measurements of the third-order nonlinear optical properties exhibited by a ZnO thin solid film deposited on a SnO2 substrate are presented. The samples were prepared by a spray pyrolysis processing route. Scanning electron microscopy analysis and UV-Vis spectroscopy studies were carried out. The picosecond response at 1064 nm was explored by the z-scan technique. A large optical Kerr effect with two-photon absorption was obtained. The inhibition of the nonlinear optical absorption together with a noticeable enhancement in the optical Kerr effect in the sample was achieved by the incorporation of Au nanoparticles into the ZnO film. Additionally, a two-wave mixing configuration at 532 nm was performed and an optical Kerr effect was identified as the main cause of the nanosecond third-order optical nonlinearity. The relaxation time of the photothermal response of the sample was estimated to be about 1 s when the sample was excited by nanosecond single-shots. The rotation of the sample during the nanosecond two-wave mixing experiments was analyzed. It was stated that a non-monotonic relation between rotating frequency and pulse repetition rate governs the thermal contribution to the nonlinear refractive index exhibited by a rotating film. Potential applications for switching photothermal interactions in rotating samples can be contemplated. A rotary logic system dependent on Kerr transmittance in a two-wave mixing experiment was proposed.

Diverse Antibiotic Resistance Genes in Dairy Cow Manure

PubMed Central

Wichmann, Fabienne; Udikovic-Kolic, Nikolina; Andrew, Sheila; Handelsman, Jo

2014-01-01

ABSTRACT Application of manure from antibiotic-treated animals to crops facilitates the dissemination of antibiotic resistance determinants into the environment. However, our knowledge of the identity, diversity, and patterns of distribution of these antibiotic resistance determinants remains limited. We used a new combination of methods to examine the resistome of dairy cow manure, a common soil amendment. Metagenomic libraries constructed with DNA extracted from manure were screened for resistance to beta-lactams, phenicols, aminoglycosides, and tetracyclines. Functional screening of fosmid and small-insert libraries identified 80 different antibiotic resistance genes whose deduced protein sequences were on average 50 to 60% identical to sequences deposited in GenBank. The resistance genes were frequently found in clusters and originated from a taxonomically diverse set of species, suggesting that some microorganisms in manure harbor multiple resistance genes. Furthermore, amid the great genetic diversity in manure, we discovered a novel clade of chloramphenicol acetyltransferases. Our study combined functional metagenomics with third-generation PacBio sequencing to significantly extend the roster of functional antibiotic resistance genes found in animal gut bacteria, providing a particularly broad resource for understanding the origins and dispersal of antibiotic resistance genes in agriculture and clinical settings. PMID:24757214

Applying functional metagenomics to search for novel lignocellulosic enzymes in a microbial consortium derived from a thermophilic composting phase of sugarcane bagasse and cow manure.

PubMed

Colombo, Lívia Tavares; de Oliveira, Marcelo Nagem Valério; Carneiro, Deisy Guimarães; de Souza, Robson Assis; Alvim, Mariana Caroline Tocantins; Dos Santos, Josenilda Carlos; da Silva, Cynthia Canêdo; Vidigal, Pedro Marcus Pereira; da Silveira, Wendel Batista; Passos, Flávia Maria Lopes

2016-09-01

Environments where lignocellulosic biomass is naturally decomposed are sources for discovery of new hydrolytic enzymes that can reduce the high cost of enzymatic cocktails for second-generation ethanol production. Metagenomic analysis was applied to discover genes coding carbohydrate-depleting enzymes from a microbial laboratory subculture using a mix of sugarcane bagasse and cow manure in the thermophilic composting phase. From a fosmid library, 182 clones had the ability to hydrolyse carbohydrate. Sequencing of 30 fosmids resulted in 12 contigs encoding 34 putative carbohydrate-active enzymes belonging to 17 glycosyl hydrolase (GH) families. One third of the putative proteins belong to the GH3 family, which includes β-glucosidase enzymes known to be important in the cellulose-deconstruction process but present with low activity in commercial enzyme preparations. Phylogenetic analysis of the amino acid sequences of seven selected proteins, including three β-glucosidases, showed low relatedness with protein sequences deposited in databases. These findings highlight microbial consortia obtained from a mixture of decomposing biomass residues, such as sugar cane bagasse and cow manure, as a rich resource of novel enzymes potentially useful in biotechnology for saccharification of lignocellulosic substrate.

Titanium mineral resources of the western U.S.: an update

USGS Publications Warehouse

Force, Eric R.; Creely, Scott

2000-01-01

Thirteen deposits or districts in the western U.S. have been examined in which titaniummineral resources have been reported or implied. These deposits are of the following general types (in probable order of importance): 1) Cretaceous shoreline placer deposits, 2) silica-sand deposits of California, 3) fluvial monazite placers of Idaho, 4) anorthositerelated deposits, and 5) clay and bauxite deposits of the northwestern U.S. Relative to previous reports, this one shows some greater and some lesser resources (table 1). In any case, titanium-mineral resources of the western U.S. (west of 103° longitude) remain modest at world scale except as unconventional (especially perovskite) and by-product (especially porphyry) resources. Some deposits, however, have enhanced value to the titanium explorationist for the geologic relations they illustrate. Among the new conclusions are: a) Loci of Cretaceous shoreline placers form linear patterns, nested as a function of age, that can be traced for thousands of kilometers, permitting focused exploration in whole new mountain ranges. b) Medial hematite-ilmenite solid-solution, which is highly magnetic, is a major carrier of TiO2 values in the Cretaceous deposits of Wyoming. This phase was previously thought to be relatively rare. c) Regressive shoreline placer deposits in indurated Cretaceous sequences expose intricate facies relations, such as the construction of shoreface sequences by long-shore drift over tidal-channel fill, without much loss of paleogeographic information. d) Due to deep weathering, virtually every Eocene sediment that accumulated in the Ione basin at the foot of the Sierra Nevada has economic value, permitting recovery of altered ilmenite and zircon along with silica, clay, coal, and gold. Ilmenite is most abundant in newly recognized shoreline sands. e) Upper Tertiary fluvial placers of Idaho formed in and filled fault-bounded basins and thus are far more voluminous than deposits in the modern valley system. Previously reported resources are thus far too low. f) Mafic igneous rocks of Proterozoic age near Bagdad, Arizona are of ophiolitic affinity, but contain nelsonitic ilmenite enrichments associated with anorthositic layers.

MR fingerprinting using the quick echo splitting NMR imaging technique.

PubMed

Jiang, Yun; Ma, Dan; Jerecic, Renate; Duerk, Jeffrey; Seiberlich, Nicole; Gulani, Vikas; Griswold, Mark A

2017-03-01

The purpose of the study is to develop a quantitative method for the relaxation properties with a reduced radio frequency (RF) power deposition by combining magnetic resonance fingerprinting (MRF) technique with quick echo splitting NMR imaging technique (QUEST). A QUEST-based MRF sequence was implemented to acquire high-order echoes by increasing the gaps between RF pulses. Bloch simulations were used to calculate a dictionary containing the range of physically plausible signal evolutions using a range of T 1 and T 2 values based on the pulse sequence. MRF-QUEST was evaluated by comparing to the results of spin-echo methods. The specific absorption rate (SAR) of MRF-QUEST was compared with the clinically available methods. MRF-QUEST quantifies the relaxation properties with good accuracy at the estimated head SAR of 0.03 W/kg. T 1 and T 2 values estimated by MRF-QUEST are in good agreement with the traditional methods. The combination of the MRF and the QUEST provides an accurate quantification of T 1 and T 2 simultaneously with reduced RF power deposition. The resulting lower SAR may provide a new acquisition strategy for MRF when RF energy deposition is problematic. Magn Reson Med 77:979-988, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Microscopic and Metallurgical Aspects of the Space Shuttle Columbia Accident Investigation and Reconstruction

NASA Technical Reports Server (NTRS)

McDaniels, Steven J.

2004-01-01

The Space Shuttle Columbia was descending for a landing at the Kennedy Space Center (KSC) on February 1, 2003. Approximately 20 minutes prior to touchdown, the Columbia began disintegrating over the western United States; the majority of debris eventually impacted in eastern Texas and western Louisiana. A monumental effort eventually recovered approximately 84,000 pieces of debris, approximately 38% of the Orbiter's original dry weight. The debris was transported to KSC, where the items were catalogued and evaluated. Critical areas of interest, such as the left and right leading edge surfaces and the underside of the ship, were placed upon a grid to aid in the reconstruction. Items of interest included metallic structures, reinforced carbon-carbon composites, and ceramic heat insulation tiles. Many of the leading edge elements had re-solidified metallic deposits spattered on them. These deposits became known as slag and were one of the main focuses of the investigation. In order to help determine the sequence of events inside the left wing during the accident, the slag's composition, layering order, and directionality of deposition were studied. A myriad of analytical tests were performed in an attempt to ascertain the compositional and depositional characteristics of selected slag deposits, including the ordering of deposited layers within each individual slag deposit harvested. Initially, Scanning Electron Microscopy and Energy Dispersive X-Ray Spectroscopy (SEM/EDX) were performed to quickly characterize the overall composition of individual slag deposits: SEM utilizes a narrowlyfocused high-energy electron beam impinging upon a specimen. The incident beam excites and liberates lower energy secondary electrons, which are detected and analyzed, providing a visual representation of the sample's surface topography. EDX also relies on an incident electron beam, except an EDX unit measures X-ray energies generated by the impinging beam. Each element generates a unique X-ray signature; the EDX detector measures these discreet energies. EDX actually penetrates approximately 2 microns into the bulk of the sample. However, random examination of various portions of slag, coupled with the semiquantitative nature of the SEM/EDX analysis, did not yield convincingly pertinent data. Therefore, X-ray dot mapping was conducted, which provided more understandable data, both in terms of slag layering and composition. An X-ray dot map is generated by performing numerous EDX scans for individual elements, then compiling the scans in a visual representation. Eventually, specimens consisting of not only the slag, but of the adjacent RCC substrate as well were cross-sectioned. X-Ray dot mapping of the materialographicallymounted and -polished cross- sections provided a visual representation of both the layering sequence and compositional characteristics of the slag. Contemporaneously, Electron Spectroscopy for Chemical Analysis/X-Ray Photoelectron Spectroscopy (ESCA/XPS) and powdered X-Ray Diffraction (XRD) were performed to further characterize the deposits and to attempt to identify what, if any, compounds were present. The ESCA/XPS analysis allowed the analyst to "sputter" into the sample with an electron gun, aiding in the identification of the layering sequence. XPS uses photons, rather than electrons, which impinge upon the surface of the sample. XPS measures the electrons emitted from within the first 5 nm of the sample's surface. The XRD measures the scatter angles of incident X-rays; the angle and intensity of scatter depend upon the crystalline structure of the pulverized sample. XRD is considered a qualitative rather than quantitative technique. ESCA/XPS revealed that the final layer to deposit was predominantly carbonaceous. XRD was successful in identifying specific compounds, such as Al 2O3, Al and/or Al3 21SiO47, mullite (3(Al2)O3 -SiO2), and nickel-aluminides. Eventually, Electron MicroProbe Analysis (EMPA) was conducted on the marialographically-prepared cross- sections of selected slag deposits. Microprobe combines SEM and Wavelength Dispersive X-Ray Spectroscopy (WDS), and, like EDX, uses a narrowly-focused high-energy electron beam impinging upon a specimen to elicit, in the case of EPMA, characteristic X-rays with specific wavelengths. This quantitative, analytical tool proved the most useful in determining depositional layering and composition of the slag deposits. This information was utilized in verifying the location of the breach in the left leading edge of the wing of the Columbia.

Low resistance thin film organic solar cell electrodes

DOEpatents

Forrest, Stephen [Princeton, NJ; Xue, Jiangeng [Piscataway, NJ

2008-01-01

A method which lower the series resistance of photosensitive devices includes providing a transparent film of a first electrically conductive material arranged on a transparent substrate; depositing and patterning a mask over the first electrically conductive material, such that openings in the mask have sloping sides which narrow approaching the substrate; depositing a second electrically conductive material directly onto the first electrically conductive material exposed in the openings of the mask, at least partially filling the openings; stripping the mask, leaving behind reentrant structures of the second electrically conductive material which were formed by the deposits in the openings of the mask; after stripping the mask, depositing a first organic material onto the first electrically conductive material in between the reentrant structures; and directionally depositing a third electrically conductive material over the first organic material deposited in between the reentrant structures, edges of the reentrant structures aligning deposition so that the third electrically conductive material does not directly contact the first electrically conductive material, and does not directly contact the second electrically conductive material.

Sedimentary processes on the Storfjorden trough-mouth fan during last deglaciation phase: the role of subglacial meltwater plumes on continental margin sedimentation

NASA Astrophysics Data System (ADS)

Lucchi, Renata G.; Camerlenghi, Angelo; Colmenero-Hidalgo, Elena; Sierro, Francisco J.; Bárcena, Maria Angeles; Flores, José-Abel; Urgeles, Roger; Macrı, Patrizia; Sagnotti, Leonardo; Caburlotto, Andrea

2010-05-01

The continental margin of the Southern Storfjorden trough-mouth fan was investigated within the SVAIS project (BIO Hesperides cruise, August 2007) as a Spanish contribution to IPY Activity N. 367 (Neogene ice streams and sedimentary processes on high- latitude continental margins - NICE STREAMS). The objectives were to investigate the glacially-dominated late-Neogene-Quaternary sedimentary architecture of the NW Barents Sea continental margin and reconstruct its sedimentary system in response to natural climate change. The paleo-ice streams in Storfjorden had a small catchment area draining ice from the southern Spitsbergen and Bear Island. The short distance from the ice source to the calving front produced a short residence time of ice, and therefore a rapid response to climatic changes. Here ground truthing recovered the last few thousands years sedimentary sequence thought to represent last deglaciation phase. Detailed palaeostratigraphic investigations together with paleomagnetic and rock magnetic analyses and AMS dating define the constraints for high-resolution inter-core correlation and dating. Most of the cores contain at the base gravity-mass deposits including debris flows and over-consolidated glacigenic diamicton. Mass deposits are overlain by an oxidized interval originated at the release and sink of fresh, cold and oxygenated melt-waters at the inception of the deglaciation phase. On the upper slope the oxidized interval is overlain by several meters of finely-stratified sediments composed of sandy-silt layers cyclically recurring within finer-grained laminated silty-clay sediments. Textural and compositional analyses suggest preferential deposition by settling from meltwater sediment-laden plumes (plumites) occurred during deglaciation with coarser layers representing episodes of subglacial meltwater discharge (glacial hyperpycnal flows) accompanying the ice streams retreat. The laminated sequence is truncated at uppermost part by a more recent gravity-mass deposit that possibly removed part of the younger sequence. In the deeper part of the slope the plumites consist of crudely laminated, terrigenous and almost barren sediments. Here the sedimentary sequence is topped by intensively bioturbated, bioclasts-bearing silty-clays representing the most recent interglacial sedimentation. On the continental shelf, the upper sedimentary sequence contains dispersed cm-thick bivalve's shells suggesting an oxygenated and nutrient-rich environment (interglacial) overlaying an interval of terrigenous, barren sediments (deglaciation). Here the short core's length suggests the presence of stiffer/coarser sediments at the base that could not be sampled. The seismic stratigraphy indicates that the slope is formed by alternating debris flow deposits and layered sediments corresponding into our cores to the fast-deposited, low-density, terrigenous plumites. Bathymetric and seismic data revealed the presence of widespread submarine landslides restricted to the southernmost part of Storfjorden continental slope. Geotechnical investigation are in progress in order to understand if such layered deposits can act on the slope as a possible preferential weak horizon favoring sediment failure.

An earthquake history derived from stratigraphic and microfossil evidence of relative sea-level change at Coos Bay, southern coastal Oregon

USGS Publications Warehouse

Nelson, A.R.; Jennings, A.E.; Kashima, K.

1996-01-01

Much of the uncertainty in determining the number and magnitude of past great earthquakes in the Cascadia subduction zone of western North America stems from difficulties in using estuarine stratigraphy to infer the size and rate of late Holocene relative sea-level changes. A sequence of interbedded peaty and muddy intertidal sediment beneath a small, protected tidal marsh in a narrow inlet of Coos Bay, Oregon, records ten rapid to instantaneous rises in relative sea level. Each rise is marked by a contact that records an upward transition from peaty to muddy sediment. But only two contacts, dating from about 1700 and 2300 yr ago, show the site-wide extent and abrupt changes in lithology and foraminiferal and diatom assemblages that can be used to infer at least half a meter of sudden coseismic subsidence. Although the characteristics of a third, gradual contact do not differ from those of some contacts produced by nonseismic processes, regional correlation with other similar sequences and high-precision 14C dating suggest that the third contact records a great plate-boundary earthquake about 300 yr ago. A fourth contact formed too slowly to have been caused by coseismic subsidence. Because lithologic and microfossil data are not sufficient to distinguish a coseismic from a nonseismic origin for the other six peatmud contacts, we cannot determine earthquake recurrence intervals at this site. Similar uncertainties in great earthquake recurrence and magnitude prevail at similar sites elsewhere in the Cascadia subduction zone, except those with sequences showing changes in fossils indicative of > 1 m of sudden subsidence, sand sheets deposited by tsunamis, or liquefaction features.

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.

Sedimentology and hydrodynamic implications of a coarse-grained hurricane sequence in a carbonate reef setting

USGS Publications Warehouse

Spiske, M.; Jaffe, B.E.

2009-01-01

Storms and associated surges are major coast-shaping processes. Nevertheless, no typical sequences for storm surge deposits in different coastal settings have been established. This study interprets a coarse-grained hurricane ridge deposit on the island of Bonaire, Netherlands Antilles. The sequence was deposited during Hurricane Lenny in November 1999. Insight is gained into the hydrodynamics of surge flow by interpreting textural trends, particle imbrication, and deposit geometry. Vertical textural variations, caused by time-dependent hydrodynamic changes, were used to subdivide the deposit into depositional units that correspond to different stages of the surge, such as setup, peak, and return flow. Particle size and imbrication trends and geometry of the units reflect landward bed-load transport of components during the setup, a nondirectional flow with sediment falling out of suspension during the peak, and a seaward bedload transport during the return flow. Formation of a ridge during setup affected the texture of the return flow unit. Changing angles of imbrication reflect alternating flow velocities during each phase. Normal grading during setup and inverse grading during return flow are caused by decelerating and accelerating flow, respectively. Hence, the interpreted deposit seems to represent the first described complete hurricane surge sequence from a carbonate environment. ?? 2009 Geological Society of America.

Effects of acid deposition on terrestrial ecosystems and their rehabilitation strategies in China.

PubMed

Feng, Zong-wei; Miao, Hong; Zhang, Fu-zhu; Huang, Yi-zong

2002-04-01

South China has become the third largest region associated with acid deposition following Europe and North America, the area subject to damage by acid deposition increased from 1.75 million km2 in 1985 to 2.8 million km2 in 1993. Acid deposition has caused serious damage to ecosystem. Combined pollution of acid rain and SO2 showed the obvious multiple effects on crops. Vegetable was more sensitive to acid deposition than foodstuff crops. Annual economic loss of crops due to acid deposition damage in eleven provinces of south China was 4.26 billion RMB Yuan. Acid deposition caused serious damage to forest. Annual economic loss of wood volume was about 1.8 billion RMB Yuan and forest ecological benefit loss 16.2 billion in eleven provinces of south China. Acid deposition in south China was typical "sulfuric acid type". According to the thoughts of sustainable development, some strategies were brought forward as follows: (1) enhancing environmental management, specifying acid-controlling region, controlling and abating the total emission amount of SO2; (2) selecting practical energy technologies of clean coal, for example, cleansing and selecting coal, sulfur-fixed-type industrial briqutting, abating sulfur from waste gas and so on; (3) developing other energy sources to replace coal, including water electricity, atomic energy and the new energy such as solar energy, wind energy and so on; (4) in acid deposition region of south China, selecting acid-resistant type of crop and tree to decrease agricultural losses, planting more green fertilizer crops, using organic fertilizers and liming, in order to improve buffer capacities of soil.

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.

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.

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.

Leg 67: the Deep Sea Drilling Project Mid-America Trench transect off Guatemala.

USGS Publications Warehouse

von Huene, Roland E.

1980-01-01

Drilling on the Cocos plate recovered a basal chalk sequence deposited during early and mid-Miocene time, a short interval of abyssal red clay, and an upper sequence of late Miocene and younger sediment deposited within an area influenced by a terrigenous source. In the trench, a mud and sand fill less than 400,000 yr old overlies the oceanic sequence. The entire section shows no evidence of compressive deformation. In contrast, the section cored on the trench's landward slope 3 km from the trench axis is affected by tectonism. The section contains a Cretaceous to Pliocene claystone sequence capped by Pliocene to Quaternary hemipelagic slope deposits.- from Authors

Correlations of nucleotide substitution rates and base composition of mammalian coding sequences with protein structure.

PubMed

Chiusano, M L; D'Onofrio, G; Alvarez-Valin, F; Jabbari, K; Colonna, G; Bernardi, G

1999-09-30

We investigated the relationships between the nucleotide substitution rates and the predicted secondary structures in the three states representation (alpha-helix, beta-sheet, and coil). The analysis was carried out on 34 alignments, each of which comprised sequences belonging to at least four different mammalian orders. The rates of synonymous substitution were found to be significantly different in regions predicted to be alpha-helix, beta-sheet, or coil. Likewise, the nonsynonymous rates also differ, although expectedly at a lower extent, in the three types of secondary structure, suggesting that different selective constraints associated with the different structures are affecting in a similar way the synonymous and nonsynonymous rates. Moreover, the base composition of the third codon positions is different in coding sequence regions corresponding to different secondary structures of proteins.

Recognizing the Albian-Cenomanian (OAE1d) sequence boundary using plant carbon isotopes: Dakota Formation, Western Interior Basin, USA

USGS Publications Warehouse

Grocke, D.R.; Ludvigson, Greg A.; Witzke, B.L.; Robinson, S.A.; Joeckel, R.M.; Ufnar, David F.; Ravn, R.L.

2006-01-01

Analysis of bulk sedimentary organic matter and charcoal from an Albian-Cenomanian fluvial-estuarine succession (Dakota Formation) at Rose Creek Pit (RCP), Nebraska, reveals a negative excursion of ???3???, in late Albian strata. Overlying Cenomanian strata have ??13C values of -24???, to -23???, that are similar to pre-excursion values. The absence of an intervening positive excursion (as exists in marine records of the Albian-Cenomanian boundary) likely results from a depositional hiatus. The corresponding positive ??13C event and proposed depositional hiatus are concordant with a regionally identified sequence boundary in the Dakota Formation (D2), as well as a major regressive phase throughout the globe at the Albian-Cenomanian boundary. Data from RCP confirm suggestions that some positive carbon-isotope excursions in the geologic record are coincident with regressive sea-level phases. We estimate using isotopic correlation that the D2 sequence boundary at RCP was on the order of 0.5 m.y. in duration. Therefore, interpretations of isotopic events and associated environmental phenomena, such as oceanic anoxic events, in the shallow-marine and terrestrial record may be influenced by stratigraphic incompleteness. Further investigation of terrestrial ??13C records may be useful in recognizing and constraining sea-level changes in the geologic record. ?? 2006 Geological Society of America.

The Midway sequence: A Timiskaming-type, pull-apart basin deposit in the western Wawa subprovince, Minnesota

USGS Publications Warehouse

Jirsa, M.A.

2000-01-01

The Midway sequence is an assemblage of subaerially deposited clastic and volcanic rocks that forms a narrow wedge within Neoarchean greenstone of the western Wawa subprovince of the Superior Province. Volcanic conglomerate in the Midway sequence contains clasts of stratigraphically older greenstone, together with clasts of a distinctive hornblende-phyric trachyandesite that is not represented among the older greenstone flows. The trachyandesite forms flows and pyroclastic units that are interbedded with lenticular deposits of volcanic conglomerate in a manner interpreted to indicate approximately coeval volcanism and alluvial fan - Fluvial sedimentation within a linear, restricted, and tectonically active depocentre. The Midway sequence unconformably overlies greenstone on one side and is bounded by a regional-scale, strike-slip fault on the other. Structural analyses show that the Midway sequence was deposited after an early, precleavage folding event (D1) in greenstone, but before the regional metamorphic cleavage-forming D2 deformation. Lithologic and structural attributes are consistent with deposition in a strike-slip "pull-apart" basin. The stratigraphic and structural characteristics of the Midway sequence are generally similar to those of the Timiskaming Group and Timiskaming-type rocks in Canada, and more specifically to those of the Shebandowan Group in the Thunder Bay district. This similarity implies that the latest Archean tectonic and magmatic history of the western Wawa subprovince may have been nearly synchronous over great distances.

Eustatic and far-field tectonic control on the development of an intra-platform carbonate-shoal complex: upper tongue of the Tanglewood Member, Upper Ordovician Lexington Limestone, central Kentucky, U.S.A.

NASA Astrophysics Data System (ADS)

Koirala, Dibya Raj; Ettensohn, Frank R.; Clepper, Marta L.

2016-11-01

The Lexington or Trenton Limestone is an Upper Ordovician (Chatfieldian-Edenian; upper Sandbian-lower Katian), temperate-water unit, averaging about 60-m thick, that was deposited in relatively shallow waters across the Lexington Platform in east-central United States during the Taconian Orogeny. Lexington/Trenton shallow-water deposition ended across most of the platform in late Chatfieldian time and from that point deepened upward into the more shale-rich Clays Ferry, Point Pleasant and Kope formations due to apparent sea-level rise. In central Kentucky, however, deposition of the Lexington Limestone continued into early Edenian time and includes up to 50 m of additional coarse calcarenites and calcirudites at the top, which form the Tanglewood buildup and reflect locally regressive conditions, apparently related to local structural uplift. Consequently, in central Kentucky, the Lexington is more than 100-m thick, and Lexington deposition on the buildup continued into early Edenian time as an intra-platform shoal complex that tongues out into deeper-water units in all directions. In an attempt to understand how this shoal complex developed, we examined the last major body of coarse skeletal sands in the central Kentucky Lexington Limestone, the upper tongue of the Tanglewood Member, a 12-m-thick succession of fossiliferous calcarenite and calcirudite that occurs across an area of 5200 km2 near the center of the Lexington Platform. Although relatively homogeneous, the upper Tanglewood is divisible into five, small-scale, fining-upward, sequence-like cycles, which contain prominent, widespread deformed horizons. Facies analysis indicates that four lithofacies, which reflect distinct depositional environments, comprise the sequences across the shoal complex. Lithofacies were correlated across the shoal complex by integrating cyclicity and widespread deformed horizons in order to delineate the locations of major depositional environments. Facies analysis shows that the thickest and coarsest parts of each sequence, and the shallowest depositional environments, coincide with basement fault blocks, which are known to have experienced uplift during earlier Lexington Limestone deposition. The occurrence of thick, coarse facies on the same blocks suggests that the blocks continued to experience uplift into shallow water, where tides and waves redistributed sediments during upper Tanglewood deposition. Although eustasy apparently controlled cyclicity, Taconian far-field forces generated by orogeny in the east seem to have influenced facies distribution in each cycle through reactivation of basement fault zones as synsedimentary growth faults. The example of the upper Tanglewood Member shows that tectonic far-field forces can exert important influences on the development of carbonate depositional environments, even in distal intracratonic settings like the Lexington Platform.

Dynamics of surges generated by hydrothermal blasts during the 6 August 2012 Te Maari eruption, Mt. Tongariro, New Zealand

NASA Astrophysics Data System (ADS)

Lube, Gert; Breard, Eric C. P.; Cronin, Shane J.; Procter, Jonathan N.; Brenna, Marco; Moebis, Anja; Pardo, Natalia; Stewart, Robert B.; Jolly, Arthur; Fournier, Nicolas

2014-10-01

The 6 August 2012 Te Maari eruption produced violent and widespread "cold" Pyroclastic Density Currents (PDCs) following unroofing of the pressurized hydrothermal system. Despite an erupted volume of only ~ 5 × 105 m3, and lacking any juvenile component, the 340,000 m3 of PDCs spread over an area of 6.1 km2 and had mobilities that were on the order of volcanic blasts or blast-like PDCs. This great mobility was due to strong lateral focussing of explosion energy, producing jets with initial velocities > 100 m/s. We present a type-stratigraphy for these hydrothermal-derived low-temperature PDCs that show a tripartite deposit sequence. Each of the deposit units dominates respectively three outward-gradational sedimentary facies, reflecting transitions in the propagating PDC transport and depositional mechanisms. The largest PDCs, directed west and east of the Upper Te Maari area were generated from outer-cone breccias and tuffs that were mostly highly hydrothermally altered. Landsliding and the geometry of the hydrothermal area led to the directed jetting. Initial particle-laden jets laid sheets, grading into lobes of proximal massive sand to gravel-rich facies dominated by unit A and extending up to 1 km from the vents. As the jets were collapsing, a vertically and longitudinally stratified PDC developed within the first few hundred metres from source. Exponential thinning and coarse-tail grading-dominated fining with radial distance of massive unit A resulted from fast deposition and progressive depletion of the most concentrated flow region behind the PDC head. Markedly slower tractional sedimentation from the passing PDC body and tail deposited the highly stratified and ripple-bedded fine-coarse ash of unit B. This formed distinctive dune fields of the medial dune-bedded ash-rich facies. Upwards in depositional sequences the waning of the current can be seen, by replacement of higher-energy bedforms to progressively lower ones. Downstream progressive waning and further depletion are characterised by the development of the distal wavy to planar-bedded ash-rich facies. This is increasingly dominated by the uppermost deposition unit C of laminated fine-med ash deposited by gently turbulent, dilute phoenix clouds. These high energy PDCs, sourced from flank hydrothermal systems should be regarded as a serious threat in any multihazard assessment of a stratovolcano, even though they may not be one of the major magmatic vent sites. In addition, further detailed studies of these hydrothermal jetting events and their deposits should be pursued in order to better understand large-volume volcanic blasts, which appear to be a larger scale sibling phenomenon.

Sequence stratigraphy of the Kingak Shale (Jurassic-Lower Cretaceous), National Petroleum Reserve in Alaska

USGS Publications Warehouse

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

2004-01-01

Beaufortian strata (Jurassic-Lower Cretaceous) in the National Petroleum Reserve in Alaska (NPRA) are a focus of exploration since the 1994 discovery of the nearby Alpine oil field (>400 MMBO). These strata include the Kingak Shale, a succession of depositional sequences influenced by rift opening of the Arctic Ocean Basin. Interpretation of sequence stratigraphy and depositional facies from a regional two-dimensional seismic grid and well data allows the definition of four sequence sets that each displays unique stratal geometries and thickness trends across NPRA. A Lower to Middle Jurassic sequence set includes numerous transgressive-regressive sequences that collectively built a clastic shelf in north-central NPRA. Along the south-facing, lobate shelf margin, condensed shales in transgressive systems tracts downlap and coalesce into a basinal condensed section that is likely an important hydrocarbon source rock. An Oxfordian-Kimmeridgian sequence set, deposited during pulses of uplift on the Barrow arch, includes multiple transgressive-regressive sequences that locally contain well-winnowed, shoreface sandstones at the base of transgressive systems tracts. These shoreface sandstones and overlying shales, deposited during maximum flooding, form stratigraphic traps that are the main objective of exploration in the Alpine play in NPRA. A Valanginian sequence set includes at least two transgressive-regressive sequences that display relatively distal characteristics, suggesting high relative sea level. An important exception is the presence of a basal transgressive systems tract that locally contains shoreface sandstones of reservoir quality. A Hauterivian sequence set includes two transgressive-regressive sequences that constitute a shelf-margin wedge developed as the result of tectonic uplift along the Barrow arch during rift opening of the Arctic Ocean Basin. This sequence set displays stratal geometries suggesting incision and synsedimentary collapse of the shelf margin. ?? 2004. The American Association of Petroleum Geologists. All rights reserved.

Structural evolution and petroleum productivity of the Baltic basin

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

Ulmishek, G.F.

The Baltic basin is an oval depression located in the western part of the Russian craton; it occupies the eastern Baltic Sea and adjacent onshore areas. The basin contains more than 5,000 m of sedimentary rocks ranging from latest Proterozoic to Tertiary in age. These rocks consist of four tectonostratigraphic sequences deposited during major tectonic episodes of basin evolution. Principal unconformities separate the sequences. The basin is underlain by a rift probably filled with Upper Proterozoic rocks. Vendian and Lower Cambrian rocks (Baikalian sequence) form two northeast-trending depressions. The principal stage of the basin development was during deposition of amore » thick Middle Cambrian-Lower Devonian (Caledonian) sequence. This stage was terminated by the most intense deformations in the basin history. The Middle Devonian-Carboniferous (Hercynian) and Permian-Tertiary (Kimmerian-Alpine) tectonic and depositional cycles only slightly modified the basin geometry and left intact the main structural framework of underlying rocks. The petroleum productivity of the basin is related to the Caledonian tectonostratigraphic sequence that contains both source rocks and reservoirs. However, maturation of source rocks, migration of oil, and formation of fields took place mostly during deposition of the Hercynian sequence.« less

Direct deposition of silver nanoplates on quartz surface by sequence pre-treatment hydroxylation and silanisation.

PubMed

Abu Bakar, Norhayati; Mat Salleh, Muhamad; Ali Umar, Akrajas; Shapter, Joseph George

2017-01-01

Silver nanoparticles deposited on quartz substrates are widely used as SERS substrates. The nanoparticles can be deposited directly from colloidal solution by dipping technique. However, the adhesion of the particles on the quartz surface is very poor. Normally the substrate is pre-treated with hydroxylation or silanisation process. In this paper, we have demonstrated that the application of the sequence pre-treatment hydroxylation and silanisation have improved the density of silver nanoplates desposited on the quartz surface. •Sequence hydroxylation and silanisation pre-treatment assists the deposition of the nanoplate on the surface.•Various immersion times of the quartz surface into the colloidal nanoplates determined size distributions and density surface of the nanoplates on the surface.

Paleo­geographic implications of molluscan assemblages in the Upper Cretaceous (Campanian) Pigeon Point Formation, California

USGS Publications Warehouse

Elder, William P.; Saul, LouElla

1993-01-01

The Pigeon Point Formation crops out along the San Mateo County coastline in a northern and southern sequence of folded and faulted strata. Correlation of the two sequences remains somewhat equivocal, although on the basis of biostratigraphy and a reversed magnetic interval both appear to have been deposited during the early to middle Campanian. Sedimentary structures suggest that the northern sequence was deposited by turbidity currents in a continental rise setting, whereas the southern sequence primarily reflects deposition in shelf and slope environments . Right-lateral offset on the San Andreas and subsidiary faults to the east of the Pigeon Point Formation can account for 100's of km of northward transport since its deposition. However, Champion and others (1984) suggested 2500 km of northward transport from a tropical setting of about 21°N. Molluscan assemblages in the formation argue strongly for a less tropical site of deposition. Relative abundances of warm and temperate taxa and the presence or absence of key species are similar to those of the Santa Ana Mountains Cretaceous section, and are indicative of a war

Buckling of pressure-loaded, long, shear deformable, cylindrical laminated shells

NASA Astrophysics Data System (ADS)

Anastasiadis, John S.; Simitses, George J.

A higher-order shell theory was developed (kinematic relations, constitutive relations, equilibrium equations and boundary conditions), which includes initial geometric imperfections and transverse shear effects for a laminated cylindrical shell under the action of pressure, axial compression and in-plane shear. Through the perturbation technique, buckling equations are derived for the corresponding 'perfect geometry' symmetric laminated configuration. Critical pressures are computed for very long cylinders for several stacking sequences, several radius-to-total-thickness ratios, three lamina materials (boron/epoxy, graphite/epoxy, and Kevlar/epoxy), and three shell theories: classical, first-order shear deformable and higher- (third-)order shear deformable. The results provide valuable information concerning the applicability (accurate prediction of buckling pressures) of the various shell theories.

Sequence analysis by iterated maps, a review.

PubMed

Almeida, Jonas S

2014-05-01

Among alignment-free methods, Iterated Maps (IMs) are on a particular extreme: they are also scale free (order free). The use of IMs for sequence analysis is also distinct from other alignment-free methodologies in being rooted in statistical mechanics instead of computational linguistics. Both of these roots go back over two decades to the use of fractal geometry in the characterization of phase-space representations. The time series analysis origin of the field is betrayed by the title of the manuscript that started this alignment-free subdomain in 1990, 'Chaos Game Representation'. The clash between the analysis of sequences as continuous series and the better established use of Markovian approaches to discrete series was almost immediate, with a defining critique published in same journal 2 years later. The rest of that decade would go by before the scale-free nature of the IM space was uncovered. The ensuing decade saw this scalability generalized for non-genomic alphabets as well as an interest in its use for graphic representation of biological sequences. Finally, in the past couple of years, in step with the emergence of BigData and MapReduce as a new computational paradigm, there is a surprising third act in the IM story. Multiple reports have described gains in computational efficiency of multiple orders of magnitude over more conventional sequence analysis methodologies. The stage appears to be now set for a recasting of IMs with a central role in processing nextgen sequencing results.

Rapid Detection of the Chlamydiaceae and Other Families in the Order Chlamydiales: Three PCR Tests

PubMed Central

Everett, Karin D. E.; Hornung, Linda J.; Andersen, Arthur A.

1999-01-01

Few identification methods will rapidly or specifically detect all bacteria in the order Chlamydiales, family Chlamydiaceae. In this study, three PCR tests based on sequence data from over 48 chlamydial strains were developed for identification of these bacteria. Two tests exclusively recognized the Chlamydiaceae: a multiplex test targeting the ompA gene and the rRNA intergenic spacer and a TaqMan test targeting the 23S ribosomal DNA. The multiplex test was able to detect as few as 200 inclusion-forming units (IFU), while the TaqMan test could detect 2 IFU. The amplicons produced in these tests ranged from 132 to 320 bp in length. The third test, targeting the 23S rRNA gene, produced a 600-bp amplicon from strains belonging to several families in the order Chlamydiales. Direct sequence analysis of this amplicon has facilitated the identification of new chlamydial strains. These three tests permit ready identification of chlamydiae for diagnostic and epidemiologic study. The specificity of these tests indicates that they might also be used to identify chlamydiae without culture or isolation. PMID:9986815

Early-mid-Cretaceous evolution in Tethyan reef communities and sea level

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

Scott, R.W.

1988-01-01

The replacement of corals by rudists in Early Cretaceous reefal communities spanned a 30-m.y. period when sea level rose and drowned continental shelves. During this time corals formed communities in the deeper parts of reefs and rudists occupied the shallow, high-energy habitats. By Aptian time rudists dominated reefs that fringed interior shelf basins and corals formed reefs with rudists on the outer shelf margins. By late Albian coral communities had virtually disappeared, presumably because of complex environmental changes and cycles of organic productivity. Two important events of eustatic sea level rise are represented by unconformities separating carbonate depositional sequences onmore » the Arabian platform that correlate with sequence boundaries on the Gulf Coast platform. Graphic correlation techniques test the synchroneity of these events. A composite standard time scale dates these sea level rises at 115.8 Ma and 94.6 Ma; a third, intra-Albian event at 104.3 Ma is present in many places and may also be eustatic. Associated with these sea level rises were apparent changes in ocean water chemistry as evidenced by changes in isotopes and trace elements, where diagenetic effects can be discounted. During this time the climate became more humid and atmospheric CO/sub 2/ increased. The concomitant environmental changes in the oceanic conditions presumably stressed the deeper coral communities on reefs. The emergence of rudists as reef contributors had a profound effect on Late Cretaceous depositional conditions and the development of hydrocarbon reservoirs.« less

Early-mid-Cretaceous evolution in Tethyan reef communities and sea level

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

Scott, R.W.

1988-02-01

The replacement of corals by rudists in Early Cretaceous reefal communities spanned a 30-m.y. period when sea level rose and drowned continental shelves. During this time corals formed communities in the deeper parts of reefs and rudists occupied the shallow, high-energy habitats. By Aptian time rudists dominated reefs that fringed interior shelf basins and corals formed reefs with rudists on the outer shelf margins. By late Albian coral communities had virtually disappeared, presumably because of complex environmental changes and cycles of organic productivity. Two important events of eustatic sea level rise are represented by unconformities separating carbonate depositional sequences onmore » the Arabian platform that correlate with sequence boundaries on the Gulf Coast platform. Graphic correlation techniques test the synchroneity of these events. A composite standard time scale dates these sea level rises at 115.8 Ma and 94.6 Ma; a third, intra-Albian event at 104.3 Ma is present in many places and may also be eustatic. Associated with these sea level rises were apparent changes in ocean water chemistry as evidenced by changes in isotopes and trace elements, where diagenetic effects can be discounted. During this time the climate became more humid and atmospheric CO/sub 2/ increased. The concomitant environmental changes in the oceanic conditions presumably stressed the deeper coral communities on reefs. The emergence of rudists as reef contributors had a profound effect on Late Cretaceous depositional conditions and the development of hydrocarbon reservoirs.« less

The Origin of Salt-Encased Sediment Packages: Observations from the SE Precaspian Basin (Kazakhstan)

NASA Astrophysics Data System (ADS)

Fernandez, Naiara; Duffy, Oliver B.; Hudec, Michael R.; Jackson, Martin P. A.; Burg, George; Jackson, Christopher A.-L.; Dooley, Tim P.

2017-04-01

Intrasalt sediment packages containing siliciclastic sediments, carbonate sediments, or non-halite evaporites such as gypsum or anhydrite are common within most salt sequences. Intrasalt sediment packages may have been deposited before, during, or after salt deposition and be incorporated into the salt by various processes. Understanding the origin and evolution of intrasalt sediment packages may yield important insights into the tectonic and geodynamic history of the basin, and also into the understanding of salt tectonics. Despite the importance of intrasalt sediment packages, currently there is no systematic description of their possible origins and their distinguishing criteria. This work is divided in three parts. First, we outline the possible origins of intrasalt sediment packages, as well as criteria to determine if they originated as subsalt, suprasalt or intrasalt sequences. Second, we examine how sediment packages that originated on top of salt, such as minibasins, can be encased within salt. We propose four key processes by which salt can be expelled and emplaced above minibasins to encase them: a) salt expulsion from beneath a minibasin experiencing density-driven subsidence; b) salt expulsion from beneath adjacent subsiding minibasins; c) salt expulsion associated with lateral shortening; d) override of minibasins by a salt sheet sourced from elsewhere. Third, we present a case study from the SE Precaspian Basin, Kazakhstan, where, using a borehole-constrained 3D seismic reflection dataset, the proposed criteria are applied to an area with abundant, newly discovered sediment packages within salt.

Radiocarbon dating with annual-resolution of subfossil trees from the Younger Dryas event in the southern French Alps

NASA Astrophysics Data System (ADS)

Capano, Manuela; Miramont, Cécile; Guibal, Frédéric; Kromer, Bernd; Tuna, Thibaut; Fagault, Yoann; Bard, Edouard

2017-04-01

Tree rings are an important archive for the calibration of radiocarbon data. The younger part of the IntCal curve is based essentially on tree-ring chronologies, absolutely dated by dendrochronological analysis. For the Northern Hemisphere (NH), a gap still exists between the absolutely dated sequences and a floating chronology. Based on the Southern Hemisphere (SH) tree-ring chronologies a link has been previously proposed (Reimer et al. 2013, Radiocarbon; see also update in Hogg et al. 2016, Radiocarbon). By measuring radiocarbon at annual resolution in French subfossil pines (Pinus sylvestris L.) we propose to improve the connection between the absolute chronology and the floating chronology. Several subfossil pines have been found in the Southern French Alps; they were buried by flood deposits, allowing their preservation. Some trees discovered in the Barbier riverbed were dated to the Younger Dryas periods by previous decadal radiocarbon measurements, performed in Heidelberg and Mannheim. The trees selected for our new study are Barb12 and Barb17 (analyzed sequences of 163 and 152 rings, respectively). These sequences were sampled at annual resolution when permitted by the ring width. As a first step, every third ring was pretreated for radiocarbon analysis. These samples were sliced in small pieces and pretreated by using the ABA-B method before being combusted, graphitized with the AGE system and measured with AixMICADAS (Bard et al. 2015, Nucl. Instr. Meth. B). From the comparison with the kauri sequence, the Barb12-17 sequence can be dated from about 12835 to 12606 cal. BP. It can also be used to calculate the interhemispheric gradient (IHG) over the overlapping period. In order to reduce the inter-annual variability, the Barb12-17 record was smoothed, grouped and averaged over the same decades as in the Kauri record. On the basis of twenty values, a mean IHG value of ca. 60 years was calculated. Quantification of the IHG around 50 yr is particularly robust during the two "age plateaux" corresponding to the time intervals 12820-12760 and 12660-12630 cal. BP. Overall, the IHG stayed relatively high throughout the studied period corresponding to the beginning of the Younger Dryas climatic event.

Laser-Assisted Cold-Sprayed Corrosion- and Wear-Resistant Coatings: A Review

NASA Astrophysics Data System (ADS)

Olakanmi, E. O.; Doyoyo, M.

2014-06-01

Laser-assisted cold spray (LACS) process will be increasingly employed for depositing coatings because of its unique advantages: solid-state deposition of dense, homogeneous, and pore-free coatings onto a range of substrates; and high build rate at reduced operating costs without the use of expensive heating and process inert gases. Depositing coatings with excellent performance indicators via LACS demands an accurate knowledge and control of processing and materials' variables. By varying the LACS process parameters and their interactions, the functional properties of coatings can be manipulated. Moreover, thermal effect due to laser irradiation and microstructural evolution complicate the interpretation of LACS mechanical deformation mechanism which is essential for elucidating its physical phenomena. In order to provide a basis for follow-on-research that leads to the development of high-productivity LACS processing of coatings, this review focuses on the latest developments in depositing corrosion- and wear-resistant coatings with the emphasis on the composition, structure, and mechanical and functional properties. Historical developments and fundamentals of LACS are addressed in an attempt to describe the physics behind the process. Typical technological applications of LACS coatings are also identified. The investigations of all process sequences, from laser irradiation of the powder-laden gas stream and the substrate, to the impingement of thermally softened particles on the deposition site, and subsequent further processes, are described. Existing gaps in the literature relating to LACS-dependent microstructural evolution, mechanical deformation mechanisms, correlation between functional properties and process parameters, processing challenges, and industrial applications have been identified in order to provide insights for further investigations and innovation in LACS deposition of wear- and corrosion-resistant coatings.

Simulating maar-diatreme volcanic systems in bench-scale experiments

NASA Astrophysics Data System (ADS)

Andrews, R. G.; White, J. D. L.; Dürig, T.; Zimanowski, B.

2015-12-01

Maar-diatreme eruptions are incompletely understood, and explanations for the processes involved in them have been debated for decades. This study extends bench-scale analogue experiments previously conducted on maar-diatreme systems and attempts to scale the results up to both field-scale experimentation and natural volcanic systems in order to produce a reconstructive toolkit for maar volcanoes. These experimental runs produced via multiple mechanisms complex deposits that match many features seen in natural maar-diatreme deposits. The runs include deeper single blasts, series of descending discrete blasts, and series of ascending blasts. Debris-jet inception and diatreme formation are indicated by this study to involve multiple types of granular fountains within diatreme deposits produced under varying initial conditions. The individual energies of blasts in multiple-blast series are not possible to infer from the final deposits. The depositional record of blast sequences can be ascertained from the proportion of fallback sedimentation versus maar ejecta rim material, the final crater size and the degree of overturning or slumping of accessory strata. Quantitatively, deeper blasts involve a roughly equal partitioning of energy into crater excavation energy versus mass movement of juvenile material, whereas shallower blasts expend a much greater proportion of energy in crater excavation.

Silurian deltaic progradation, Tassili n'Ajjer plateau, south-eastern Algeria: Sedimentology, ichnology and sequence stratigraphy

NASA Astrophysics Data System (ADS)

Djouder, Hocine; Lüning, Sebastian; Da Silva, Anne-Christine; Abdallah, Hussein; Boulvain, Frédéric

2018-06-01

The economic potential for unconventional shale oil and gas production in the Silurian of the Berkine - Ghadames and Illizi basins (BGI) in south-eastern Algeria has been recently confirmed through exploration drilling. The aim of the present paper attempts a better understanding of the Intra-Tassilian depression within the entire Silurian of the Tassili n'Ajjer plateau. The continuous deposits of the Silurian are exposed at the southern margin of the prolific BGI basins, in the Tassili n'Ajjer plateau, offering the chance to understand the sedimentology, ichnology, and to present a detailed sequence stratigraphy framework for the region. The 410 m-thick clastic Silurian sedimentary strata are subdivided into three formations in the context of sequence stratigraphy, namely: (i) the Oued Imihrou Fm. (Llandoverian) overlain by (ii) the Atafaïtafa Fm. (late Llandoverian to Wenlockian), and (iii) the Oued Tifernine Fm. (late Wenlockian to Pridolian). These can be also distinguished across the entire investigated area and laterally traceable over kilometers. Clear cyclic stacking patterns are identified within the four studied sections showing progressively a general trend of thickening- and coarsening-upward, over a complete 2nd-order megasequence (SIL-1 MS). This transgressive-regressive succession suggests deltaic progradation, shallowing and basin infilling as evidenced by numerous diagnostic sedimentary features and trace fossils, largely from eastern-to western-Tassili plateau. Indeed, the wealth of outcrop data in the Silurian siliciclastic succession enables us to distinct thirteen facies (facies A-M), ranging from shallow-to marginal-marine facies, and in turn, grouped into six facies associations (FA1-FA6). The lowermost part of the succession, which is the most prolific sources of hydrocarbons in North Africa, consists of thick organic-rich graptolite-yielding black 'hot' shales and 'lean' shales with sparse bioturbation with small Thalassinoides belonging to the distal Cruziana ichnofacies. In contrast, the uppermost part of the Silurian deposits becomes progressively coarser and fluvial in response to the progradation of the North African Akakus deltaic system, during regional sea level fall and uplifting of the region. These progradational deposits exhibit well-preserved trace fossils with moderate to high degree of bioturbation, such as Skolithos or the so-called "Tigillites" pipe-rock, Cruziana isp., Rusophycus isp., Monocraterion isp., and Syringomorpha. The SIL-1 MS is bounded by a post-glacial latest Hirnantian unconformity on the basal (SB1), as confirmed by the moderately diverse early Silurian graptolite faunas, and by the Caledonian unconformity on the top (SB7). Each of the three formations of SIL-1 MS reveals two major 3rd-order progradational sequences, commonly delineated by discontinuity surfaces (in ascending order, SB1 to SB7), and in turn, these six sequences (i.e. Si-1 to Si-6) are subdivided into at least ten shorter-term cycles. The regional extent of each unconformity is directly linked to significant facies changes and to inflection points on the global sea level curve.

Climatic-oceanic forcing on the organic accumulation across the shelf during the Early Cambrian (Age 2 through 3) in the mid-upper Yangtze Block, NE Guizhou, South China

NASA Astrophysics Data System (ADS)

Yeasmin, Rumana; Chen, Daizhao; Fu, Yong; Wang, Jianguo; Guo, Zenghui; Guo, Chuan

2017-02-01

The organic-rich sediments were widely deposited over the entire Yangtze Block during the Early Cambrian (late Nemakit-Daldynian to Botomian). In the mid-upper Yangtze region, northeastern Guizhou, South China, they comprise, in ascending order, the Niutitang, Jiumenchong and lower Bianmachong formations which are dominated by black shales except the middle one characterized by interbedded shales-limestones. Three third-order depositional sequences are identified in the two studied sections located on the upper slope to basin of the open shelf. The organic-rich sediments were mostly deposited notably during transgressions on the shallower upper slope-margin (TOC up to 25 wt.%) where they are characterized by co-increases in C, P, Fe, and Ba concentrations, indicating the highest organic productivity and coupled C, P and Fe cycling there. In contrast, in the shelf basin, the concomitant organic-rich sediments yield lower organic (TOC <10 wt.% mostly) and Ba abundances, and generally show antithetic relationship of TOC with P and Fe variations, indicative of a relatively low organic productivity and transient decoupled C, P and Fe cycling in the deeper basin. This spatial difference in C, P, Fe and Ba cycling as a whole thus indicate that the highest organic productivity wedge on the shallower shelf upper slope-margin was likely induced by the oceanic upwelling from the restricted basin where the P and Fe nutrients were transiently depleted without timely renewal. Meanwhile, multiple redox proxies, including V/Al, Ni/Al and Cr/Al ratios vs. TOC contents, together with V/(V + Ni) and V/Cr ratios, generally characterize a more severe euxinic water wedge localized on the shallower upper slope-margin of shelf where the organic production culminated, but a nonsulfidic (ferruginous) anoxic state in the basin due to the relatively low sulfate level. Meanwhile, episodic depletion of trace elements in the deeper basin during the higher organic productivity also reconciles the concomitantly enhanced upwelling from the somewhat restricted deep watermass likely silled by the underwater upland seaward. The coincidence of organic-rich intervals with more arid climate epoches, as shown by increased Ti/Al ratios indicative of increased aeolian fluxes, reconciles a subtropical arid climate of Yangtze Block within the north mid-low-latitude trade-wind zone during deposition (the Early Cambrian). As such, enhanced offshore currents driven by the trade winds could have further induced the upwelling of nutrient-rich deep waters along the shelf during the transgressions, although tended to wane onwards, leading to the tempo-spatial heterogeneities in organic production and redox state across the shelf sea.

Inverse bilayer magnetoelectric thin film sensor

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

Yarar, E.; Piorra, A.; Quandt, E., E-mail: eq@tf.uni-kiel.de

2016-07-11

Prior investigations on magnetoelectric (ME) thin film sensors using amorphous FeCoSiB as a magnetostrictive layer and AlN as a piezoelectric layer revealed a limit of detection (LOD) in the range of a few pT/Hz{sup 1/2} in the mechanical resonance. These sensors are comprised of a Si/SiO{sub 2}/Pt/AlN/FeCoSiB layer stack, as dictated by the temperatures required for the deposition of the layers. A low temperature deposition route of very high quality AlN allows the reversal of the deposition sequence, thus allowing the amorphous FeCoSiB to be deposited on the very smooth Si substrate. As a consequence, the LOD could be enhancedmore » by almost an order of magnitude reaching 400 fT/Hz{sup 1/2} at the mechanical resonance of the sensor. Giant ME coefficients (α{sub ME}) as high as 5 kV/cm Oe were measured. Transmission electron microscopy investigations revealed highly c-axis oriented growth of the AlN starting from the Pt-AlN interface with local epitaxy.« less

Analysis on the overpressure characterization with respect to depositional environment facies: Case Study in Miri Area, Baram Delta

NASA Astrophysics Data System (ADS)

Mhd Hanapiah, N.; Yusoff, W. I. Wan; Zakariah, M. N. A.

2017-10-01

Overpressure studies in oil and gas exploration and production are carried out in order to mitigate any losses that could happen while drilling. These concerns can be addressed by enhancing the understanding of overpressure characterization in the fields. This research emphasizes in determining the pore pressure trend in Miri area to assist pore pressure prediction for future hydrocarbon exploration and production. Generally, pore pressure trends are related to mechanisms that contribute to the overpressure generation. In the region predominant overpressure are disequilibrium compaction within the prodelta shales meanwhile in outer shelf overpressure generation controlled by fluid expansion in deltaic sequence of inner shelf area. The objective of this research is to analyze the pore pressure profile of wells for determining vertical trends of pore pressure for various depositional environment facies of Miri area. Integration of rock physics and pore pressure analysis and relating the trends to environment depositional environment facies within shale underlying sand interval. Analysis done shows that overpressure top is characterize by depositional environment facies within shale underlying sand interval.

Investigating the microbial community responsible for unusually high soil N2O and NOx emissions in the Colorado Desert

NASA Astrophysics Data System (ADS)

Eberwein, J. R.; Carey, C.; Aronson, E. L.; Jenerette, D.

2016-12-01

Although the importance of soil nitrogenous emissions are well accepted in terms of local and global ecological relevance, there remain considerable knowledge gaps concerning the mechanisms regulating production, particularly in arid systems. This study aimed to connect desert soil trace gas emissions of nitrous oxide (N2O) and nitrogen oxides (NOx) with compositional changes in the microbial community. We quantified real-time soil trace gas emissions at two sites in the Colorado Desert experiencing contrasting anthropogenic nitrogen (N) deposition loads (<5 and 15 kg N ha-1 y-1). Measurements were made through 48 hours following water (to simulate a 2 cm rain event) and N additions (at 30 kg NH4NO3 ha-1). In conjunction with flux measurements, soil samples were collected for 16S rRNA gene sequencing to characterize the soil microbial community. N2O fluxes reached as high as 1200 ng N2O-N m-2 s-1, well above most published emissions, but returned to pre-wetting conditions within 12 hours. NOx emissions reached as high as 350 ng NOx-N m-2 s-1 and remained elevated past 24 hours post-wetting. Results from the 16S analysis indicate distinct differences in the microbial community composition between the high and low N deposition sites, with less than 50% of operational taxonomic units (OTUs) in common between sites. N addition had a significant effect on the soil microbial community at the low deposition site, but not at the high deposition site. Furthermore, significant shifts in the bacterial community occurred after wetting, with only one third of the community remaining constant between time points. These results suggest that gaseous N export, particularly N2O emission, is a greater form of nitrogen loss in this system than is currently assumed. Experimental N additions and anthropogenic N deposition show potential for shifting soil microbial community composition, with implications for soil N emissions. Furthermore, shifts in the microbial community can occur as quickly as 15 minutes post-wetting, representing a remarkable ability for soil microorganisms to recover from extreme water stress. As aridlands cover approximately one third of the Earth's land surface, understanding the mechanisms that contribute to soil N emissions in these systems is of important global relevance.

Composition and origin of Early Cambrian Tiantaishan phosphorite-Mn carbonate ores, Shaanxi Province, China

USGS Publications Warehouse

Hein, J.R.; Fan, D.; Ye, J.; Liu, T.; Yeh, H.-W.

1999-01-01

The Tiantaishan phosphorite-Mn carbonate ores occur in the Early Cambrian Tananpo Formation in complexly folded and faulted rocks located in southern Shaanxi Province. About 65 x 106 tonnes of 17% P2O5 ore reserves exist and Mn-ore reserves are about 8.3 x 106 tonnes of +18% Mn. The stratigraphic sequence in ascending order consists of black phyllite, black to gray phosphorite ore, black phyllite, rhodochrostone ore, Mn mixed-carbonates, and dolostone. Data are presented from microprobe mineral chemistry, whole-rock chemistry, stable isotopes of carbonates, X-ray mineralogy, petrographic and SEM observations, and statistical analysis of chemical data. The dominant ore-forming minerals are hydroxy- and carbonate fluorapatite and Ca rhodochrosite, with Mg kutnahorite and dolomite comprising the Mn mixed-carbonate section. Pyrite occurs in all rock types and alabandite (MnS) occurs throughout the rhodochrostone section. The mean P2O5 content of phosphorite is 31% and argillaceous phosphorite is 16%, while the mean MnO content of rhodochrostone ore is 37%. Phosphorite ores are massive, spheroidal, laminated, and banded, while rhodochrostone ores have oolitic, spheroidal, and granular fabrics. The most distinguishing characteristics of the ores are high total organic carbon (TOC) contents (mean 8.4%) in the phosphorite and high P2O5 contents (mean 2.7%) in the rhodochrostone ore. The atypically high TOC contents in the Tiantaishan phosphorite probably result from very strong productivity leading to high sedimentation rates accompanied by weak reworking of sediments; poor utilization of the organic matter by bacteria; and/or partial replacement of bacterial or algal mats by the apatite. The depositional setting of the ores was the margin of an epicontinental seaway created as a direct consequence of global processes that included break-up of a supercontinent, formation of narrow seaways, creation of extensive continental shelves, overturn of stagnant, metal-rich deep-ocean waters, and marine transgression. Water depth increased from deposition of the black phyllite sequence through deposition of the Mn mixed-carbonate sequence, then shallowed again during deposition of the overlying dolostone sequence. Bottom waters were mostly dysoxic to suboxic, but fluctuated from oxic to anoxic. Productivity was high during deposition of the black phyllite sequence, increased during precipitation of phosphorite, and then decreased to moderate levels during precipitation of rhodochrostone ores. Biosilica contributions occur in each lithology, but are greatest in rhodochrostone. Changes in sedimentation were determined by changes in water depth, productivity, upwelling, sea-level change, and ventilation of the depositional basin. The source of the phosphorus was organic matter produced in great quantities during deposition of the black phyllite and phosphorite sequences in a zone of coastal upwelling. Organic matter accumulation was rapid. Globally, Mn was supplied by overturn of stagnant, metal-rich deep-ocean waters, which were redistributed to areas of coastal upwelling and seaways; that process may have been initiated by latest Proterozoic glaciations which would have promoted density stratification and accumulation and storage of metals. Regionally, Mn was supplied by terrigenous input into the shallow seaway and hydrothermal input into the deeper water parts of that seaway. Locally, Mn sources included leaching and transport of metals from the sediment column. Manganese was stored locally in low-oxygen (not anoxic) seawater prior to Mn-ore formation. The source of the carbon in the Mn carbonates and dolostones was predominantly seawater bicarbonate and secondarily CO2 derived from the oxidation of organic matter in the bacterially mediated diagenetic zone of sulfate reduction.

Complete genome sequence of Streptobacillus moniliformis type strain (9901T)

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

Nolan, Matt; Gronow, Sabine; Lapidus, Alla L.

2009-01-01

Streptobacillus moniliformis Levaditi et al. 1925 is the sole and type species of the genus, and is of phylogenetic interest because of its isolated location in the sparsely populated and neither taxonomically nor genomically much accessed family 'Leptotrichiaceae' within the phylum 'Fusobacteria'. S. moniliformis, a Gram-negative, non-motile and pleomorphic bacterium, is the etiologic agent of rat bite fever and Haverhill fever. Strain 9901T, the type strain of the species, was isolated from a patient with rat bite fever. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is only the second completedmore » genome sequence of the order 'Fusobacteriales' and no more than the third sequence from the phylum 'Fusobacteria'. The 1,662,578 bp long chromosome and the 10,702 bp plasmid with a total of 1511 protein-coding and 55 RNA genes are part of the Genomic Encyclopedia of Bacteria and Archaea project.« less

[Big Data Revolution or Data Hubris? : On the Data Positivism of Molecular Biology].

PubMed

Gramelsberger, Gabriele

2017-12-01

Genome data, the core of the 2008 proclaimed big data revolution in biology, are automatically generated and analyzed. The transition from the manual laboratory practice of electrophoresis sequencing to automated DNA-sequencing machines and software-based analysis programs was completed between 1982 and 1992. This transition facilitated the first data deluge, which was considerably increased by the second and third generation of DNA-sequencers during the 2000s. However, the strategies for evaluating sequence data were also transformed along with this transition. The paper explores both the computational strategies of automation, as well as the data evaluation culture connected with it, in order to provide a complete picture of the complexity of today's data generation and its intrinsic data positivism. This paper is thereby guided by the question, whether this data positivism is the basis of the big data revolution of molecular biology announced today, or it marks the beginning of its data hubris.

High resolution luminescence chronology for Xiashu Loess deposits of Southeastern China

NASA Astrophysics Data System (ADS)

Yi, Shuangwen; Li, Xusheng; Han, Zhiyong; Lu, Huayu; Liu, Jinfeng; Wu, Jiang

2018-04-01

Loess deposits in Xiashu are representative of such deposits in Southeastern China that are mainly distributed in the middle and lower reaches of the Yangtze River valley. These loess-paleosol sequences provide a key archive of past climate change in humid, subtropical regions. However, the ages of the sequences are not well constrained. In this study, the standard quartz single-aliquot regenerative (SAR) dose optically stimulated luminescence (OSL) and K-feldspar post-infrared infrared stimulated luminescence (post-IR IRSL; pIRIR290) methods are used to date two loess sequences in Nanjing region. Our results show that quartz SAR OSL and K-feldspar pIRIR290 ages are more or less indistinguishable from one another up to ∼50 ka. Beyond this age, the K-feldspar pIRIR ages increased systematically with deposition depth, agreeing well with the expected ages as far as ∼200 ka. On the basis of a fully independently-dated timescale, we are therefore able to propose, for the first time, a new age model for the Xiashu Loess deposits accumulated since the penultimate interglacial period. Using our newly obtained luminescence dating ages, we observe a marked difference between the loess accumulation rates in the two sequences, potentially forced by regional depositional processes and loess preservation.

A buried marine depositional sequence (Presumpscot FM. ) N. of the marine limit, Waterboro, Maine

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

Morency, R.E.

Subsurface investigations conducted in Waterboro, ME (York Co.) in connection with studies of two hazardous waste sites and a municipal water supply exploration project, have demonstrated that a laterally extensive sequence of marine deposits underlies surficial sediments mapped as non-esker ice contact glacio-fluvial deposits. The marine deposits consist of a fining-downwards sequence of grey, micaceous sands (fine to medium, grading down to a silty-fine sand), which grade downward into a thick ([plus minus] 30 feet) grey silt/clay unit, which itself shows a fining-downward trend. The stratigraphy is likely correlative to the Presumpscot Formation, as described by Bloom (1963). The bottommore » of the regressive marine sequence is marked at several locations by a thin layer of sand-sized biotite mica. Lodgement till was encountered only at scattered localities (in boreholes) at each site. The bedrock surface is of considerable relief, with changes of 200--300 feet over short distances detected. The sequence appears to be the record of a rapidly transgressing sea which inundated a valley where outwash had been deposited by meltwater ahead of retreating ice. As the sea retreated, up to 70 feet of sediment was deposited in a continuous, coarsening-upwards sequence. Subsequent to the marine regression, the sediments were reworked in a subaerial (braided stream) environment. The Surficial Geologic Map of Maine shows that the inland limit of late-glacial marine submergence is located approximately 8 miles southwest of Waterboro, in Alfred, Maine. The marine limit in Alfred takes the form of a NNE trending, blunt-ended embayment. The results of this study suggest that the marine embayment once extended northward from Alfred, and is now a buried feature, possibly representing a preglacial valley, which hosted an estuary in late Wisconsonian time.« less

Characterization of geologic deposits in the vicinity of US Ecology, Amargosa Basin, southern Nevada

USGS Publications Warehouse

Taylor, Emily M.

2010-01-01

Multiple approaches have been applied to better understand the characteristics of geologic units exposed at the surface and buried at depth in the vicinity of US Ecology (USE), a low-level commercial waste site in the northern Amargosa Desert, Nevada. Techniques include surficial geologic mapping and interpretation of the subsurface using borehole data. Dated deposits at depth were used to estimate rates of sediment accumulation. The subsurface lithologies have been modeled in three dimensions. Lithologic cross sections have been created from the three-dimensional model and have been compared to resistivity data at the same location. Where deposits appear offset, a fault was suspected. Global Positioning System elevation transects were measured and trenches were excavated to locate a strand of the Carrara Fault. The presence of the fault helps to better understand the shape of the potentiometric surface. These data will be used to better understand the hydrologic parameters controlling the containment of the waste at US Ecology.Quaternary geologic units exposed at the surface, in the vicinity of US Ecology, are derived from the alluvium shed off the adjacent range front and the Amargosa River. These deposits vary from modern to early Pleistocene in age. At depth, heterogeneous sands and gravel occur. Observed in deep trenches and boreholes, the subsurface deposits are characterized as fining-upward sequence of sediment from 5- to 8-meters thick. No volcanic units or fine-grained playa deposits were described in the boreholes to a depth of 200 meters. Based on Infrared Stimulated Luminescence dated core samples, short-term rates of sediment accumulation (<70,000 years) are an average of 2.7 millimeters per year, however, long-term rates (<3,900,000 years) are orders of magnitude less. Resistivity data, when compared to lithologic cross sections, generally are consistent with lithology grain size and probable soil carbonate accumulations. Surface resistivity displays a fining-upward sequence of sediments at the surface with a soil carbonate imprint. Finally, trenching north of US Ecology successfully exposed offset Quaternary deposits on a splay of the Carrara Fault. Holocene deposits do not appear to be faulted, however, a fault zone does intersect middle and late Pleistocene aged units.

Moussa virus: a new member of the Rhabdoviridae family isolated from Culex decens mosquitoes in Côte d’Ivoire

PubMed Central

Quan, Phenix-Lan; Junglen, Sandra; Tashmukhamedova, Alla; Conlan, Sean; Hutchison, Stephen K.; Kurth, Andreas; Ellerbrok, Heinz; Egholm, Michael; Briese, Thomas; Leendertz, Fabian H.; Ian Lipkin, W

2009-01-01

Characterization of arboviruses at the interface of pristine habitats and anthropogenic landscapes is crucial to comprehensive emergent disease surveillance and forecasting efforts. In context of surveillance campaign in and around a West African rainforest, particles morphologically consistent with rhabdoviruses were identified in cell cultures infected with homogenates of trapped mosquitoes. RNA recovered from these cultures was used to derive the first complete genome sequence of a rhabdovirus isolated from Culex decens mosquitoes in Côte d’Ivoire, tentatively named Moussa virus (MOUV). MOUV shows the classical genome organization of rhabdoviruses, with five open reading frames (ORF) in a linear order. However, sequences show only limited conservation (12–33% identity at amino acid level), and ORF2 and ORF3 have no significant similarity to sequences deposited in GenBank. Phylogenetic analysis indicates a potential new species with distant relationship to Tupaia and Tibrogargan virus. PMID:19804801

Moussa virus: a new member of the Rhabdoviridae family isolated from Culex decens mosquitoes in Côte d'Ivoire.

PubMed

Quan, Phenix-Lan; Junglen, Sandra; Tashmukhamedova, Alla; Conlan, Sean; Hutchison, Stephen K; Kurth, Andreas; Ellerbrok, Heinz; Egholm, Michael; Briese, Thomas; Leendertz, Fabian H; Lipkin, W Ian

2010-01-01

Characterization of arboviruses at the interface of pristine habitats and anthropogenic landscapes is crucial to comprehensive emergent disease surveillance and forecasting efforts. In context of a surveillance campaign in and around a West African rainforest, particles morphologically consistent with rhabdoviruses were identified in cell cultures infected with homogenates of trapped mosquitoes. RNA recovered from these cultures was used to derive the first complete genome sequence of a rhabdovirus isolated from Culex decens mosquitoes in Côte d'Ivoire, tentatively named Moussa virus (MOUV). MOUV shows the classical genome organization of rhabdoviruses, with five open reading frames (ORF) in a linear order. However, sequences show only limited conservation (12-33% identity at amino acid level), and ORF2 and ORF3 have no significant similarity to sequences deposited in GenBank. Phylogenetic analysis indicates a potential new species with distant relationship to Tupaia and Tibrogargan virus.

Salt lake Laguna de Fuente de Piedra (S-Spain) as Late Quaternary palaeoenvironmental archive

NASA Astrophysics Data System (ADS)

Höbig, Nicole; Melles, Martin; Reicherter, Klaus

2014-05-01

This study deals with Late Quaternary palaeoenvironmental variability in Iberia reconstructed from terrestrial archives. In southern Iberia, endorheic basins of the Betic Cordilleras are relatively common and contain salt or fresh-water lakes due to subsurface dissolution of Triassic evaporites. Such precipitation or ground-water fed lakes (called Lagunas in Spanish) are vulnerable to changes in hydrology, climate or anthropogenic modifications. The largest Spanish salt lake, Laguna de Fuente de Piedra (Antequera region, S-Spain), has been investigated and serves as a palaeoenvironmental archive for the Late Pleistocene to Holocene time interval. Several sediment cores taken during drilling campaigns in 2012 and 2013 have revealed sedimentary sequences (up to 14 m length) along the shoreline. A multi-proxy study, including sedimentology, geochemistry and physical properties (magnetic susceptibility) has been performed on the cores. The sedimentary history is highly variable: several decimetre thick silty variegated clay deposits, laminated evaporites, and even few-centimetre thick massive gypsum crystals (i.e., selenites). XRF analysis was focussed on valuable palaeoclimatic proxies (e.g., S, Zr, Ti, and element ratios) to identify the composition and provenance of the sediments and to delineate palaeoenvironmental conditions. First age control has been realized by AMS-radiocarbon dating. The records start with approximately 2-3 m Holocene deposits and reach back to the middle of MIS 3 (GS-3). The sequences contain changes in sedimentation rates as well as colour changes, which can be summarized as brownish-beige deposits at the top and more greenish-grey deposits below as well as highly variegated lamination and selenites below ca. 6 m depth. The Younger Dryas, Bølling/Allerød, and the so-called Mystery Interval/Last Glacial Maximum have presumably been identified in the sediment cores and aligned to other climate records. In general, the cores of the Laguna de Fuente de Piedra show cyclic deposition including evaporitic sequences throughout the Holocene and Late Pleistocene, indicating higher fluxes and reworking of organic/inorganic carbon as well as other indicative proxy elements like Ti, Zr and Ca/Sr ratio during Late Pleistocene times. In order to achieve a better understanding of the palaeoenvironmental history in the study area further studies are planned which encompass biological/palaeontological indicators (e.g., pollen, diatoms) as well as another geochemical isotopic techniques on evaporitic deposits such as fluid inclusion analysis.

A colluvium - travertine sedimentary succession from the Tibetan Plateau: dating and climatic significance

NASA Astrophysics Data System (ADS)

Meyer, Michael; Wang, Zhijun; Schlütz, Frank; Hoffmann, Dirk; May, Jan-Hendrik; Aldenderfer, Mark

2014-05-01

Morphodynamics and sedimentation on the Tibetan Plateau are strongly controlled by cold-arid climate conditions and distinct freeze-thaw cycles. In such a periglacial environment mass-wasting processes are dominant on mountain slopes, causing thick successions of talus and colluvium to accumulate. While periglacial slope dynamics are ubiquitous on the plateau today, they were probably much more intense during the various cold stages of the Late Pleistocene. However, the exact nature as well as the timing and duration of such temperature controlled slope dynamics on the Tibetan plateau are not well constrained. Travertines are secondary carbonates precipitated from hydrothermal springs. On the Tibetan Plateau these types of spring deposits form along neotectonic faults, where super-saturated ground water can penetrate onto the surface, facilitating degassing and carbonate precipitation. Spring carbonate formation further requires non-permanently frozen ground and reasonable humid conditions in order to recharge the ground water aquifer. Travertines hold potential for palaeoenvironmental reconstruction, because they are dateable via U-series techniques and their geochemical, biological and petrographic signature can be used to extract high resolution palaeoenvironmental information. Due to a dense network of neotectonic faults on the Tibetan plateau, travertines are relatively common. Nevertheless, the potential of these hydrothermal spring deposits as an archive for palaeoenvironmental change on the plateau has yet to be explored. Here we present the first results obtained for an unusual, non-continuous sediment sequence encountered in southern Tibet at an altitude of 4200 m asl. near Chusang village, i.e. a ca. 200 m thick succession of periglacial colluvium alternating with travertine deposits. Preliminary data indicate that travertine deposition at the Chusang hydrothermal spring occurred periodically throughout the Late Pleistocene and extensive travertine precipitation was also responsible for preserving old colluvial sediment. We combine U-series disequilibrium dating with optically stimulated luminescence dating and radiocarbon dating to constrain the depositional history of this unique sediment sequence. Sedimentological logging and geomorphological mapping is used to understand past depositional processes and environmental constraints. Comparison to published high resolution climate records that are continuous in nature (e.g. speleothem records from adjacent catchments and regions) will allow us to link this clastic-chemical sediment sequence into the broader palaeoclimatic framework of High Asia.

Austrian phase on the northern African margin inferred from sequence stratigraphy and sedimentary records in southern Tunisia (Chotts and Djeffara areas)

NASA Astrophysics Data System (ADS)

Lazzez, Marzouk; Zouaghi, Taher; Ben Youssef, Mohamed

2008-08-01

A multidisciplinary study concerning Aptian and Albian deposits is reported from petroleum wells and the exposed section. The biostratigraphic and sedimentological analysis defined four sedimentary units. Well-logging signals' analysis allows us to refine the record resolution on Aptian series and reveals, in the Djeffara field, a transgressive system tract (TST) and a highstand system tract (HST). Exceptionally, the first sequence (S1) in the Mareth 1 well and the fifth sequence in the two wells Mareth 1 and Gourine 1 reveal the lower-stand system tract (LST). The unconformities characterized by the absence of Upper Aptian (Clansayesian) and Lower to Middle Albian deposits signed by a significant gamma-ray reduction. The Middle and Upper Albian is represented by only one deposit sequence (S6) in Mareth 1. Towards the south, in the Gourine well, two deposit sequences were identified (S6 and S7); to specify the Aptian and Albian evolution of the deposit sequences, a tentative correlation has been established between the Chotts and Djeffara areas. This correlation allows us to characterize the sedimentary unconformities related to the tectonics and eustatic events. The Chotts and the Djeffara deposition areas were developed, characterized by an irregular subsidence and separated by the Tebaga Medenine high area. The Aptian-Albian subsidence platform of southern Tunisia may be considered as a block diagram of environmental deposit with regressive and transgressive trends, showing the impact of tectonic deformations on the palaeogeographic evolution of southeastern Tunisia during the Austrian phase. This study also must be replaced within regional structural patterns that may explain both the sequential and sedimentological evolution of the area. Deformations regionally identified are integrated in the more general context of both Tethyan and Atlantic areas related to the drift of the African platform.

Identification of the skeletal remains of Martin Bormann by mtDNA analysis.

PubMed

Anslinger, K; Weichhold, G; Keil, W; Bayer, B; Eisenmenger, W

2001-01-01

Contrary to statements of an eye-witness who reported that Martin Bormann, the second most powerful man in the Third Reich, died on 2 May 1945 in Berlin, rumours persisted over the years that he had escaped from Germany after World War II. In 1972, skeletal remains were found during construction work, and by investigating the teeth and the bones experts concluded that they were from Bormann. Nevertheless, new rumours arose and in order to end this speculation we were commissioned to identify the skeletal remains by mitochondrial DNA analysis. The comparison of the sequence of HV1 and HV2 from the skeletal remains and a living maternal relative of Martin Bormann revealed no differences and this sequence was not found in 1,500 Caucasoid reference sequences. Based on this investigation, we support the hypothesis that the skeletal remains are those of Martin Bormann.

Paleocurrents of the Middle-Upper Jurassic strata in the Paradox Basin, Colorado, inferred from anisotropy of magnetic susceptibility (AMS)

NASA Astrophysics Data System (ADS)

Ejembi, J. I.; Ferre, E. C.; Potter-McIntyre, S. L.

2017-12-01

The Middle-Upper Jurassic sedimentary strata in the southwestern Colorado Plateau recorded pervasive eolian to fluvio-lacustrine deposition in the Paradox Basin. While paleocurrents preserved in the Entrada Sandstone, an eolian deposition in the Middle Jurassic, has been well constrained and show a northwesterly to northeasterly migration of ergs from the south onto the Colorado Plateau, there is yet no clear resolution of the paleocurrents preserved in the Wanakah Formation and Tidwell Member of the Morrison Formation, both of which are important sedimentary sequences in the paleogeographic framework of the Colorado Plateau. New U-Pb detrital zircon geochronology of sandstones from these sequences suggests that an abrupt change in provenance occurred in the early Late Jurassic, with sediments largely sourced from eroding highlands in central Colorado. We measured the anisotropy of magnetic susceptibility (AMS) of sediments in oriented sandstone samples from these three successive sequences; first, to determine the paleocurrents from the orientations of the AMS fabrics in order to delineate the source area and sediments dispersal pattern and second, to determine the depositional mechanisms of the sediments. Preliminary AMS data from two study sites show consistency and clustering of the AMS axes in all the sedimentary sequences. The orientations of the Kmin - Kint planes in the Entrada Sandstone sample point to a NNE-NNW paleocurrent directions, which is in agreement with earlier studies. The orientations of the Kmin - Kint planes in the Wanakah Formation and Tidwell Member samples show W-SW trending paleocurrent directions, corroborating our hypothesis of a shift in provenance to the eroding Ancestral Front Range Mountain, located northeast of the Paradox Basin, during the Late Jurassic. Isothermal remanence magnetization (IRM) of the samples indicate that the primary AMS carriers are detrital, syndepositional ferromagnetic minerals. Thus, we contend that AMS can be successfully deployed in constraining paleocurrents in lacustrine sedimentary strata, which lacks traditional sedimentary structures for paleocurrent analyses.

Sedimentological imprints of environmental variability at the Balkan Peninsula on the sediment sequence of Lake Ohrid (Macedonia, Albania) between the Mid Pleistocene Transition and present days: The ICDP SCOPSCO project

NASA Astrophysics Data System (ADS)

Francke, Alexander; Wagner, Bernd; Leicher, Niklas; Raphael, Gromig; Leng, Melanie; Lacey, Jack; Vogel, Hendrik; Baumgarten, Henrike; Thomas, Wonik; Zanchetta, Giovanni; Roberto, Sulpizio; Krastel, Sebastian; Lindhorst, Katja

2015-04-01

The UNESCO World Heritage site of Lake Ohrid in the Balkans is thought to be the oldest, continuously existing lake in Europe. In order to unravel the geological and evolutionary history of the lake, a deep drilling campaign was conducted in spring 2013 under the umbrella of the ICDP SCOPSCO project. At the coring site "DEEP" in central parts of the lake, more than 1,500 m of sediments were recovered down to a penetration depth of 569 m blf. This sediment sequence is assumed to be more than 1.2 Ma old and likely covers the entire lacustrine deposits of the Lake Ohrid Basin. Currently, an age model for the upper 260m of the DEEP- site sequence is available. This age model is based on chronological tie points (tephrochronology), and wiggle matching of down hole logging data and (bio-)geochemistry data (XRF, TIC, TOC) from the core sequence to the global benthic stack LR04 and local insolation patterns. The data suggests that the upper 260 m of the DEEP-site sequence corresponds to the time period between the Mid Pleistocene Transition (MPT) and present days. During this period, the sedimentological properties of the sediments show a strong dependency on environmental variability in the area. Interglacial deposits appear massive or marbled, contain up to 80 % of CaCO3 (high TIC), high amounts of organic matter (high TOC) and biogenic silica (high BSi), and low contents of clastic material. Glacial deposits are predominantly marbled and calcite is generally absent. Similarly, the amounts of organic matter and biogenic silica are low, and glacial sediments predominately consist of clastic matter. Distinct layers of siderite and uniformly distributed Fe- or Mn- oxides occur in the glacial deposits, vivianite concretions occur in both the glacial and interglacial periods. High CaCO3 contents in deposits formed during warm (interglacial) periods are also known from studies on short pilot cores from Lake Ohrid and are triggered by increased productivity in the lake, such as also indicated by enhanced contents of organic matter and biogenic silica. Thereby, CaCO3 precipitation is caused by photosynthesis induced calcite precipitation during algae blooms in spring and early summer. Negligible contents of TIC in deposits formed during glacial periods can be explained by an overall low productivity (low TOC and BSi) and, in addition, by dilution of CaCO3. Dilution of CaCO3 might be a result of more acid bottom water conditions, triggered by improved mixing conditions (less thermal stratification), oxidation of OM and CO2 release from the surface sediments. Oxygenated surface sediments and degradation of organic matter are indicated by the marbled structure of the glacial sediments implying intensive bioturbation, and by TOC/TN ratios around 4, respectively. The high amount of clastic material in deposits from cold (glacial) periods can be a result of mutual dilution with calcite, organic matter and biogenic silica, but might also indicate more intensive erosion in the catchment due to a less dense vegetation cover.

Multiple episodes of mineralization revealed by Re-Os molybdenite geochronology in the Lala Fe-Cu deposit, SW China

NASA Astrophysics Data System (ADS)

Zhu, Zhimin; Tan, Hongqi; Liu, Yingdong; Li, Chao

2018-03-01

The Lala Fe-Cu deposit is one of the largest iron oxide-copper-gold (IOCG) deposits in the Kangdian copper belt, southwest China. The paragenetic sequence of the Lala deposit includes six hydrothermal stages: pre-ore pervasive Na alteration (I); magnetite stage with K-feldspar and apatite (II); polymetallic disseminated/massive magnetite-sulfide stage (III); banded magnetite-sulfide stage (IV); sulfide vein stage (V); and late quartz-carbonate vein stage (VI). Fifteen molybdenite separates from stages III to VI were analyzed for Re-Os dating. Our new Re-Os data, together with previous studies, identify four distinct hydrothermal events at the Lala deposit. Molybdenite from the stage III disseminated to massive chalcopyrite-magnetite ores yielded a weighted average Re-Os age of 1306 ± 8 Ma (MSWD = 1.1, n = 6) which represents the timing of main ore formation. Molybdenite from the stage IV-banded magnetite-chalcopyrite ores yielded a weighted average Re-Os age of 1086 ± 8 Ma (MSWD = 2.2, n = 7), i.e., a second ore-forming event. Molybdenite from the stage V sulfide veins yielded a weighted average Re-Os age of 988 ± 8 Ma (MSWD = 1.3, n = 7) which represents the timing of a third hydrothermal event. Molybdenite from the quartz-carbonate veins (stage VI) yielded a weighted average Re-Os age at 835 ± 4 Ma (MSWD = 0.66, n = 10) and documented the timing of a late hydrothermal event. Our results indicate that the Lala deposit formed during multiple, protracted mineralization events over several hundred million years. The first three Mesoproterozoic mineralization events are coeval with intra-continental rifting (breakup of the supercontinent Nuna) and share a temporal link to other IOCG-style deposits within the Kangdian Copper Belt, and the last Neoproterozoic hydrothermal event is coeval with the Sibao orogeny which culminated with the amalgamation of the Yangtze Block with the Cathaysia Block at 860-815 Ma.

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

The September 14, 2015 phreatomagmatic eruption of Nakadake first crater, Aso Volcano, Japan: Eruption sequence inferred from ballistic, pyroclastic density current and fallout deposits

NASA Astrophysics Data System (ADS)

Miyabuchi, Yasuo; Iizuka, Yoshiyuki; Hara, Chihoko; Yokoo, Akihiko; Ohkura, Takahiro

2018-02-01

An explosive eruption occurred at Nakadake first crater, Aso Volcano in central Kyushu, southwestern Japan, on September 14, 2015. The sequence and causes of the eruption were reconstructed from the distribution, textures, grain-size, component and chemical characteristics of the related deposits, and video record. The eruptive deposits are divided into ballistics, pyroclastic density current and ash-fall deposits. A large number of ballistic clasts (mostly < 10 cm in diameter; maximum size 1.6 m) are scattered within about 500 m from the center of the crater. Almost half of the ballistics appear as fresh and unaltered basaltic andesite rocks interpreted to be derived from a fresh batch of magma, while the rest is weakly to highly altered clasts. A relatively thin ash derived from pyroclastic density currents covered an area of 2.3 km2 with the SE-trending main axis and two minor axes to the NE and NW. The pyroclastic density current deposit (maximum thickness < 10 cm even at the crater rim) is wholly fine grained, containing no block-sized clasts. Based on the isopach map, the mass of the pyroclastic density current deposit was estimated at ca. 5.2 × 104 tons. The ash-fall deposit is finer grained and clearly distributed to about 8 km west of the source crater. The mass of the ash-fall deposit was calculated at about 2.7 × 104 tons. Adding the mass of the pyroclastic density current deposit, the total discharged mass of the September 14, 2015 eruption was 7.9 × 104 tons. The September 14 pyroclastic density current and ash-fall deposits consist of glass shards (ca. 30%), crystals (20-30%) and lithic (40-50%) grains. Most glass shards are unaltered poorly crystallized pale brown glasses which probably resulted from quenching of juvenile magma. This suggests that the September 14, 2015 event at the Nakadake first crater was a phreatomagmatic eruption. Similar phreatomagmatic eruptions occurred at the same crater on September 6, 1979 and April 20, 1990 whose eruptive masses were one order larger than that of the September 14, 2015 eruption. These events highlight the potential hazard from phreatic or phreatomagmatic eruptions at Nakadake first crater, and provide useful information that will assist in preventing or mitigating future disasters at other similar volcanoes worldwide.

Fluvial sedimentary styles and associated depositional environments in the buntsandstein west of river rhine in saar area and pfalz (F.R. Germany) and vosges (France)

NASA Astrophysics Data System (ADS)

Dachroth, Wolfgang

The Buntsandstein west of river Rhine in Saar area, Pfalz and Vosges consists of three fluvial magnacycles which are characterized by different associated non-alluvial environments. The stratigraphic sequence is divided by several unconformities reflecting tectonic movements which were connected with periods of extension of the depositional area. Two major phases and two minor events are recognized by the evaluation of the Pfalz unconformity and the Lothringen unconformity, and the Leuter unconformity and the Saar unconformity, respectively. The Lower Buntsandstein (including Zechstein) compries the first magnacycle and is built up of alluvial-fan deposits, fluvial braidplain sediments and marine to lagoonal deposits. Some aeolian sands as well as several palaeosols are also present. The palaeolandscape consists of alluvial fans seaming the margin of the basin and fluvial braidplains reaching from the toes of the fan belt to the centre of the depositional area which is occupied by a lagoonal sea that partially evolves into a playa-lake with progressive refreshment. The Middle Buntsandstein comprises the second magnacycle and is composed of an alternation of aeolian Dünnschichten and fluvial Felsbänke. The third facies are alluvial-fan deposits of palaeogeographically restricted distribution along the margins of the basin. The aeolian Dünnschichten originate in the marginal parts of chott-type depressions (in comparison with the recent Chott Djerid in Tunesia) where rising ground water moistens the dry sediments that are laid down on the playa floor and thus allows their enhanced preservation. In dry periods, wind-blown sand is spread out as plane sheets or as migrating wind ripple trains, or accumulates to barchanoid-type dunes that advance across the flat. Depending on supply of sand, all stages of transition between dune fields with only narrow interdune corridors between the ridges and interdune playas with isolated widely-spaced dunes are developed. The individual sand storms operating in the erg are recorded in a mm-scale graded grain-size lamination. The desert-type setting is divided into depositional sand ergs where aeolian bedforms migrate, and deflationary gravel serirs where pebbly fluvial sediments are winnowed, resulting in concentration of the gravel to residual lags and in abundant grinding of clasts to ventifacts. During time of flooding of the chotts by atmospheric precipitation, fluvial incursions or rising ground water level, lacustrine playa deposits settle out in shallow stagnant water. The fluvial Felsbänke originate in wadi-type braided river systems intersecting the erg and serir zones and often redepositing aeolian sand which is derived from undercutting during abandonment and displacement of the watercourses. The stream complexes are partially fed at their proximal ends by runoff from local alluvial fans which are aligned along parts of the margins of the basin. The Upper Buntsandstein comprises the third magnacycle which is split into three megacycles that in turn are divided into several phases. A change from generally arid to primarily semi-arid climate along with tectonical up-lift in the source area results in extinction of aeolian deposition and gives rise to formation of Violette Horizonte calcrete palaeosols which are widespread throughout the Upper Buntsandstein, if their origin was not inhibited by the dynamics of the fluvial systems. The palaeosols occur in different evolutionary stages and are mainly characterized by the typical blue-violet colour, presence of root tubes, carbonate nodules and carbonate crusts, destratification and polyedric jointing. The fluvial fining-upwards cyclothems are formed in braided river systems which partially pass into meandering stream complexes. At the top of the Upper Buntsandstein, the alluvial inland plain is converted into a delta complex in the coastal plain along the approaching sea, and with a sequence of alternating progradation and recession events, the Muschelkalk transgression finally inundates the continental setting.

Mushroom Flora of Ulleung-gun and a Newly Recorded Bovista Species in the Republic of Korea

PubMed Central

Kim, Chang Sun; Jo, Jong Won; Kwag, Young-Nam; Sung, Gi-Ho; Lee, Sle-gee; Kim, Sang-Yong; Shin, Chang-Ho

2015-01-01

We conducted five times surveys, in June, September and October in 2012; June and September 2013, to catalog the mushroom flora in Ulleung-gun, Republic of Korea. More than 400 specimens were collected, and 317 of the specimens were successfully sequenced using the ribosomal DNA internal transcribed spacer barcode marker. We also surveyed the morphological characteristics of the sequenced specimens. The specimens were classified into 2 phyla, 7 classes, 21 orders, 59 families, 122 genera, and 221 species, and were deposited in the herbarium of Korea National Arboretum. Among the collected species, 72% were saprophytic, 25% were symbiotic, and 3% were parasitic. The most common order was Agaricales (189 specimens, 132 species), followed by Polyporales (47 specimens, 27 species), Russulales (31 specimens, 22 species), Boletales (10 specimens, 7 species), and so on. Herein, we also reported the first Bovista species in Korea, which was collected from Dokdo, the far-eastern island of Korea. PMID:26539040

Essai de corrélations séquentielles au Barrémien-Aptien dans un système plateforme-bassin-plateforme le long d'un transect Danube-Gabrovo (Bulgarie du Centre-Nord)

NASA Astrophysics Data System (ADS)

Ivanov, Marin; Peybernès, Bernard; Nikolov, Todor; Ciszak, Richard; Stoykova, Krystalina; Minkovska, Vera

1997-12-01

Along a Danube-Gabrovo cross-section, from Central Fore Balkan to Moesian Platform, the Barremian-Aptian deposits are distributed within three distinct paleogeographic domains: a central terrigenous: basin (Pleven-Polski Trămbeš) and, laterally (N: Danube, S: Gabrovo) two carbonate-dominated platforms where "Urgonian" fades can be well-developed. This pattern is induced by synsedimentary extensional tectonics already active from the end of Jurassic times. The subdivision of the various series into eight 3 d order depositional sequences and the recent discovery of ammonites allow us to propose new and more reliable correlations between the traditional lithologic formations characterizing those three domains.

Suspected Offshore Chalcolithic/Early Bronze Age Tsunamigenic Sediments: Jisr al Zarka, Israel

NASA Astrophysics Data System (ADS)

Tiulienieva, N.; Braun, Y.; Katz, T.; Goodman-Tchernov, B. N.; Suchkov, I.

2017-12-01

Offshore tsunami deposits are a potentially important sedimentological archive for past tsunamis. They have been identified offshore of Israel using granulometric, geoarchaeological, and micropaleontological indicators. Recent advances in tsunami sedimentological research have put forth a series of new proxies that may be useful tools for tsunami deposit identification. The well-studied offshore deposits of Israel provide a unique opportunity to test some of these proxies because they present good distinction between tsunami and non-tsunami deposits and they can be associated with a rich historical record and archaeological artifacts. In this study, a 219 cm long sediment core, retrieved from a 15.3 m water depth, situated in about 5 km to the north from well studied shallow shelf, offshore Caesarea. Based on the previously used criteria three layers in the new core were identified as tsunami-generated. Two of these correlated to previously described tsunami events in Caesarea; 749 AD and 1500 BC. The third layer gave the time frame from 5.6 to 6 ka BP, making this event the oldest identified in the Eastern Mediterranean to date. Identified unusual layers were attributed to tsunami-generated sedimentary sequences, based on both visually recognizable indicators and the results of laboratory analyses. FT-IR, XRD, and XRF analysis were also applied. The results of this study allow to make following conclusions: (1) visual tsunami indicators in the studied core are similar to those in Caesarea, but lack archaeological debris; (2) while distinct deviation of granulometric coefficients (mean, median, standard deviation, skewness, kurtosis) correlated to tsunami layers, the additional proxies of deposition rate and mollusk assemblage excluded one deviated layer from tsunamigenic-designation; (3) the results of XRF, FT-IR, XRD showed that they are not useful as independent methods at this study site.

GFinisher: a new strategy to refine and finish bacterial genome assemblies

NASA Astrophysics Data System (ADS)

Guizelini, Dieval; Raittz, Roberto T.; Cruz, Leonardo M.; Souza, Emanuel M.; Steffens, Maria B. R.; Pedrosa, Fabio O.

2016-10-01

Despite the development in DNA sequencing technology, improving the number and the length of reads, the process of reconstruction of complete genome sequences, the so called genome assembly, is still complex. Only 13% of the prokaryotic genome sequencing projects have been completed. Draft genome sequences deposited in public databases are fragmented in contigs and may lack the full gene complement. The aim of the present work is to identify assembly errors and improve the assembly process of bacterial genomes. The biological patterns observed in genomic sequences and the application of a priori information can allow the identification of misassembled regions, and the reorganization and improvement of the overall de novo genome assembly. GFinisher starts generating a Fuzzy GC skew graphs for each contig in an assembly and follows breaking down the contigs in critical points in order to reassemble and close them using jFGap. This has been successfully applied to dataset from 96 genome assemblies, decreasing the number of contigs by up to 86%. GFinisher can easily optimize assemblies of prokaryotic draft genomes and can be used to improve the assembly programs based on nucleotide sequence patterns in the genome. The software and source code are available at http://gfinisher.sourceforge.net/.

GFinisher: a new strategy to refine and finish bacterial genome assemblies.

PubMed

Guizelini, Dieval; Raittz, Roberto T; Cruz, Leonardo M; Souza, Emanuel M; Steffens, Maria B R; Pedrosa, Fabio O

2016-10-10

Despite the development in DNA sequencing technology, improving the number and the length of reads, the process of reconstruction of complete genome sequences, the so called genome assembly, is still complex. Only 13% of the prokaryotic genome sequencing projects have been completed. Draft genome sequences deposited in public databases are fragmented in contigs and may lack the full gene complement. The aim of the present work is to identify assembly errors and improve the assembly process of bacterial genomes. The biological patterns observed in genomic sequences and the application of a priori information can allow the identification of misassembled regions, and the reorganization and improvement of the overall de novo genome assembly. GFinisher starts generating a Fuzzy GC skew graphs for each contig in an assembly and follows breaking down the contigs in critical points in order to reassemble and close them using jFGap. This has been successfully applied to dataset from 96 genome assemblies, decreasing the number of contigs by up to 86%. GFinisher can easily optimize assemblies of prokaryotic draft genomes and can be used to improve the assembly programs based on nucleotide sequence patterns in the genome. The software and source code are available at http://gfinisher.sourceforge.net/.

A short review of paleoenvironments for Lower Beaufort (Upper Permian) Karoo sequences from southern to central Africa: A major Gondwana Lacustrine episode

NASA Astrophysics Data System (ADS)

Yemane, K.; Kelts, K.

This paper compares Karoo deposits within the Lower Beaufort (Late Permian) time interval from southern to central Africa. Facies aspects are summarized for selected sequences and depositional environments assessed in connection with the palaeogeography. The comparison shows that thickness of Lower Beaufort sequences varies greatly; sequences are over a kilometre thick at the southern tip, but decrease drastically to the north, northwest and northeast, and is commonly absent from the western part of the subcontinent. Depositional environments are continental except for small estuarine intervals from a sequence in Tanzania. The commonest lithologies comprise mudstones, siltstones, arkoses and carbonates. In spite of the dominance of fluvial facies, the records preserved by intervals of lacustrine sequences suggest that large lakes were major features of the palaeogeography, and that lacustrine environments may have been dominant deposition environments. The Lower Beaufort landscape is generally interpreted as an expansive cratonic lowland with meandering rivers and streams crossing vast floodplains, which were indented by concomitant shallow lakes of various sizes. The lakes from the Karoo tectono-sedimentary terrain were often ephemeral and closely linked with fluvial processes, but large, anoxic lakers are also documented. On the other hand, giant, freshwater lakes, covered large areas of the Zambezian tectono-sedimentary terrain and may have been locally connected. Evidence from abundant freshwater fossil assemblages, particularly from the Zambezian tectono-sedimentary terrain suggest that in spite of the generally semi-arid global climate of the Upper Permian, seasonal precipitation (monsoonal?) supplied enough moisture to sustain large perennial lakes. Because of the unique nature of the Permian cotinental configuration and palaeogeography, however, modern analogues of large systems are lacking. The general lithological and palaeontological correlability of Lower Beaufort sequences suggests a similar regional palaeoclimate, whereas the differences in distribution are taken to be a result of control of tectonic settings. From the widespread occurrences of lake deposits in the African subcontinent, over relatively long interval, we conclude that lake deposits provide more information for a better understanding of Karoo palaeogeography than previously thought, since such lacustrine sequences should hold sensitive, high resolution records for palaeoenvironmental interpretations.

Tectonostratigraphy and depositional history of the Neoproterozoic volcano-sedimentary sequences in Kid area, southeastern Sinai, Egypt: Implications for intra-arc to foreland basin in the northern Arabian-Nubian Shield

NASA Astrophysics Data System (ADS)

Khalaf, E. A.; Obeid, M. A.

2013-09-01

This paper presents a stratigraphic and sedimentary study of Neoproterozoic successions of the South Sinai, at the northernmost segment of the Arabian-Nubian Shield (ANS), including the Kid complex. This complex is composed predominantly of thick volcano-sedimentary successions representing different depositional and tectonic environments, followed by four deformational phases including folding and brittle faults (D1-D4). The whole Kid area is divisible from north to south into the lower, middle, and upper rock sequences. The higher metamorphic grade and extensive deformational styles of the lower sequence distinguishes them from the middle and upper sequences. Principal lithofacies in the lower sequence include thrust-imbricated tectonic slice of metasediments and metavolcanics, whereas the middle and upper sequences are made up of clastic sediments, intermediate-felsic lavas, volcaniclastics, and dike swarms. Two distinct Paleo- depositional environments are observed: deep-marine and alluvial fan regime. The former occurred mainly during the lower sequence, whereas the latter developed during the other two sequences. These alternations of depositional conditions in the volcano-sedimentary deposits suggest that the Kid area may have formed under a transitional climate regime fluctuating gradually from warm and dry to warm and humid conditions. Geochemical and petrographical data, in conjunction with field relationships, suggest that the investigated volcano-sedimentary rocks were built from detritus derived from a wide range of sources, ranging from Paleoproterozoic to Neoproterozoic continental crust. Deposition within the ancient Kid basin reflects a complete basin cycle from rifting and passive margin development, to intra-arc and foreland basin development and, finally, basin closure. The early phase of basin evolution is similar to various basins in the Taupo volcanics, whereas the later phases are similar to the Cordilleran-type foreland basin. The progressive change in lithofacies from marine intra-arc basin to continental molasses foreland basin and from compression to extension setting respectively, imply that the source area became peneplained, where the Kid basin became stabilized as sedimentation progressed following uplift. The scenario proposed of the study area supports the role of volcanic and tectonic events in architecting the facies and stratigraphic development.

Atomic layer deposition in nanostructured photovoltaics: tuning optical, electronic and surface properties

NASA Astrophysics Data System (ADS)

Palmstrom, Axel F.; Santra, Pralay K.; Bent, Stacey F.

2015-07-01

Nanostructured materials offer key advantages for third-generation photovoltaics, such as the ability to achieve high optical absorption together with enhanced charge carrier collection using low cost components. However, the extensive interfacial areas in nanostructured photovoltaic devices can cause high recombination rates and a high density of surface electronic states. In this feature article, we provide a brief review of some nanostructured photovoltaic technologies including dye-sensitized, quantum dot sensitized and colloidal quantum dot solar cells. We then introduce the technique of atomic layer deposition (ALD), which is a vapor phase deposition method using a sequence of self-limiting surface reaction steps to grow thin, uniform and conformal films. We discuss how ALD has established itself as a promising tool for addressing different aspects of nanostructured photovoltaics. Examples include the use of ALD to synthesize absorber materials for both quantum dot and plasmonic solar cells, to grow barrier layers for dye and quantum dot sensitized solar cells, and to infiltrate coatings into colloidal quantum dot solar cell to improve charge carrier mobilities as well as stability. We also provide an example of monolayer surface modification in which adsorbed ligand molecules on quantum dots are used to tune the band structure of colloidal quantum dot solar cells for improved charge collection. Finally, we comment on the present challenges and future outlook of the use of ALD for nanostructured photovoltaics.

Repairing the sickle cell mutation. I. Specific covalent binding of a photoreactive third strand to the mutated base pair.

PubMed

Broitman, S; Amosova, O; Dolinnaya, N G; Fresco, J R

1999-07-30

A DNA third strand with a 3'-psoralen substituent was designed to form a triplex with the sequence downstream of the T.A mutant base pair of the human sickle cell beta-globin gene. Triplex-mediated psoralen modification of the mutant T residue was sought as an approach to gene repair. The 24-nucleotide purine-rich target sequence switches from one strand to the other and has four pyrimidine interruptions. Therefore, a third strand sequence favorable to two triplex motifs was used, one parallel and the other antiparallel to it. To cope with the pyrimidine interruptions, which weaken third strand binding, 5-methylcytosine and 5-propynyluracil were used in the third strand. Further, a six residue "hook" complementary to an overhang of a linear duplex target was added to the 5'-end of the third strand via a T(4) linker. In binding to the overhang by Watson-Crick pairing, the hook facilitates triplex formation. This third strand also binds specifically to the target within a supercoiled plasmid. The psoralen moiety at the 3'-end of the third strand forms photoadducts to the targeted T with high efficiency. Such monoadducts are known to preferentially trigger reversion of the mutation by DNA repair enzymes.

Miocene unconformities in the Central Apennines: geodynamic significance and sedimentary basin evolution

NASA Astrophysics Data System (ADS)

Cipollari, Paola; Cosentino, Domenico

1995-12-01

This paper shows the results obtained from an integrated study (geology, biostratigraphy and geochemistry) carried out on the Miocene edimentary deposits in Central Italy in order to define the timing of the sedimentary basin evolution. This paper deals also with the causes of the unconformities recorded in these basins. In the Miocene deposits of the Latina Valley and the Ernici-Simbruini Mts. several unconformities which distinguish different stratigraphic sequences have been recognized (D 0, D 1, D 2 D 3 and D 4). For each unconformity a general description together with a geodynamical significance is provided. In particular, D 0 unconformity appears to be related to a regional tectonic event (Adria-Europe collision). As a consequence, the Adria lithosphere folded and the area underwent a regional erosive event. D 1, D 2 and D 3 unconformities have had a more local tectonic control since they represent the stratigraphic record of the migration of the Apennines thrust belt/foredeep system. D 1 and D 2 unconformities are related to the late Tortonian foredeep stage, whereas D 3 is linked to the early Messinian piggy-back stage. Moreover, the D 4 unconformity, which took place during the Messinian piggy-back stage, is strictly linked to the sea-level drop of the Messinian salinity crisis. In this paper the genesis and evolution of a late Tortonian foreland basin is also stressed (Latina Valley foredeep basin). Finally, taking into account sequence boundaries, nannofossil biostratigraphy and geochemistry isotopic data, a comparison with the curve of the 3rd order of the relative coastal onlap (Haq et al., 1988) has been attempted in order to distinguish the unconformities controlled either by tectonic or eustatic processes.

Structural, optical and nonlinear optical studies of AZO thin film prepared by SILAR method for electro-optic applications

NASA Astrophysics Data System (ADS)

Edison, D. Joseph; Nirmala, W.; Kumar, K. Deva Arun; Valanarasu, S.; Ganesh, V.; Shkir, Mohd.; AlFaify, S.

2017-10-01

Aluminium doped (i.e. 3 at%) zinc oxide (AZO) thin films were prepared by simple successive ionic layer adsorption and reaction (SILAR) method with different dipping cycles. The structural and surface morphology of AZO thin films were studied by using X-ray diffraction (XRD) and scanning electron microscopy (SEM). The optical parameters such as, transmittance, band gap, refractive index, extinction coefficient, dielectric constant and nonlinear optical properties of AZO films were investigated. XRD pattern revealed the formation of hexagonal phase ZnO and the intensity of the film was found to increase with increasing dipping cycle. The crystallite size was found to be in the range of 29-37 nm. Scanning Electron Microscope (SEM) images show the presence of small sized grains, revealing that the smoothest surface was obtained at all the films. The EDAX spectrum of AZO conforms the presence of Zn, O and Al. The optical transmittance in the visible region is high 87% and the band gap value is 3.23 eV. The optical transmittance is decreased with respect to dipping cycles. The room temperature PL studies revealed that the AZO films prepared at (30 cycles) has good film quality with lesser defect density. The third order nonlinear optical parameters were also studied using Z-scan technique to know the applications of deposited films in nonlinear devices. The third order nonlinear susceptibility value is found to be 1.69 × 10-7, 3.34 × 10-8, 1.33 × 10-7and 2.52 × 10-7 for AZO films deposited after 15, 20, 25 and 30 dipping cycles.

Third-order optical nonlinearity studies of bilayer Au/Ag metallic films

NASA Astrophysics Data System (ADS)

Mezher, M. H.; Chong, W. Y.; Zakaria, R.

2016-05-01

This paper presents nonlinear optical studies of bilayer metallic films of gold (Au) and silver (Ag) on glass substrate prepared using electron beam evaporation. The preparation of Au and Ag nanoparticles (NPs) on the substrate involved the use of electron beam deposition, then thermal annealing at 600 °C and 270 °C, respectively, to produce a randomly distributed layer of Au and a layer of Ag NPs. Observation of field-effect scanning electron microscope images indicated the size of the NPs. Details of the optical properties related to peak absorption of surface plasmon resonance of the nanoparticle were revealed by use of UV-Vis spectroscopy. The Z-scan technique was used to measure the nonlinear absorption and nonlinear refraction of the fabricated NP layers. The third-order nonlinear refractive index coefficients for Au and Ag are (-9.34 and  -1.61)  ×  10-11 cm2 W-1 given lower n 2, in comparison with bilayer (Au and Ag) NPs at  -1.24  ×  10-10 cm2 W-1. The results show bilayer NPs have higher refractive index coefficients thus enhance the nonlinearity effects.

Radiocarbon Dates from Volcanic Deposits of the Chaos Crags and Cinder Cone Eruptive Sequences and Other Deposits, Lassen Volcanic National Park and Vicinity, California

USGS Publications Warehouse

Clynne, Michael A.; Christiansen, Robert L.; Trimble, Deborah A.; McGeehin, John P.

2008-01-01

This contribution reports radiocarbon ages obtained from charcoal, wood and other samples collected between 1979 and 2001 in Lassen Volcanic National Park and vicinity and a few samples from other nearby localities. Most of the samples are from the Chaos Crags and Cinder Cone eruptive sequences. Brief summaries are given of the Chaos Crags and Cinder Cone eruptive sequences.

Gene Discovery through Genomic Sequencing of Brucella abortus

PubMed Central

Sánchez, Daniel O.; Zandomeni, Ruben O.; Cravero, Silvio; Verdún, Ramiro E.; Pierrou, Ester; Faccio, Paula; Diaz, Gabriela; Lanzavecchia, Silvia; Agüero, Fernán; Frasch, Alberto C. C.; Andersson, Siv G. E.; Rossetti, Osvaldo L.; Grau, Oscar; Ugalde, Rodolfo A.

2001-01-01

Brucella abortus is the etiological agent of brucellosis, a disease that affects bovines and human. We generated DNA random sequences from the genome of B. abortus strain 2308 in order to characterize molecular targets that might be useful for developing immunological or chemotherapeutic strategies against this pathogen. The partial sequencing of 1,899 clones allowed the identification of 1,199 genomic sequence surveys (GSSs) with high homology (BLAST expect value < 10−5) to sequences deposited in the GenBank databases. Among them, 925 represent putative novel genes for the Brucella genus. Out of 925 nonredundant GSSs, 470 were classified in 15 categories based on cellular function. Seven hundred GSSs showed no significant database matches and remain available for further studies in order to identify their function. A high number of GSSs with homology to Agrobacterium tumefaciens and Rhizobium meliloti proteins were observed, thus confirming their close phylogenetic relationship. Among them, several GSSs showed high similarity with genes related to nodule nitrogen fixation, synthesis of nod factors, nodulation protein symbiotic plasmid, and nodule bacteroid differentiation. We have also identified several B. abortus homologs of virulence and pathogenesis genes from other pathogens, including a homolog to both the Shda gene from Salmonella enterica serovar Typhimurium and the AidA-1 gene from Escherichia coli. Other GSSs displayed significant homologies to genes encoding components of the type III and type IV secretion machineries, suggesting that Brucella might also have an active type III secretion machinery. PMID:11159979

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

Chen, Zheng; Huang, Hongying; Yan, Jue

We develop 3rd order maximum-principle-satisfying direct discontinuous Galerkin methods [8], [9], [19] and [21] for convection diffusion equations on unstructured triangular mesh. We carefully calculate the normal derivative numerical flux across element edges and prove that, with proper choice of parameter pair (β 0,β 1) in the numerical flux formula, the quadratic polynomial solution satisfies strict maximum principle. The polynomial solution is bounded within the given range and third order accuracy is maintained. There is no geometric restriction on the meshes and obtuse triangles are allowed in the partition. As a result, a sequence of numerical examples are carried outmore » to demonstrate the accuracy and capability of the maximum-principle-satisfying limiter.« less

External quality assurance project report for the National Atmospheric Deposition Program’s National Trends Network and Mercury Deposition Network, 2013–14

USGS Publications Warehouse

Wetherbee, Gregory A.; Martin, RoseAnn

2016-07-05

The Mercury Deposition Network programs include the system blank program and an interlaboratory comparison program. System blank results indicated that maximum total mercury contamination concentrations in samples were less than the third percentile of all Mercury Deposition Network sample concentrations. The Mercury Analytical Laboratory produced chemical concentration results with low bias and variability compared with other domestic and international laboratories that support atmospheric-deposition monitoring.

Learning strategy preference of 5XFAD transgenic mice depends on the sequence of place/spatial and cued training in the water maze task.

PubMed

Cho, Woo-Hyun; Park, Jung-Cheol; Chung, ChiHye; Jeon, Won Kyung; Han, Jung-Soo

2014-10-15

Learning strategy preference was assessed in 5XFAD mice, which carry 5 familial Alzheimer's disease (AD) mutations. Mice were sequentially trained in cued and place/spatial versions of the water maze task. After training, a strategy preference test was conducted in which mice were required to choose between the spatial location where the platform had previously been during the place/spatial training, and a visible platform in a new location. 5XFAD and non-transgenic control mice showed equivalent escape performance in both training tasks. However, in the strategy preference test, 5XFAD mice preferred a cued strategy relative to control mice. When the training sequence was presented in the reverse order (i.e., place/spatial training before cued training), 5XFAD mice showed impairments in place/spatial training, but no differences in cued training or in the strategy preference test comparing to control. Analysis of regional Aβ42 deposition in brains of 5XFAD mice showed that the hippocampus, which is involved in the place/spatial learning strategy, had the highest levels of Aβ42 and the dorsal striatum, which is involved in cued learning strategy, showed a small increase in Aβ42 levels. The effect of training protocol order on performance, and regional differences in Aβ42 deposition observed in 5XFAD mice, suggest differential functional recruitment of brain structures related to learning in healthy and AD individuals. Copyright © 2014 Elsevier B.V. All rights reserved.

Differentiated evolutionary relationships among chordates from comparative alignments of multiple sequences of MyoD and MyoG myogenic regulatory factors.

PubMed

Oliani, L C; Lidani, K C F; Gabriel, J E

2015-10-16

MyoD and MyoG are transcription factors that have essential roles in myogenic lineage determination and muscle differentiation. The purpose of this study was to compare multiple amino acid sequences of myogenic regulatory proteins to infer evolutionary relationships among chordates. Protein sequences from Mus musculus (P10085 and P12979), human Homo sapiens (P15172 and P15173), bovine Bos taurus (Q7YS82 and Q7YS81), wild pig Sus scrofa (P49811 and P49812), quail Coturnix coturnix (P21572 and P34060), chicken Gallus gallus (P16075 and P17920), rat Rattus norvegicus (Q02346 and P20428), domestic water buffalo Bubalus bubalis (D2SP11 and A7L034), and sheep Ovis aries (Q90477 and D3YKV7) were searched from a non-redundant protein sequence database UniProtKB/Swiss-Prot, and subsequently analyzed using the Mega6.0 software. MyoD evolutionary analyses revealed the presence of three main clusters with all mammals branched in one cluster, members of the order Rodentia (mouse and rat) in a second branch linked to the first, and birds of the order Galliformes (chicken and quail) remaining isolated in a third. MyoG evolutionary analyses aligned sequences in two main clusters, all mammalian specimens grouped in different sub-branches, and birds clustered in a second branch. These analyses suggest that the evolution of MyoD and MyoG was driven by different pathways.

Surface water acidification responses and critical loads of sulfur and nitrogen deposition in Loch Vale watershed, Colorado

USGS Publications Warehouse

Sullivan, T.J.; Cosby, B.J.; Tonnessen, K.A.; Clow, D.W.

2005-01-01

We evaluated the sensitivity of The Loch, a subalpine lake in Rocky Mountain National Park in Colorado, to acidification in response to increased atmospheric loading of sulfur (S) and nitrogen (N) using the Model of Acidification of Groundwater in Catchments (MAGIC). Lake water acid‐base chemistry was moderately sensitive to changes in both S and N deposition. However, the loads of S deposition that would drive chronic lake water acid neutralizing capacity (ANC) to below 0 or 20 μeq L−1 were estimated to be 11 and 8 kg S ha−1 yr−1, respectively, assuming constant future N deposition at current levels. Comparable loads for N deposition, assuming constant future S deposition, were estimated to be 21 and 12 kg N ha−1 yr−1, respectively. Modeling results for Andrews Creek, an alpine tributary to The Loch, suggested critical loads for surface water acidification that averaged about one third lower. Surface water ANC = 50 μeq L−1 was projected to occur in 50 years in The Loch if S or N deposition increased by a moderate amount (<40%) but could not be achieved in Andrews Creek by reducing either S or N deposition to zero. On the basis of the results of synoptic surveys of lake water chemistry, about one fifth of the wilderness lakes in the Colorado Front Range are more acid‐sensitive than The Loch. This modeling exercise suggests the need for a regional analysis of critical loads for the larger population of acid‐sensitive aquatic resources in order to provide part of the scientific foundation for federally mandated land management decisions.

Linear and nonlinear optical properties of Sb-doped GeSe2 thin films

NASA Astrophysics Data System (ADS)

Zhang, Zhen-Ying; Chen, Fen; Lu, Shun-Bin; Wang, Yong-Hui; Shen, Xiang; Dai, Shi-Xun; Nie, Qiu-Hua

2015-06-01

Sb-doped GeSe2 chalcogenide thin films are prepared by the magnetron co-sputtering method. The linear optical properties of as-deposited films are derived by analyzing transmission spectra. The refractive index rises and the optical band gap decreases from 2.08 eV to 1.41 eV with increasing the Sb content. X-ray photoelectron spectra further confirm the formation of a covalent Sb-Se bond. The third-order nonlinear optical properties of thin films are investigated under femtosecond laser excitation at 800 nm. The results show that the third-order nonlinear optical properties are enhanced with increasing the concentration of Sb. The nonlinear refraction indices of these thin films are measured to be on the order of 10-18 m2/W with a positive sign and the nonlinear absorption coefficients are obtained to be on the order of 10-10 m/W. These excellent properties indicate that Sb-doped Ge-Se films have a good prospect in the applications of nonlinear optical devices. Project supported by the National Key Basic Research Program of China (Grant No. 2012CB722703), the National Natural Science Foundation of China (Grant No. 61377061), the Young Leaders of Academic Climbing Project of the Education Department of Zhejiang Province, China (Grant No. pd2013092), the Program for Innovative Research Team of Ningbo City, China (Grant No. 2009B217), and the K. C. Wong Magna Fund in Ningbo University, China.

Sequence stratigraphic controls on reservoir characterization and architecture: case study of the Messinian Abu Madi incised-valley fill, Egypt

NASA Astrophysics Data System (ADS)

Abdel-Fattah, Mohamed I.; Slatt, Roger M.

2013-12-01

Understanding sequence stratigraphy architecture in the incised-valley is a crucial step to understanding the effect of relative sea level changes on reservoir characterization and architecture. This paper presents a sequence stratigraphic framework of the incised-valley strata within the late Messinian Abu Madi Formation based on seismic and borehole data. Analysis of sand-body distribution reveals that fluvial channel sandstones in the Abu Madi Formation in the Baltim Fields, offshore Nile Delta, Egypt, are not randomly distributed but are predictable in their spatial and stratigraphic position. Elucidation of the distribution of sandstones in the Abu Madi incised-valley fill within a sequence stratigraphic framework allows a better understanding of their characterization and architecture during burial. Strata of the Abu Madi Formation are interpreted to comprise two sequences, which are the most complex stratigraphically; their deposits comprise a complex incised valley fill. The lower sequence (SQ1) consists of a thick incised valley-fill of a Lowstand Systems Tract (LST1)) overlain by a Transgressive Systems Tract (TST1) and Highstand Systems Tract (HST1). The upper sequence (SQ2) contains channel-fill and is interpreted as a LST2 which has a thin sandstone channel deposits. Above this, channel-fill sandstone and related strata with tidal influence delineates the base of TST2, which is overlain by a HST2. Gas reservoirs of the Abu Madi Formation (present-day depth ˜3552 m), the Baltim Fields, Egypt, consist of fluvial lowstand systems tract (LST) sandstones deposited in an incised valley. LST sandstones have a wide range of porosity (15 to 28%) and permeability (1 to 5080mD), which reflect both depositional facies and diagenetic controls. This work demonstrates the value of constraining and evaluating the impact of sequence stratigraphic distribution on reservoir characterization and architecture in incised-valley deposits, and thus has an important impact on reservoir quality evolution in hydrocarbon exploration in such settings.

Revealing the microbial community structure of clogging materials in dewatering wells differing in physico-chemical parameters in an open-cast mining area.

PubMed

Wang, Juanjuan; Sickinger, Maren; Ciobota, Valerian; Herrmann, Martina; Rasch, Helfried; Rösch, Petra; Popp, Jürgen; Küsel, Kirsten

2014-10-15

Iron rich deposits cause clogging the pumps and pipes of dewatering wells in open-cast mines, interfering with their function; however, little is known about either the microbial community structure or their potential role in the formation of these deposits. The microbial diversity and abundance of iron-oxidizing and -reducing bacteria were compared in pipe deposit samples with different levels of encrustation from 16 wells at three lignite mining sites. The groundwater varied in pH values from slightly acidic (4.5) to neutral (7.3), Fe(II) concentrations from 0.48 to 7.55 mM, oxygen content from 1.8 to 5.8 mg L(-1), and dissolved organic carbon (DOC) from 1.43 to 12.59 mg L(-1). There were high numbers of bacterial 16S rRNA gene copies in deposits, up to 2.5 × 10(10) copies g(-1) wet weight. Pyrosequencing analysis of bacterial 16S rRNA genes revealed that Proteobacteria was the most abundant phylum (63.3% of the total reads on average), followed by Actinobacteria (10.2%) and Chloroflexi (6.4%). Gallionella-related sequences dominated the bacterial community of pipe deposits and accounted for 48% of total sequence reads. Pipe deposits with amorphous ferrihydrite and schwertmannite mostly contained Gallionella (up to 1.51 × 10(10) 16S rRNA gene copies g(-1) wet weight), while more crystalline deposits showed a higher bacterial diversity. Surprisingly, the abundance of Gallionella was not correlated with groundwater pH, oxygen, or DOC content. Sideroxydans-related 16S rRNA gene copy numbers were one order of magnitude less than Gallionella, followed by acidophilic Ferrovum-related groups. Iron reducing bacteria were detected at rather low abundance, as was expected given the low iron reduction potential, although they could be stimulated by lactate amendment. The overall high abundance of Gallionella suggests that microbes may make major contributions to pipe deposit formation irrespective of the water geochemistry. Their iron oxidation activity might initiate the formation of amorphous iron oxides, potentially providing niches for other microorganisms later after crystallization, and leading to higher bacterial diversity along with deposit accumulation in later stages of clogging. Copyright © 2014 Elsevier Ltd. All rights reserved.

Mega-features at the Table Rock phreatomagmatic complex in Christmas Valley, Oregon; Law of original horizontality need not apply

NASA Astrophysics Data System (ADS)

Brand, B. D.; Clarke, A.

2006-12-01

The Table Rock Complex (TRC; Pliocene-Pleistocene), first documented and described by (Heiken, 1971, J. Geophy Res, 76, 5615-5626) is a large and well exposed phreatomagmatic complex in the Fort Rock- Christmas Lake Valley Basin, south-central Oregon. It is ~7 by 5 km and contains two large phreatomagmatic edifices; a large southern tuff cone with a capping lava lake (TRC1), and a large broad tuff ring in the northeast (TRC2). At least five additional, smaller tuff rings were identified along the flanks of the complex, yielding a complicated network of tuff ring-tuff cone deposits. Based on the low accidental component and evidence for a lake during this time, the cause of the explosive eruptions is interpreted to be due to interaction of magma with shallow standing water. The TRC1 consists of fining-up sequences, large erosive channel scour and fill deposits, massive tuff breccias, and abundant soft sediment deformation, which suggests deposition within a standing body of water. Subaerial TRC1 deposits are found south of the edifice, but are not exposed in the north. A significant repose period occurred between the TRC1 and TRC2 eruptions, evidenced by a wave-cut terrace and 25-50 cm of diatomitic lake sediments. TRC2 produced multiple, extremely erosive pyroclastic surges, which cut and scour the TRC1 deposits. Surge deposits consist of 50-200 m wavelength cross-beds, in some areas form large U-shaped features (10-100 m deep), and can be seen plastering up and around large obstacles from previous vents. The surge-deposits blanket all other sequences and create a hummocky topography around the edifice. This suggests that TRC2 was the last eruption in the sequence. The weight of the TRC2 sediments caused the water-saturated TRC1 sediments to plastically deform into large ball and pillow features and overturned slump blocks on the order of 20-50 m thick. The smaller flank tuff-ring eruptions likely occurred sometime between the TRC1 and TRC2 events. The inner-craters of these vents are well exposed and show features such as near-vertical plastered beds, large-scale convolute bedding, and in some places deformed and folded slump blocks up to 20-120 m thick. The features observed in both TRC deposits and in the smaller flank tuff rings (e.g., large-scale soft sediment deformation, plastered-vertical bedding, accretionary/armored lapilli) are consistent with a high water-magma ratio. The highly erosive surge beds of TRC2 represent the most energetic pulse of the eruptions.

Internet-accessible DNA sequence database for identifying fusaria from human and animal infections.

PubMed

O'Donnell, Kerry; Sutton, Deanna A; Rinaldi, Michael G; Sarver, Brice A J; Balajee, S Arunmozhi; Schroers, Hans-Josef; Summerbell, Richard C; Robert, Vincent A R G; Crous, Pedro W; Zhang, Ning; Aoki, Takayuki; Jung, Kyongyong; Park, Jongsun; Lee, Yong-Hwan; Kang, Seogchan; Park, Bongsoo; Geiser, David M

2010-10-01

Because less than one-third of clinically relevant fusaria can be accurately identified to species level using phenotypic data (i.e., morphological species recognition), we constructed a three-locus DNA sequence database to facilitate molecular identification of the 69 Fusarium species associated with human or animal mycoses encountered in clinical microbiology laboratories. The database comprises partial sequences from three nuclear genes: translation elongation factor 1α (EF-1α), the largest subunit of RNA polymerase (RPB1), and the second largest subunit of RNA polymerase (RPB2). These three gene fragments can be amplified by PCR and sequenced using primers that are conserved across the phylogenetic breadth of Fusarium. Phylogenetic analyses of the combined data set reveal that, with the exception of two monotypic lineages, all clinically relevant fusaria are nested in one of eight variously sized and strongly supported species complexes. The monophyletic lineages have been named informally to facilitate communication of an isolate's clade membership and genetic diversity. To identify isolates to the species included within the database, partial DNA sequence data from one or more of the three genes can be used as a BLAST query against the database which is Web accessible at FUSARIUM-ID (http://isolate.fusariumdb.org) and the Centraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Center (http://www.cbs.knaw.nl/fusarium). Alternatively, isolates can be identified via phylogenetic analysis by adding sequences of unknowns to the DNA sequence alignment, which can be downloaded from the two aforementioned websites. The utility of this database should increase significantly as members of the clinical microbiology community deposit in internationally accessible culture collections (e.g., CBS-KNAW or the Fusarium Research Center) cultures of novel mycosis-associated fusaria, along with associated, corrected sequence chromatograms and data, so that the sequence results can be verified and isolates are made available for future study.

A review of stratigraphy and sedimentary environments of the Karoo Basin of South Africa

NASA Astrophysics Data System (ADS)

Smith, R. M. H.

The Karoo Supergroup covers almost two thirds of the present land surface of southern Africa. Its strata record an almost continuous sequence of continental sedimentation that began in the Permo-Carboniferous (280 Ma) and terminated in the early Jurassic 100 million years later. The glacio-marine to terrestrial sequence accumulated in a variety of tectonically controlled depositories under progressively more arid climatic conditions. Numerous vertebrate fossils are preserved in these rocks, including fish, amphibians, primitive aquatic reptiles, primitive land reptiles, more advanced mammal-like reptiles, dinosaurs and even the earliest mammals. Palaeoenvironmental analysis of the major stratigraphic units of the Karoo sequence demonstrates the effects of more localised tectonic basins in influencing depositional style. These are superimposed on a basinwide trend of progressive aridification attributed to the gradual northward migration of southwestern Gondwanaland out of polar climes and accentuated by the meteoric drying effect of the surrounding land masses. Combined with progressive climatic drying was a gradual shrinking of the basin brought about by the northward migration of the subducting palaeo-Pacific margin to the south. Following deposition of the Cape Supergroup in the pre-Karoo basin there was a period of uplift and erosion. At the same time the southern part of Gondwana migrated over the South Pole resulting in a major ice-sheet over the early Karoo basin and surrounding highlands. Glacial sedimentation in both upland valley and shelf depositories resulted in the basal Karoo Dwyka Formation. After glaciation, an extensive shallow sea remained over the gently subsiding shelf fed by large volumes of meltwater. Black clays and muds accumulated under relatively cool climatic conditions (Lower Ecca) with perhaps a warmer "interglacial" during which the distinctive Mesosaurus-bearing, carbonaceous shales of the Whitehill Formation were deposited. Deformation of the southern rim of the basin, caused by the subducting palaeo-Pacific plate, resulted in mountain ranges far to the south. Material derived from this source, as well as granitic uplands to the west and morth-east, was deposited on large deltas that built out into the Ecca sea (Upper Ecca). The relatively cool climate and lowland setting promoted thick accumulations of peat on the coastal and delta plains and which now constitute the major coal reserves of southern Africa. Later the prograding deltas coalesced to fill most of the basin after which fluvial sedimentation of the Beaufort Group dominated. The climate by this time (Late Permian) had warmed to become semi-arid with highly seasonal rainfall. The central parts of the basin were for the most part drained by fine-grained meanderbelts and semi-permanent lakes. Significant stratabound uranium reserves have been delimited in the channel sandstones of the Beaufort Group in the southwestern parts of the basin. Pulses of uplift in the southern source areas combined with a possible orogenic effect resulted in two coarser-grained alluvial fans prograding into the more central parts of the basin (Katberg Sandstone Member and Molteno Formation). In the upper Karoo sequence progressive aridification dominated depositional style with playa lake and wadi-type environments (Elliot Formation) that finally gave way to a dune sand dominated system (Clarens Formation). Basinwide volcanic activity of the early Jurassic Drakensberg Group brought deposition in the Karoo Basin to a close.

Seismic sequence stratigraphy and platform to basin reservoir structuring of Lower Cretaceous deposits in the Sidi Aïch-Majoura region (Central Tunisia)

NASA Astrophysics Data System (ADS)

Azaïez, Hajer; Bédir, Mourad; Tanfous, Dorra; Soussi, Mohamed

2007-05-01

In central Tunisia, Lower Cretaceous deposits represent carbonate and sandstone reservoir series that correspond to proven oil fields. The main problems for hydrocarbon exploration of these levels are their basin tectonic configuration and their sequence distribution in addition to the source rock availability. The Central Atlas of Tunisia is characterized by deep seated faults directed northeast-southwest, northwest-southeast and north-south. These faults limit inherited tectonic blocks and show intruded Triassic salt domes. Lower Cretaceous series outcropping in the region along the anticline flanks present platform deposits. The seismic interpretation has followed the Exxon methodologies in the 26th A.A.P.G. Memoir. The defined Lower Cretaceous seismic units were calibrated with petroleum well data and tied to stratigraphic sequences established by outcrop studies. This allows the subsurface identification of subsiding zones and thus sequence deposit distribution. Seismic mapping of these units boundary shows a structuring from a platform to basin blocks zones and helps to understand the hydrocarbon reservoir systems-tract and horizon distribution around these domains.

Recognition of maximum flooding events in mixed siliciclastic-carbonate systems: Key to global chronostratigraphic correlation

USGS Publications Warehouse

Mancini, E.A.; Tew, B.H.

1997-01-01

The maximum flooding event within a depositional sequence is an important datum for correlation because it represents a virtually synchronous horizon. This event is typically recognized by a distinctive physical surface and/or a significant change in microfossil assemblages (relative fossil abundance peaks) in siliciclastic deposits from shoreline to continental slope environments in a passive margin setting. Recognition of maximum flooding events in mixed siliciclastic-carbonate sediments is more complicated because the entire section usually represents deposition in continental shelf environments with varying rates of biologic and carbonate productivity versus siliciclastic influx. Hence, this event cannot be consistently identified simply by relative fossil abundance peaks. Factors such as siliciclastic input, carbonate productivity, sediment accumulation rates, and paleoenvironmental conditions dramatically affect the relative abundances of microfossils. Failure to recognize these complications can lead to a sequence stratigraphic interpretation that substantially overestimates the number of depositional sequences of 1 to 10 m.y. duration.

Oligocene lacustrine tuff facies, Abu Treifeya, Cairo-Suez Road, Egypt

NASA Astrophysics Data System (ADS)

Abdel-Motelib, Ali; Kabesh, Mona; El Manawi, Abdel Hamid; Said, Amir

2015-02-01

Field investigations in the Abu Treifeya area, Cairo-Suez District, revealed the presence of Oligocene lacustrine volcaniclastic deposits of lacustrine sequences associated with an Oligocene rift regime. The present study represents a new record of lacustrine zeolite deposits associated with saponite clay minerals contained within reworked clastic vitric tuffs. The different lithofacies associations of these clastic sequences are identified and described: volcaniclastic sedimentary facies represent episodic volcaniclastic reworking, redistribution and redeposition in a lacustrine environment and these deposits are subdivided into proximal and medial facies. Zeolite and smectite minerals are mainly found as authigenic crystals formed in vugs or crusts due to the reaction of volcanic glasses with saline-alkaline water or as alteration products of feldspars. The presence of abundant smectite (saponite) may be attributed to a warm climate, with alternating humid and dry conditions characterised by the existence of kaolinite. Reddish iron-rich paleosols record periods of non-deposition intercalated with the volcaniclastic tuff sequence.

Sequence stratigraphic interpretation of parts of Anambra Basin, Nigeria using geophysical well logs and biostratigraphic data

NASA Astrophysics Data System (ADS)

Anakwuba, E. K.; Ajaegwu, N. E.; Ejeke, C. F.; Onyekwelu, C. U.; Chinwuko, A. I.

2018-03-01

The Anambra basin constitutes the southeastern lower portion of the Benue Trough, which is a large structural depression that is divided into lower, middle and upper parts; and is one of the least studied inland sedimentary basins in Nigeria. Sequence stratigraphic interpretation had been carried out in parts of the Anambra Basin using data from three wells (Alo-1 Igbariam-1 and Ajire-1). Geophysical well logs and biostratigraphic data were integrated in order to identify key bounding surfaces, subdivide the sediment packages, correlate sand continuity and interpret the environment of deposition in the fields. Biostratigraphic interpretation, using foraminifera and plankton population and diversity, reveals five maximum flooding surfaces (MFS) in the fields. Five sequence boundaries (SB) were also identified using the well log analysis. Four 3rd order genetic sequences bounded by maximum flooding surfaces (MFS-1 to MFS-6) were identified in the areas; four complete sequences and one incomplete sequence were identified in both Alo-1 and Igbariam-1 wells while Ajire-1 has an no complete sequence. The identified system tracts delineated comprises Lowstand Systems Tracts (progradational to aggradational to retrogradational packages), Transgressive Systems Tracts (retrogradational packages) and Highstand Systems Tracts (aggradational to progradational packages) in each well. The sand continuity across the fields reveal sands S1 to S5 where S1 is present in Ajire-1 well and Igbariam-1 well but not in Alo-1 well. The sands S4 to S5 run across the three fields at different depths. The formations penetrated by the wells starting from the base are; Nkporo Formation (Campanian), Mamu Formation (Late Campanian to Early Maastrichtian), Ajali Sandstone (Maastrichtian), Nsukka Formation (Late Maastrichtian to Early Palaeocene), Imo Formation (Palaeocene) and Nanka Sand (Eocene). The environments of deposition revealed are from coastal to bathyal. The sands of lowstand system tract and highstand system tract found in Ajali, Nsukka, Nkporo and Imo (Ebenebe Sandstone) Formations show good continuity and as such good reservoir qualities while the shales of the transgressive system tracts which includes the Imo Formation, Mamu, and Nkporo Formations where most of the maximum flooding surfaces were delineated, can serve as seals to the numerous reservoir units. Combinations of the reservoir sands of the lowstand system tract and highstand system tract and the shale units of the transgressive system tract can form good stratigraphic traps for hydrocarbon and hence should be hydrocarbon exploration targets.

Ramp Creek and Harrodsburg Limestones: A shoaling-upward sequence with storm-produced features in southern Indiana, U.S.A.. Carbonate petrology seminar, Indiana University

NASA Astrophysics Data System (ADS)

1987-05-01

Most previously described examples of storm-produced stratification have been reported from siliciclastic rocks. However, such features should also be common in carbonate rocks. The Mississippian (Valmeyeran) Ramp Creek and Harrodsburg Limestones, deposited on the east margin of the Illinois Basin on top of the Borden Delta, contain storm-produced features. The dolomitic, geode-bearing Ramp Creek Limestone contains muddying-upward sequences, commonly with scoured bases overlain by grainstones, packstones, wackestones, and burrowed mudstones. These sequences are similar to hummocky sequences formed by storm waves below fair-weather wave base. The middle portion of the section including the upper Ramp Creek and lower Harrodsburg Limestones contains dolomitized mud lenses of uncertain origin. They may have formed by the baffling effect of bryozoans and/or unpreserved algae. The Harrodsburg is gradational with the Ramp Creek and consists predominantly of grainstones and packstones deposited in shallower water. Low-angle cross-stratification and truncation surfaces suggest a foreshore depositional environment for the Harrodsburg. Neither formation contains any indication of supratidal deposition as has been previously suggested. Open marine conditions during deposition of both formations are indicated by the fauna which includes crinoids, bryozoans, brachiopods, corals, ostracods, echinoids, trilobites, molluscs, fish (sharks), and trace fossils.

Laser-induced periodic surface structures on zinc oxide crystals upon two-colour femtosecond double-pulse irradiation

NASA Astrophysics Data System (ADS)

Höhm, S.; Rosenfeld, A.; Krüger, J.; Bonse, J.

2017-03-01

In order to study the temporally distributed energy deposition in the formation of laser-induced periodic surface structures (LIPSS) on single-crystalline zinc oxide (ZnO), two-colour double-fs-pulse experiments were performed. Parallel or cross-polarised double-pulse sequences at 400 and 800 nm wavelength were generated by a Mach-Zehnder interferometer, exhibiting inter-pulse delays up to a few picoseconds between the sub-ablation 50-fs-pulses. Twenty two-colour double-pulse sequences were collinearly focused by a spherical mirror to the sample surface. The resulting LIPSS periods and areas were analysed by scanning electron microscopy. The delay-dependence of these LIPSS characteristics shows a dissimilar behaviour when compared to the semiconductor silicon, the dielectric fused silica, or the metal titanium. A wavelength-dependent plasmonic mechanism is proposed to explain the delay-dependence of the LIPSS on ZnO when considering multi-photon excitation processes. Our results support the involvement of nonlinear processes for temporally overlapping pulses. These experiments extend previous two-colour studies on the indirect semiconductor silicon towards the direct wide band-gap semiconductor ZnO and further manifest the relevance of the ultrafast energy deposition for LIPSS formation.

Workflow and web application for annotating NCBI BioProject transcriptome data

PubMed Central

Vera Alvarez, Roberto; Medeiros Vidal, Newton; Garzón-Martínez, Gina A.; Barrero, Luz S.; Landsman, David

2017-01-01

Abstract The volume of transcriptome data is growing exponentially due to rapid improvement of experimental technologies. In response, large central resources such as those of the National Center for Biotechnology Information (NCBI) are continually adapting their computational infrastructure to accommodate this large influx of data. New and specialized databases, such as Transcriptome Shotgun Assembly Sequence Database (TSA) and Sequence Read Archive (SRA), have been created to aid the development and expansion of centralized repositories. Although the central resource databases are under continual development, they do not include automatic pipelines to increase annotation of newly deposited data. Therefore, third-party applications are required to achieve that aim. Here, we present an automatic workflow and web application for the annotation of transcriptome data. The workflow creates secondary data such as sequencing reads and BLAST alignments, which are available through the web application. They are based on freely available bioinformatics tools and scripts developed in-house. The interactive web application provides a search engine and several browser utilities. Graphical views of transcript alignments are available through SeqViewer, an embedded tool developed by NCBI for viewing biological sequence data. The web application is tightly integrated with other NCBI web applications and tools to extend the functionality of data processing and interconnectivity. We present a case study for the species Physalis peruviana with data generated from BioProject ID 67621. Database URL: http://www.ncbi.nlm.nih.gov/projects/physalis/ PMID:28605765

The Miocene Sommières basin, SE France: Bioclastic carbonates in a tide-dominated depositional system

NASA Astrophysics Data System (ADS)

Reynaud, Jean-Yves; James, Noël P.

2012-12-01

The Miocene Sommières Basin in SE France is a semi-enclosed depression that was connected to the Mediterranean Sea by a flooded paleo-incised valley and then filled by a suite of sediments comprising carbonate grains coming from temperate factories that were largely deposited in tidal-dominated paleoenvironments. The strata are partitioned into two sequences that reflect repeated flooding of the incised valley system, one of several similar situations in this region of France. The carbonate grains are mostly bioclasts, namely from barnacles, bryozoans, coralline algae (encrusting, branching, and rhodoliths), echinoids, and benthic foraminifers (large and small) with ostracods, sponge spicules and planktic foraminifers prominent in muddy facies. Particles were produced by shallow water carbonate factories on hard substrates (valley walls in particular), associated with subaqueous dunes, and in deeper water basinal settings. Each depositional sequence is underlain by an eroded and bored hard surface that is progressively overlain by TST subaqueous tidal dunes or storm deposits that grade up, in one case, into HST marls (the HST of the upper sequence has been removed by erosion). The lower sequence is ebb tide dominated whereas the upper sequence is flood tide dominated. The succession is interpreted to represent a TST whose tidal currents were focused by the narrow valley and a HST that reflected flooding of the overbanks. This stratigraphic and depositional motif is comparable to that in other spatially separated Neogene paleovalleys that are filled with tide-dominated clastic carbonates in the region. Together with other recently documented similar systems, these limestones constitute an important new group of carbonate sand bodies in the carbonate depositional realm.

Statistical analyses of soil properties on a quaternary terrace sequence in the upper sava river valley, Slovenia, Yugoslavia

USGS Publications Warehouse

Vidic, N.; Pavich, M.; Lobnik, F.

1991-01-01

Alpine glaciations, climatic changes and tectonic movements have created a Quaternary sequence of gravely carbonate sediments in the upper Sava River Valley, Slovenia, Yugoslavia. The names for terraces, assigned in this model, Gu??nz, Mindel, Riss and Wu??rm in order of decreasing age, are used as morphostratigraphic terms. Soil chronosequence on the terraces was examined to evaluate which soil properties are time dependent and can be used to help constrain the ages of glaciofluvial sedimentation. Soil thickness, thickness of Bt horizons, amount and continuity of clay coatings and amount of Fe and Me concretions increase with soil age. The main source of variability consists of solutions of carbonate, leaching of basic cations and acidification of soils, which are time dependent and increase with the age of soils. The second source of variability is the content of organic matter, which is less time dependent, but varies more within soil profiles. Textural changes are significant, presented by solution of carbonate pebbles and sand, and formation is silt loam matrix, which with age becomes finer, with clay loam or clayey texture. The oldest, Gu??nz, terrace shows slight deviation from general progressive trends of changes of soil properties with time. The hypothesis of single versus multiple depositional periods of deposition was tested with one-way analysis of variance (ANOVA) on a staggered, nested hierarchical sampling design on a terrace of largest extent and greatest gravel volume, the Wu??rm terrace. The variability of soil properties is generally higher within subareas than between areas of the terrace, except for the soil thickness. Observed differences in soil thickness between the areas of the terrace could be due to multiple periods of gravel deposition, or to the initial differences of texture of the deposits. ?? 1991.

Carbonate sedimentation in an extensional active margin: Cretaceous history of the Haymana region, Pontides

NASA Astrophysics Data System (ADS)

Okay, Aral I.; Altiner, Demir

2016-10-01

The Haymana region in Central Anatolia is located in the southern part of the Pontides close to the İzmir-Ankara suture. During the Cretaceous, the region formed part of the south-facing active margin of the Eurasia. The area preserves a nearly complete record of the Cretaceous system. Shallow marine carbonates of earliest Cretaceous age are overlain by a 700-m-thick Cretaceous sequence, dominated by deep marine limestones. Three unconformity-bounded pelagic carbonate sequences of Berriasian, Albian-Cenomanian and Turonian-Santonian ages are recognized: Each depositional sequence is preceded by a period of tilting and submarine erosion during the Berriasian, early Albian and late Cenomanian, which corresponds to phases of local extension in the active continental margin. Carbonate breccias mark the base of the sequences and each carbonate sequence steps down on older units. The deep marine carbonate deposition ended in the late Santonian followed by tilting, erosion and folding during the Campanian. Deposition of thick siliciclastic turbidites started in the late Campanian and continued into the Tertiary. Unlike most forearc basins, the Haymana region was a site of deep marine carbonate deposition until the Campanian. This was because the Pontide arc was extensional and the volcanic detritus was trapped in the intra-arc basins and did not reach the forearc or the trench. The extensional nature of the arc is also shown by the opening of the Black Sea as a backarc basin in the Turonian-Santonian. The carbonate sedimentation in an active margin is characterized by synsedimentary vertical displacements, which results in submarine erosion, carbonate breccias and in the lateral discontinuity of the sequences, and differs from blanket like carbonate deposition in the passive margins.

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.

The recent pumice eruptions of Mt. Pelée volcano, Martinique. Part I: Depositional sequences, description of pumiceous deposits

NASA Astrophysics Data System (ADS)

Traineau, Hervé; Westercamp, Denis; Bardintzeff, Jacques-Marie; Miskovsky, Jean-Claude

1989-08-01

Mount Pelée is one of the most active volcanoes of the Lesser Antilles arc, with more than twenty eruptions over the last 5000 years. Both nuée ardente-type eruptions, which are well known, and pumice eruptions, although little known, are very common in the stratigraphic record. The four younger pumice eruptions, P4 (2440 y.B.P.), P3 (2010 y.B.P.), P2 (1670 y.B.P.) and P1 (650 y.B.P.) can be used to reconstruct the eruption sequences. The various pumiceous deposits can be described as fine lithic ash layer, Plinian fall deposits, pumice and ash flow deposits with associated ash cloud fall deposits, and pumice surge deposits. Three kinds of depositional sequences have been defined. The distinctions between them are based on the occurrence of an initial Plinian phase and the generation of intraflow pyroclastic surges. The pumice eruptions of Mt. Pelée are small in intensity and magnitude, as expressed by the dispersal of their products and by the total mass of erupted material which is estimated to be less than 1 km 3 in each case. The pumice fall deposits have dispersal characteristics of small Plinian eruptions, close to the sub-Plinian type. Nevertheless, the probability of an occurrence of a new pumice eruption at Mt. Pelée is high, and the widespread distribution of pumice deposits around the volcano suggests that such an eruption is a major volcanic risk during the present stage of activity.

Solid Lubrication of Laser Deposited Carbon Nanotube Reinforced Nickel Matrix Nanocomposites Preprint

DTIC Science & Technology

2009-03-01

others [24-27], involves third body processes. Third bodies are formed by the relative motion of the two parent (first body ) materials in the...into wear particles. By separating the two first bodies , third bodies take on the chore of transmitting stresses and accommodate the relative...motion between the counterfaces. Thus friction and wear behavior is controlled by the third body processes, as opposed to the first body properties

The ICDP Hotspot Scientific Drilling Program: Overview of geophysical logging and seismic imaging through basaltic and rhyolitic volcanic deposits

NASA Astrophysics Data System (ADS)

Schmitt, D. R.; Liberty, L. M.; Kessler, J. A.; Kueck, J.; Kofman, R. S.; Bishop, R. A.; Shervais, J. W.; Evans, J. P.; Champion, D. E.

2012-12-01

The recently completed ICDP Hotspot drilling program consisted of drilling of three scientific drill holes each to at least 1800 m depth across the Snake River Plain of Idaho. The three boreholes include i) Kimama: thick sequences of basalt flows with sediment interbeds; ii) Kimberley: near surface basalt flows overlying rhyolite deposits, and iii) Mountain Home: geothermally altered basalts overlain by lacustrine sediments. The program consisted of high resolution 2D surface tied to vertical and walk-a-way borehole seismic profiles and an extensive suite of full waveform sonic, ultrasonic televiewer, electrical resistivity, magnetic susceptibility, and hydrogen index neutron logging. There are a number of highlights out of this work. First, seismic imaging beneath basalt flows is a classic problem in reflection seismology and has long been believed to be due to rapid attenuation of the downgoing seismic pulse. Here, however, we observed strong arrivals at all depths suggesting that seismic energy is penetrating such formations and that issues in imaging may be a result of the heterogeneous nature of the formations. Second, the neutron log responses correlate well with the structure of individual basalt flows. High and low backscattered neutron counts correspond to massive low porosity basalt rock and with the higher porosity and sediment filled flow tops, respectively. Third, the ultrasonic borehole televiewer information is being used to orient the nearly complete sets of core in order to obtain information on the azimuths of natural and drilling induced core fractures. This together with examination of borehole breakouts and drilling induced tensile fractures on the wellbore wall will allow for semi-quantitative stress estimates across the Snake River Plain. Finally, the Mountain Home borehole provides an unique opportunity to study the geothermally altered basalts. There are a number of correlations between, for example, the sonic and electrical logs that must relate to the style of alteration.

Interstratified arkosic and volcanic rocks of the Miocene Spanish Canyon Formation, Alvord Mountain area, California: descriptions and interpretations

USGS Publications Warehouse

Buesch, David C.

2014-01-01

The Spanish Canyon Foundation in the Alvord Mountain area, California, varies from about 50 to 120 m thick and records the interstratification of arkosic sandstone and conglomerate with tuffaceous deposits and lava flows. In the lower third of the formation, arkosic sandstone and conglomerate are interstratified with tuffaceous deposits. Some tuffs might have been deposited as primary, nonwelded to partially welded ignimbrites or fallout tephra. Many of the tuffaceous deposits represent redeposited material that formed tuffaceous sandstone, and many of these deposits contain arkosic grains that represent mixing of different source matieral. Arkosic sandstone, and especially conglomerate (some with maximum clast lengths up to 1 m), represent intermittent incursions of coarser plutoniclastic fan deposits into other finer grained and mostly volcaniclastic basin deposits. After deposition of the 18.78 Ma Peach Spring Tuff, the amount of tuffaceous material decreased. The upper two-thirds of the formation has arkosic sandstone and conglomerate interstratified with two olivine basalt lave flows. locally, conglomerate clasts in this part of the section have maximum lengths up to 1 m. Many tuffaceous and arkosic sandstone beds of the Spanish Canyon Formation have tabular to broad (low-relief) lenticular geometry, and locally, some arkosic conglomerate fills channels as much as 1.5 m deep. These bedforms are consistent with deposition in medial to distal alluvial-fan or fluvial environments; some finer-grained deposits might have formed in lacustrine environments.

Complete Genome Sequence of Leptospirillum ferrooxidans Strain C2-3, Isolated from a Fresh Volcanic Ash Deposit on the Island of Miyake, Japan

PubMed Central

Fujimura, Reiko; Sato, Yoshinori; Nishizawa, Tomoyasu; Oshima, Kenshiro; Kim, Seok-Won; Hattori, Masahira; Kamijo, Takashi

2012-01-01

A diazotrophic, acidophilic, iron-oxidizing bacterium, Leptospirillum ferrooxidans, known to be difficult to cultivate, was isolated from a fresh volcanic ash deposit on the island of Miyake, Japan. Here, we report the complete genome sequence of a cultured strain, C2-3. PMID:22815442

Complete genome sequence of Leptospirillum ferrooxidans strain C2-3, isolated from a fresh volcanic ash deposit on the island of Miyake, Japan.

PubMed

Fujimura, Reiko; Sato, Yoshinori; Nishizawa, Tomoyasu; Oshima, Kenshiro; Kim, Seok-Won; Hattori, Masahira; Kamijo, Takashi; Ohta, Hiroyuki

2012-08-01

A diazotrophic, acidophilic, iron-oxidizing bacterium, Leptospirillum ferrooxidans, known to be difficult to cultivate, was isolated from a fresh volcanic ash deposit on the island of Miyake, Japan. Here, we report the complete genome sequence of a cultured strain, C2-3.

The age of the Keystone thrust: laser-fusion 40Ar/39Ar dating of foreland basin deposits, southern Spring Mountains, Nevada

USGS Publications Warehouse

Fleck, R.J.; Carr, M.D.

1990-01-01

Nonmarine sedimentary and volcaniclastic foreland-basin deposits in the Spring Mountains are cut by the Contact and Keystone thrusts. These synorogenic deposits, informally designated the Lavinia Wash sequence by Carr (1980), previously were assigned a Late Jurassic to Early Cretaceous(?) age. New 40Ar.39Ar laser-fusion and incremental-heating studies of a tuff bed in the Lavinia Wash sequence support a best estimate age of 99.0 ?? 0.4 Ma, indicating that the Lavinia Wash sequence is actually late Early Cretaceous in age and establishing a maximum age for final emplacement of the Contact and Keystone thrust plates consistent with the remainder of the Mesozoic foreland thrust belt. -from Authors

Deciphering natural to anthropogenic control on sedimentation: the Late Holocene Magdala (Kinneret Lake, Israel) harbour hystory

NASA Astrophysics Data System (ADS)

Sarti, G.; Rossi, V.; Amorosi, A.; Bertoni, D.; Ribolini, A.; Sammartino, I.; Zanchetta, G.

2012-04-01

Using a multidisciplinary approach involving geologists, geomorphologists and archeologists, the late Holocene sedimentary succession buried beneath the ancient Magdala harbour area (Kinneret Lake, Israel) was studied, in order to highlight the strict relationships among harbour evolutive phases (e.g. foundation, siltation, abandonment), natural events (e.g. sea-level variations, climatic changes and earthquakes among the most important) and, obviously, archaeological history. Recent excavations performed within the "Magdala Project" have discovered a harbour structure with late Hellenistic-Roman mooring stones at altitudes of 208.100 m and 208.320 m bsl respectively, suggestive of a higher lake-level (about 212 m bsl) than previously hypothesized. Along the most representative sections of trenches, integrated sedimentological, micropalaeontological (benthic meiofauna and pollen) and geochemical analyses were carried out on sedimentary deposits underlying and overlying the harbour structures, to define the main depositional facies and evolution phases that took place during the last millennia. Spatial variability of coeval palaeoenvironments across the archaeological site allowed to reconstruct a comprehensive picture of the harbour complex, evidencing the occurrence of three main evolution phases, similar to those reported from several Mediterranean Sea harbour systems: 1) a pre-harbor foundation phase; 2) a sin-harbor activity phase and 3) an harbor-abandonment phase. The first phase corresponds to the development of a natural lacustrine sandy beach barren in archaeological remains and containing an ostracod fauna very similar to the one observed within the present-day lake basin at ca. 5 m water depth. The second phase was characterized by the formation of an early Hellenistic sheltered lacustrine basin, recording the first anthropogenic control exerted on coastal sedimentation by the construction of harbour structures ("anthropogenically forced sheltered basin"). Dark, fine-grained deposits formed during the sin-harbour activity phase are rich in osteological remains (sheep, cattles) and archaeological artifacts (coins, pottery etc.). Moreover, the very high proportion of noded forms of Cyprideis torosa with respect to the smooth ones reflects stressed conditions, possibly connected to high pollution levels induced by harbor activities or, more generally, to a dense human frequentation. According to this interpretation, a sharp increase in concentration of trace metals Zn, Pb and Cu, along with P2O5, is recorded at the very base of the sin-harbour sequence on which Late Hellenistic and early Roman harbour structures rest on. The third phase, dated to the middle Roman period onwards, marks the siltation of the harbour basin and the end of Magdala harbour activities. The harbour-abandonment sequence is constituted by shoreface sands sharply overlain by foreshore-backshore well-sorted pebble conglomerates bearing middle Roman age remains. Another very similar conglomerate layer crops out in the sequence and covers Byzantine anthropogenic structures. From a sedimentological point of view the abrupt transition from sands to conglomerates indicates that major changes in sediment supply occurred after the late Roman age. We tentatively correlate this lithofacies change to climatic fluctuations (from a rainy to an arid phase) or to tectonic events, such as the destructive earthquakes occurred in the 349 AD and in 749 AD.

A Survey of Protein Structures from Archaeal Viruses

PubMed Central

Dellas, Nikki; Lawrence, C. Martin; Young, Mark J.

2013-01-01

Viruses that infect the third domain of life, Archaea, are a newly emerging field of interest. To date, all characterized archaeal viruses infect archaea that thrive in extreme conditions, such as halophilic, hyperthermophilic, and methanogenic environments. Viruses in general, especially those replicating in extreme environments, contain highly mosaic genomes with open reading frames (ORFs) whose sequences are often dissimilar to all other known ORFs. It has been estimated that approximately 85% of virally encoded ORFs do not match known sequences in the nucleic acid databases, and this percentage is even higher for archaeal viruses (typically 90%–100%). This statistic suggests that either virus genomes represent a larger segment of sequence space and/or that viruses encode genes of novel fold and/or function. Because the overall three-dimensional fold of a protein evolves more slowly than its sequence, efforts have been geared toward structural characterization of proteins encoded by archaeal viruses in order to gain insight into their potential functions. In this short review, we provide multiple examples where structural characterization of archaeal viral proteins has indeed provided significant functional and evolutionary insight. PMID:25371334

The problems and promise of DNA barcodes for species diagnosis of primate biomaterials

PubMed Central

Lorenz, Joseph G; Jackson, Whitney E; Beck, Jeanne C; Hanner, Robert

2005-01-01

The Integrated Primate Biomaterials and Information Resource (www.IPBIR.org) provides essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing DNA and RNA derived from primate cell cultures. The IPBIR uses mitochondrial cytochrome c oxidase subunit I sequences to verify the identity of samples for quality control purposes in the accession, cell culture, DNA extraction processes and prior to shipping to end users. As a result, IPBIR is accumulating a database of ‘DNA barcodes’ for many species of primates. However, this quality control process is complicated by taxon specific patterns of ‘universal primer’ failure, as well as the amplification or co-amplification of nuclear pseudogenes of mitochondrial origins. To overcome these difficulties, taxon specific primers have been developed, and reverse transcriptase PCR is utilized to exclude these extraneous sequences from amplification. DNA barcoding of primates has applications to conservation and law enforcement. Depositing barcode sequences in a public database, along with primer sequences, trace files and associated quality scores, makes this species identification technique widely accessible. Reference DNA barcode sequences should be derived from, and linked to, specimens of known provenance in web-accessible collections in order to validate this system of molecular diagnostics. PMID:16214744

Factorized Runge-Kutta-Chebyshev Methods

NASA Astrophysics Data System (ADS)

O'Sullivan, Stephen

2017-05-01

The second-order extended stability Factorized Runge-Kutta-Chebyshev (FRKC2) explicit schemes for the integration of large systems of PDEs with diffusive terms are presented. The schemes are simple to implement through ordered sequences of forward Euler steps with complex stepsizes, and easily parallelised for large scale problems on distributed architectures. Preserving 7 digits for accuracy at 16 digit precision, the schemes are theoretically capable of maintaining internal stability for acceleration factors in excess of 6000 with respect to standard explicit Runge-Kutta methods. The extent of the stability domain is approximately the same as that of RKC schemes, and a third longer than in the case of RKL2 schemes. Extension of FRKC methods to fourth-order, by both complex splitting and Butcher composition techniques, is also discussed. A publicly available implementation of FRKC2 schemes may be obtained from maths.dit.ie/frkc

Regional stratigraphy of the south polar layered deposits (Promethei Lingula, Mars): "Discontinuity-bounded" units in images and radargrams

NASA Astrophysics Data System (ADS)

Guallini, Luca; Rossi, Angelo Pio; Forget, François; Marinangeli, Lucia; Lauro, Sebastian Emanuel; Pettinelli, Elena; Seu, Roberto; Thomas, Nicolas

2018-07-01

The Mars South Polar Layered Deposits (SPLD) are the result of depositional and erosional events, which are marked by different stratigraphic sequences and erosional surfaces. To unambiguously define the stratigraphic units at regional scale, we mapped the SPLD on the basis of observed discontinuities (i.e., unconformities, correlative discontinuities and conformities), as commonly done in terrestrial modern stratigraphy. This methodology is defined as "Discontinuity-Bounded Units" or allostratigraphy, and is complemented by geomorphological mapping. Our study focuses on Promethei Lingula (PL) and uses both high-resolution images (CTX, HiRISE) and radargrams (SHARAD) to combine surface and sub-surface observations and obtain a 3D geological reconstruction of the SPLD. One regional discontinuity (named AUR1) was defined within the studied stratigraphic succession and is exposed in several non-contiguous outcrops around PL as well as observed at depth within the ice sheet. This is the primary contact between two major depositional sequences, showing a different texture at CTX resolution. The lower sequence is characterized mainly by a "ridge and trough" morphology (Ridge and Trough Sequence; RTS) and the upper sequence shows mainly by a "stair-stepped" morphology (Stair-Stepped Sequence; SSS). On the basis of the observations, we defined two regional "discontinuity-bounded" units in PL, respectively coinciding with RTS and SSS sequences. Our stratigraphic reconstruction provides new hints on the major scale events that shaped this region. Oscillations in Martian axial obliquity could have controlled local climate conditions in the past, affecting the PL geological record.

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.

PubMed

Schoch, Conrad L; Robbertse, Barbara; Robert, Vincent; Vu, Duong; Cardinali, Gianluigi; Irinyi, Laszlo; Meyer, Wieland; Nilsson, R Henrik; Hughes, Karen; Miller, Andrew N; Kirk, Paul M; Abarenkov, Kessy; Aime, M Catherine; Ariyawansa, Hiran A; Bidartondo, Martin; Boekhout, Teun; Buyck, Bart; Cai, Qing; Chen, Jie; Crespo, Ana; Crous, Pedro W; Damm, Ulrike; De Beer, Z Wilhelm; Dentinger, Bryn T M; Divakar, Pradeep K; Dueñas, Margarita; Feau, Nicolas; Fliegerova, Katerina; García, Miguel A; Ge, Zai-Wei; Griffith, Gareth W; Groenewald, Johannes Z; Groenewald, Marizeth; Grube, Martin; Gryzenhout, Marieka; Gueidan, Cécile; Guo, Liangdong; Hambleton, Sarah; Hamelin, Richard; Hansen, Karen; Hofstetter, Valérie; Hong, Seung-Beom; Houbraken, Jos; Hyde, Kevin D; Inderbitzin, Patrik; Johnston, Peter R; Karunarathna, Samantha C; Kõljalg, Urmas; Kovács, Gábor M; Kraichak, Ekaphan; Krizsan, Krisztina; Kurtzman, Cletus P; Larsson, Karl-Henrik; Leavitt, Steven; Letcher, Peter M; Liimatainen, Kare; Liu, Jian-Kui; Lodge, D Jean; Luangsa-ard, Janet Jennifer; Lumbsch, H Thorsten; Maharachchikumbura, Sajeewa S N; Manamgoda, Dimuthu; Martín, María P; Minnis, Andrew M; Moncalvo, Jean-Marc; Mulè, Giuseppina; Nakasone, Karen K; Niskanen, Tuula; Olariaga, Ibai; Papp, Tamás; Petkovits, Tamás; Pino-Bodas, Raquel; Powell, Martha J; Raja, Huzefa A; Redecker, Dirk; Sarmiento-Ramirez, J M; Seifert, Keith A; Shrestha, Bhushan; Stenroos, Soili; Stielow, Benjamin; Suh, Sung-Oui; Tanaka, Kazuaki; Tedersoo, Leho; Telleria, M Teresa; Udayanga, Dhanushka; Untereiner, Wendy A; Diéguez Uribeondo, Javier; Subbarao, Krishna V; Vágvölgyi, Csaba; Visagie, Cobus; Voigt, Kerstin; Walker, Donald M; Weir, Bevan S; Weiß, Michael; Wijayawardene, Nalin N; Wingfield, Michael J; Xu, J P; Yang, Zhu L; Zhang, Ning; Zhuang, Wen-Ying; Federhen, Scott

2014-01-01

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353. Published by Oxford University Press 2013. This work is written by US Government employees and is in the public domain in the US.

Gravity-Driven Deposits in an Active Margin (Ionian Sea) Over the Last 330,000 Years

NASA Astrophysics Data System (ADS)

Köng, Eléonore; Zaragosi, Sébastien; Schneider, Jean-Luc; Garlan, Thierry; Bachèlery, Patrick; Sabine, Marjolaine; San Pedro, Laurine

2017-11-01

In the Ionian Sea, the subduction of the Nubia plate underneath the Eurasia plate leads to an important sediment remobilization on the Calabrian Arc and the Mediterranean Ridge. These events are often associated with earthquakes and tsunamis. In this study, we analyze gravity-driven deposits in order to establish their recurrence time on the Calabrian Arc and the western Mediterranean Ridge. Four gravity cores collected on ridges and slope basins of accretionary prisms record turbidites, megaturbidites, slumping and micro-faults over the last 330,000 years. These turbidites were dated by correlation with a hemipelagic core with a multi-proxy approach: radiometric dating, δ18O, b* colour curve, sapropels and tephrochronology. The origin of the gravity-driven deposits was studied with a sedimentary approach: grain-size, lithology, thin section, geochemistry of volcanic glass. The results suggest three periods of presence/absence of gravity-driven deposits: a first on the western lobe of the Calabrian Arc between 330,000 and 250,000 years, a second between 120,000 years and present day on the eastern lobe of the Calabrian Arc and over the last 60,000 years on the western lobe, and a third on the Mediterranean Ridge over the last 37,000 years. Return times for gravity-driven deposits are around 1,000 years during the most important record periods. The turbidite activity also highlights the presence of volcaniclastic turbidites that seems to be link to the Etna changing morphology over the last 320,000 years.

Identification of a third feline Demodex species through partial sequencing of the 16S rDNA and frequency of Demodex species in 74 cats using a PCR assay.

PubMed

Ferreira, Diana; Sastre, Natalia; Ravera, Iván; Altet, Laura; Francino, Olga; Bardagí, Mar; Ferrer, Lluís

2015-08-01

Demodex cati and Demodex gatoi are considered the two Demodex species of cats. However, several reports have identified Demodex mites morphologically different from these two species. The differentiation of Demodex mites is usually based on morphology, but within the same species different morphologies can occur. DNA amplification/sequencing has been used effectively to identify and differentiate Demodex mites in humans, dogs and cats. The aim was to develop a PCR technique to identify feline Demodex mites and use this technique to investigate the frequency of Demodex in cats. Demodex cati, D. gatoi and Demodex mites classified morphologically as the third unnamed feline species were obtained. Hair samples were taken from 74 cats. DNA was extracted; a 330 bp fragment of the 16S rDNA was amplified and sequenced. The sequences of D. cati and D. gatoi shared >98% identity with those published on GenBank. The sequence of the third unnamed species showed 98% identity with a recently published feline Demodex sequence and only 75.2 and 70.9% identity with D. gatoi and D. cati sequences, respectively. Demodex DNA was detected in 19 of 74 cats tested; 11 DNA sequences corresponded to Demodex canis, five to Demodex folliculorum, three to D. cati and two to Demodex brevis. Three Demodex species can be found in cats, because the third unnamed Demodex species is likely to be a distinct species. Apart from D. cati and D. gatoi, DNA from D. canis, D. folliculorum and D. brevis was found on feline skin. © 2015 ESVD and ACVD.

Additional support for Afrotheria and Paenungulata, the performance of mitochondrial versus nuclear genes, and the impact of data partitions with heterogeneous base composition.

PubMed

Springer, M S; Amrine, H M; Burk, A; Stanhope, M J

1999-03-01

We concatenated sequences for four mitochondrial genes (12S rRNA, tRNA valine, 16S rRNA, cytochrome b) and four nuclear genes [aquaporin, alpha 2B adrenergic receptor (A2AB), interphotoreceptor retinoid-binding protein (IRBP), von Willebrand factor (vWF)] into a multigene data set representing 11 eutherian orders (Artiodactyla, Hyracoidea, Insectivora, Lagomorpha, Macroscelidea, Perissodactyla, Primates, Proboscidea, Rodentia, Sirenia, Tubulidentata). Within this data set, we recognized nine mitochondrial partitions (both stems and loops, for each of 12S rRNA, tRNA valine, and 16S rRNA; and first, second, and third codon positions of cytochrome b) and 12 nuclear partitions (first, second, and third codon positions, respectively, of each of the four nuclear genes). Four of the 21 partitions (third positions of cytochrome b, A2AB, IRBP, and vWF) showed significant heterogeneity in base composition across taxa. Phylogenetic analyses (parsimony, minimum evolution, maximum likelihood) based on sequences for all 21 partitions provide 99-100% bootstrap support for Afrotheria and Paenungulata. With the elimination of the four partitions exhibiting heterogeneity in base composition, there is also high bootstrap support (89-100%) for cow + horse. Statistical tests reject Altungulata, Anagalida, and Ungulata. Data set heterogeneity between mitochondrial and nuclear genes is most evident when all partitions are included in the phylogenetic analyses. Mitochondrial-gene trees associate cow with horse, whereas nuclear-gene trees associate cow with hedgehog and these two with horse. However, after eliminating third positions of A2AB, IRBP, and vWF, nuclear data agree with mitochondrial data in supporting cow + horse. Nuclear genes provide stronger support for both Afrotheria and Paenungulata. Removal of third positions of cytochrome b results in improved performance for the mitochondrial genes in recovering these clades.

Geological Setting of Diamond Drilling for the Archean Biosphere Drilling Project, Pilbara Craton, Western Australia

NASA Astrophysics Data System (ADS)

Hickman, A.

2004-12-01

The Archean Biosphere Drilling Project (ABDP) is a collaborative international research project conducting systematic (bio)geochemical investigations to improve our understanding of the biosphere of the early Earth. The Pilbara Craton of Western Australia, which includes exceptionally well preserved 3.52 to 2.70 Ga sedimentary sequences, was selected for an innovative sampling program commencing in 2003. To avoid near-surface alteration and contamination effects, sampling was by diamond drilling to depths of between 150 and 300 m, and was located at sites where the target lithologies were least deformed and had lowest metamorphic grade (below 300°C). The first of five successful drilling sites (Jasper Deposit) targeted red, white and black chert in the 3.46 Ga Marble Bar Chert Member. This chert marks the top of a thick mafic-felsic volcanic cycle, the third of four such cycles formed by mantle plumes between 3.52 and 3.43 Ga. The geological setting was a volcanic plateau founded on 3.72 to 3.60 Ga sialic crust (isotopic evidence). The second hole (Salgash) was sited on the basal section of the fourth cycle, and sampled sulfidic (Cu-Zn-Fe), carbon-rich shale and sandstone units separated by flows of peridotite. The third hole (Eastern Creek) was sited on the margin of a moderately deep-water rift basin, the 2.95 to 2.91 Ga Mosquito Creek Basin. This is dominated by turbidites, but the sandstones and carbon-rich shales intersected at the drilling site were deposited in shallower water. The fourth and fifth holes, located 300 km apart, sampled 2.77 to 2.76 Ga continental formations of the Fortescue Group; both holes included black shales.

A palynostratigraphic approach to the SW Anatolian molasse basin: Kale-Tavas molasse and Denizli molasse

NASA Astrophysics Data System (ADS)

Akgün, Funda; Sözbilir, Hasan

The study, explains stratigraphy of the Oligo-Miocene molasse around the Denizli province (SW Anatolia), based on the palynology which is also supported by the detailed mapping and correlation of the measured sections from the coal-bearing sequences of the molasse deposits. For this purpose, two huge depressions named as the Kale-Tavas molasse and Denizli molasse basins were examined. The Kale-Tavas molasse deposits has a basal unconformity with the underlying pre-Oligocene basement and begins with the Chattian Karadere and Mortuma formations which are covered unconformably by the Aquitanian Yenidere formation. An angular unconformity between the Chattian and the Burdigalian is only observed in the middle part of the basin, around Kale. In the Tavas section, the Aquitanian and the Burdigalian are absent. The Denizli molasse is characterized by Chattian-Aquitanian sequence consisting of distinctive sedimentary facies, alluvial fan and deltaic-shallow marine deposits with carbonate patch reefs. Palynostratigraphic studies, which have given the Chattian age, have been carried out from the coal lenses of alluvial fan and delta plain deposits. In addition to the palynological determinations, coral and foraminiferal content of the carbonate patch reefs which rest conformably on the coal-bearing sequences have yielded the Chattian-Aquitanian age. Two different palynomorph associations have been determined from the molasse deposits. The first palynomorph association which is established in the samples from the Sağdere and Mortuma formations, corresponds to the Chattian age, whilst the second is of the Aquitanian age. The Late Oligocene-Early Miocene which is claimed as the time of N-S-extensional tectonics in western Turkey, is related to the depositional time of the molasse sequences in the study area. Thus, the molasse is older than the basal deposits of the Gediz and Büyük Menderes grabens.

Valley-fill sequences and onlap geometries, Lower Cretaceous Muddy Sandstone, Kitty Field, Powder River basin, Wyoming

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

Gardner, M.H.; Gustason, E.R.

1987-05-01

The Muddy Sandstone at Kitty field is a valley-fill sequence that records a late Albian sea level rise and accompanying transgression. The valley was cut during a preceding sea level lowstand. Stratal geometries and facies successions within the valley fill demonstrate the history of transgression was not gradual and progressive. Rather, the valley fill comprises a series of discrete, time-bounded, depositional units which onlap the erosional surface. Five time-bounded depositional units were defined by facies successions and were used to define onlap geometries. Facies successions within individual units record progressive shoaling. Capping each succession, there may be a planar disconformity,more » a thin bioturbated interval, or the deepest water facies of the next depositional event. Thus, the termination of each depositional event is marked by an episode of rapid deepening. At a single geographic location, stratal successions within older depositional units represent more landward facies than those within younger units. Therefore, the onlap geometry of the valley-fill sequence consists of a landward-stepping arrangement of depositional units. The primary reservoirs within the valley-fill sequence, at Kitty field, are laterally coalesced, channel-belt sandstones at the base and barrier island sandstones at the top. Reservoir sandstones of lesser quality occur within the intermediate estuarine facies. The stacking pattern, developed by onlap of the units, results in multiple pay zones within mid-valley reaches. The boundaries of each depositional unit define a high-resolution, chronostratigraphic correlation of valley-fill strata, a correlation corroborated by bentonites. This correlation method gives an accurate description of the internal geometry of valley-fill strata and, therefore, provides a basis for understanding the process of transgressive onlap.« less

Prevalence of monosodium urate deposits in a population of rheumatoid arthritis patients with hyperuricemia.

PubMed

Petsch, Christina; Araujo, Elizabeth G; Englbrecht, Matthias; Bayat, Sara; Cavallaro, Alexander; Hueber, Axel J; Lell, Michael; Schett, Georg; Manger, Bernhard; Rech, Juergen

2016-06-01

To investigate the prevalence of monosodium urate (MSU) crystal deposits, indicative for gout, in a population of rheumatoid arthritis (RA) patients with concomitant hyperuricemia and to analyze the clinical and disease-specific characteristics of RA patients who exhibit MSU crystal deposits. Overall, 100 consecutive patients with the diagnosis of RA and a serum urate level above 6mg/dl underwent dual energy computed tomography (DECT) of both feet and hands to search for MSU crystals in a prospective study between October 2011 and July 2013. Presence and extent of MSU crystal deposits on DECT was assessed by automated volume measurement. Demographic and disease-specific characteristics were recorded and included into two logistic regression models to test for the factors associated with MSU crystal deposits in RA. Hyperuricemic RA patients were mostly male (55%), over 60 years of age (63 ± 11 years), had established disease (8.7 ± 10.5 years) and a mean disease activity score 28 (DAS 28) of 3.2. In total, 20 out of 100 patients displayed MSU crystal deposits in DECT. Interestingly, the majority (70%) of the RA patients positive for MSU crystal deposits were seronegative RA patients. Hence, every third seronegative RA patient had MSU crystal deposits. According to logistic regression model analysis, seronegative status correlated positively with presence of urate deposits (p = 0.019). These data show that a considerable number of RA patients display periarticular MSU crystal deposits. Seronegative patients were shown to be predominantly affected with every third patient being positive for urate deposits. Copyright © 2016 Elsevier Inc. All rights reserved.

The story of landscape evolution in Lower Austria told by sedimentological analysis and luminescence dating

NASA Astrophysics Data System (ADS)

Hofer, Ingo; Thiel, Christine; Terhorst, Birgit; Jaburova, Iva; Buylaert, Jan-Pieter; Murray, Andrew; Frechen, Manfred

2010-05-01

Loess/palaeosol sequences contain detailed information about palaeoenvironmental changes during the Quaternary. Furthermore, because of its long distance aeolian transport, which resets the luminescence signal to zero prior to deposition, loess is highly suitable for luminescence dating. This allows the determination of geodynamic processes with time. The loess deposits in the Kremser Feld (Lower Austria) are up to 30 m thick. The loess/paleosol sequence of Stratzing is situated at the eastern margin of the west-east elongated hill of the ‘Galgenberg'; this location is famous for its archaeological finds, e.g. the sculpture "Fanny", one of the oldest identifiable representations of the human figure (Neugebauer-Maresch, 1993). The loess profile examined here has a total depth of 7.5 m and is subdivided into 19 prominent horizons. For each horizon the grain size distribution, pH-value, total carbonate content, total organic content and sulphur content was derived in order to reconstruct the environmental conditions leading to sedimentation and soil formation. To set up a geochronological framework for the loess deposition and the subsequent soil formation, nine samples were dated by means of elevated temperature post-IR IRSL (Thiel et al., submitted). Besides a general discussion about the sedimentological data we will discuss horizon 18 in more detail; this is a paleosol rich in clay and poor in mineralic carbonate. The sulphur content is relatively high and indicates higher humidity and warmer climate, all making the unexpectedly low organic carbon content of particular interest. The luminescence ages reveal an important hiatus above this well-developed palaeosol (from ~ 100 to ~ at least 200 ka) clearly showing that this loess/palaeosol sequence is not a continuous record. This implies either significant erosion or lack of loess deposition in this area. Neugebauer-Maresch, C., 1993. Kunst und geistige Welt. - In: Neugebauer-Maresch, C., (ed): Altsteinzeit im Osten Österreichs. Wissenschaftliche Schriftenreihe Niederösterreich 95/96/97 (St. Pölten). Thiel, C., Buylaert, J. P., Terhorst, B., Murray, A. S., Hofer, I., Tsukamoto, S., Frechen, M., submitted. Luminescence dating of the Stratzing loess profile (Austria) - Testing the potential of an elevated temperature post-IR IRSL protocol. Quaternary International.

Tectonics and metallogenesis of Proterozoic rocks of the Reading Prong

USGS Publications Warehouse

Gundersen, L.C.S.

2004-01-01

Detailed geologic mapping, petrography, and major and trace-element analyses of Proterozoic rocks from the Greenwood Lake Quadrangle, New York are compared with chemical analyses and stratigraphic information compiled for the entire Reading Prong. A persistent regional stratigraphy is evident in the mapped area whose geochemistry indicates protoliths consistent with a back-arc marginal basin sequence. The proposed marginal basin may have been floored by an older sialic basement and overlain by a basin-fill sequence consisting of a basal tholeiitic basalt, basic to intermediate volcanic or volcaniclastic rocks and carbonate sediments, a bimodal calc-alkaline volcanic sequence, and finally volcaniclastic, marine, and continental sediments. The presence of high-chlorine biotite and scapolite may indicate circulation of brine fluids or the presence of evaporite layers in the sequence. Abundant, stratabound magnetite deposits with a geologic setting very unlike that of cratonic, Proterozoic banded-iron formations are found throughout the proposed basin sequence. Associated with many of the magnetite deposits is unusual uranium and rare-earth element mineralization. It is proposed here that these deposits formed in an exhalative, volcanogenic, depositional environment within an extensional back-arc marginal basin. Such a tectonic setting is consistent with interpretations of protoliths in other portions of the Reading Prong, the Central Metasedimentary Belt of the Canadian Grenville Province, and recent interpretation of the origin of the Franklin lead-zinc deposits, suggesting a more cohesive evolving arc/back-arc tectonic model for the entire Proterozoic margin of the north-eastern portion of the North American craton. Published by Elsevier Ltd.

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

Molecular detection of Toxoplasma gondii in snakes.

PubMed

Nasiri, Vahid; Teymurzadeh, Shohreh; Karimi, Gholamreza; Nasiri, Mehdi

2016-10-01

Toxoplasma gondii, an obligate intracellular protozoan parasite, is responsible for one of the most common zoonotic parasitic diseases in almost all warm-blooded vertebrates worldwide, and it is estimated that about one-third of the world human population is chronically infected with this parasite. Little is known about the circulation of T. gondii in snakes and this study for the first time aimed to evaluate the infection rates of snakes by this parasite by PCR methods. The brain of 68 Snakes, that were collected between May 2012 and September 2015 and died after the hold in captivity, under which they were kept for taking poisons, were examined for the presence of this parasite. DNA was extracted and Nested-PCR method was carried out with two of pairs of primers to detect the 344 bp fragment of T. gondii GRA6 gene. Five positive nested-PCR products were directly sequenced in the forward and reverse directions by Sequetech Company (Mountain View, CA). T. gondii GRA6 gene were detected from 55 (80.88%) of 68 snakes brains. Sequencing of the GRA6 gene revealed 98-100% of similarity with T. gondii sequences deposited in GenBank. To our knowledge, this is the first study of molecular detection of T. gondii in snakes and our findings show a higher frequency of this organism among them. Copyright © 2016 Elsevier Inc. All rights reserved.

Cyanobacterial Diversity in Microbial Mats from the Hypersaline Lagoon System of Araruama, Brazil: An In-depth Polyphasic Study.

PubMed

Ramos, Vitor M C; Castelo-Branco, Raquel; Leão, Pedro N; Martins, Joana; Carvalhal-Gomes, Sinda; Sobrinho da Silva, Frederico; Mendonça Filho, João G; Vasconcelos, Vitor M

2017-01-01

Microbial mats are complex, micro-scale ecosystems that can be found in a wide range of environments. In the top layer of photosynthetic mats from hypersaline environments, a large diversity of cyanobacteria typically predominates. With the aim of strengthening the knowledge on the cyanobacterial diversity present in the coastal lagoon system of Araruama (state of Rio de Janeiro, Brazil), we have characterized three mat samples by means of a polyphasic approach. We have used morphological and molecular data obtained by culture-dependent and -independent methods. Moreover, we have compared different classification methodologies and discussed the outcomes, challenges, and pitfalls of these methods. Overall, we show that Araruama's lagoons harbor a high cyanobacterial diversity. Thirty-six unique morphospecies could be differentiated, which increases by more than 15% the number of morphospecies and genera already reported for the entire Araruama system. Morphology-based data were compared with the 16S rRNA gene phylogeny derived from isolate sequences and environmental sequences obtained by PCR-DGGE and pyrosequencing. Most of the 48 phylotypes could be associated with the observed morphospecies at the order level. More than one third of the sequences demonstrated to be closely affiliated (best BLAST hit results of ≥99%) with cyanobacteria from ecologically similar habitats. Some sequences had no close relatives in the public databases, including one from an isolate, being placed as "loner" sequences within different orders. This hints at hidden cyanobacterial diversity in the mats of the Araruama system, while reinforcing the relevance of using complementary approaches to study cyanobacterial diversity.

Cyanobacterial Diversity in Microbial Mats from the Hypersaline Lagoon System of Araruama, Brazil: An In-depth Polyphasic Study

PubMed Central

Ramos, Vitor M. C.; Castelo-Branco, Raquel; Leão, Pedro N.; Martins, Joana; Carvalhal-Gomes, Sinda; Sobrinho da Silva, Frederico; Mendonça Filho, João G.; Vasconcelos, Vitor M.

2017-01-01

Microbial mats are complex, micro-scale ecosystems that can be found in a wide range of environments. In the top layer of photosynthetic mats from hypersaline environments, a large diversity of cyanobacteria typically predominates. With the aim of strengthening the knowledge on the cyanobacterial diversity present in the coastal lagoon system of Araruama (state of Rio de Janeiro, Brazil), we have characterized three mat samples by means of a polyphasic approach. We have used morphological and molecular data obtained by culture-dependent and -independent methods. Moreover, we have compared different classification methodologies and discussed the outcomes, challenges, and pitfalls of these methods. Overall, we show that Araruama's lagoons harbor a high cyanobacterial diversity. Thirty-six unique morphospecies could be differentiated, which increases by more than 15% the number of morphospecies and genera already reported for the entire Araruama system. Morphology-based data were compared with the 16S rRNA gene phylogeny derived from isolate sequences and environmental sequences obtained by PCR-DGGE and pyrosequencing. Most of the 48 phylotypes could be associated with the observed morphospecies at the order level. More than one third of the sequences demonstrated to be closely affiliated (best BLAST hit results of ≥99%) with cyanobacteria from ecologically similar habitats. Some sequences had no close relatives in the public databases, including one from an isolate, being placed as “loner” sequences within different orders. This hints at hidden cyanobacterial diversity in the mats of the Araruama system, while reinforcing the relevance of using complementary approaches to study cyanobacterial diversity. PMID:28713360

Upper Lower Cambrian depositional sequence in Avalonian New Brunswick

USGS Publications Warehouse

Landing, E.; Westrop, S.R.

1996-01-01

The Hanford Brook Formation (emended) is a thin (up to 42+ m), upper Lower Cambrian depositional sequence that is unconformably bounded by the lower Lower Cambrian (Random Formation) and the middle Middle Cambrian (Fossil Brook Member of the Chamberlain's Brook Formation). These stratigraphic relationships of the trilobite-bearing Hanford Brook Formation indicate deposition on the Avalonian marginal platform in the Saint John, New Brunswick, region and provide more evidence for a uniform, latest Precambrian-Cambrian epeirogenic history and cover sequence in Avalon. The Hanford Brook Formation is a deepening - shoaling sequence with (i) lower, transgressive sandstone deposited in episodically high-energy environments (St. Martins Member, new); (ii) highstand-regressive, dysaerobic mudstone - fine-grained sandstone with volcanic ashes (Somerset Street Member, new); and (iii) upper, regressive, planar and hummocky cross-stratified sandstone (Long Island Member, new). Trilobites are common in the distal Somerset Street Member, and ostracodes and brachiopods dominate the St. Martins and Long Island members. Condensation of the St. Martins Member and absence of the Long Island Member where the Random Formation and Fossil Brook Member are thinnest suggest onlap of the Hanford Brook and pronounced, sub-Middle Cambrian erosion across epeirogenically active blocks in southern New Brunswick.

Biodiversity hot spot on a hot spot: novel extremophile diversity in Hawaiian fumaroles.

PubMed

Wall, Kate; Cornell, Jennifer; Bizzoco, Richard W; Kelley, Scott T

2015-01-06

Fumaroles (steam vents) are the most common, yet least understood, microbial habitat in terrestrial geothermal settings. Long believed too extreme for life, recent advances in sample collection and DNA extraction methods have found that fumarole deposits and subsurface waters harbor a considerable diversity of viable microbes. In this study, we applied culture-independent molecular methods to explore fumarole deposit microbial assemblages in 15 different fumaroles in four geographic locations on the Big Island of Hawai'i. Just over half of the vents yielded sufficient high-quality DNA for the construction of 16S ribosomal RNA gene sequence clone libraries. The bacterial clone libraries contained sequences belonging to 11 recognized bacterial divisions and seven other division-level phylogenetic groups. Archaeal sequences were less numerous, but similarly diverse. The taxonomic composition among fumarole deposits was highly heterogeneous. Phylogenetic analysis found cloned fumarole sequences were related to microbes identified from a broad array of globally distributed ecotypes, including hot springs, terrestrial soils, and industrial waste sites. Our results suggest that fumarole deposits function as an "extremophile collector" and may be a hot spot of novel extremophile biodiversity. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Biodiversity hot spot on a hot spot: novel extremophile diversity in Hawaiian fumaroles

PubMed Central

Wall, Kate; Cornell, Jennifer; Bizzoco, Richard W; Kelley, Scott T

2015-01-01

Fumaroles (steam vents) are the most common, yet least understood, microbial habitat in terrestrial geothermal settings. Long believed too extreme for life, recent advances in sample collection and DNA extraction methods have found that fumarole deposits and subsurface waters harbor a considerable diversity of viable microbes. In this study, we applied culture-independent molecular methods to explore fumarole deposit microbial assemblages in 15 different fumaroles in four geographic locations on the Big Island of Hawai'i. Just over half of the vents yielded sufficient high-quality DNA for the construction of 16S ribosomal RNA gene sequence clone libraries. The bacterial clone libraries contained sequences belonging to 11 recognized bacterial divisions and seven other division-level phylogenetic groups. Archaeal sequences were less numerous, but similarly diverse. The taxonomic composition among fumarole deposits was highly heterogeneous. Phylogenetic analysis found cloned fumarole sequences were related to microbes identified from a broad array of globally distributed ecotypes, including hot springs, terrestrial soils, and industrial waste sites. Our results suggest that fumarole deposits function as an “extremophile collector” and may be a hot spot of novel extremophile biodiversity. PMID:25565172

Magnetic susceptibility variations in Loess sequences and their relationship to astronomical forcing

NASA Technical Reports Server (NTRS)

Verosub, Kenneth L.; Singer, Michael J.

1992-01-01

The long, well-exposed and often continuous sequences of loess found throughout the world are generally thought to provide an excellent opportunity for studying long-term, large-scale environmental change during the last few million years. In recent years, the most fruitful loess studies have been those involving the deposits of the loess in China. One of the most intriguing results of that work has been the discovery of an apparent correlation between variations in the magnetic susceptibility of the loess sequence and the oxygen isotope record of the deep sea. This correlation implies that magnetic susceptibility variations are being driven by astronomical parameters. However, the basic data have been interpreted in various ways by different authors, most of whom assumed that the magnetic minerals in the loess have not been affected by post-depositional processes. Using a chemical extraction procedure that allows us to separate the contribution of secondary pedogenic magnetic minerals from primary inherited magnetic minerals, we have found that the magnetic susceptibility of the Chinese paleosols is largely due to a pedogenic component which is present to a lesser degree in the loess. We have also found that the smaller inherited component of the magnetic susceptibility is about the same in the paleosols and the loess. These results demonstrate the need for additional study of the processes that create magnetic susceptibility variations in order to interpret properly the role of astronomical forcing in producing these variations.

Erosion and deposition on a debris-flow fan

NASA Astrophysics Data System (ADS)

Densmore, A. L.; Schuerch, P.; Rosser, N. J.; McArdell, B. W.

2011-12-01

The ability of a debris flow to entrain or deposit sediment controls the downstream evolution of flow volume, and ultimately dictates both the geomorphic impact of the flow and the potential hazard that it represents. Our understanding of the patterns of, and controls on, such flow volume changes remains extremely limited, however, partly due to a poor mechanistic grasp of the interactions between debris flows and their bed and banks. In addition, we lack a good understanding of the cumulative long-term effects of sequences of flows in a single catchment-fan system. Here we begin to address these issues by using repeated terrestrial laser scanning (TLS) to characterize the detailed surface change associated with the passage of multiple debris flows on the Illgraben fan, Switzerland. We calculate surface elevation change along a 300 m study reach, and from this derive the downfan rate of flow volume change, or lag rate; for comparison, we also derive the spatially-averaged lag rate over the entire ~2 km length of the fan. Lag rates are broadly comparable over both length scales, indicating that flow behavior does not vary significantly across the fan for most flows, but importantly we find that flow volume at the fan head is a poor predictor of volume at the fan toe. The sign and magnitude of bed elevation change scale with local flow depth; at flow depths < 2 m, erosion and deposition are approximately equally likely, but erosion becomes increasingly dominant for flow depths > 2 m. On the Illgraben fan, this depth corresponds to a basal shear stress of 3-4 kPa. Because flow depth is in part a function of channel cross-sectional topography, which varies strongly both within and between flows, this result indicates that erosion and deposition are likely to be highly dynamic. The dependence of flow volume change on both the channel topography and the flow history may thus complicate efforts to predict debris-flow inundation areas by simple flow routing. We then apply a 2d numerical model of debris-flow fan evolution to explore the key controls on debris-flow routing and topographic development over sequences of multiple flows. We find that fan topographic roughness plays an important role in both channel development and fan surface stability. We also find that, while first-order fan shape is largely insensitive to the input flow sequence, second-order variables such as the pattern of surface exposure ages and the distribution of channel characteristics hold more promise as robust recorders of past flow conditions. Further work is needed to understand the degree to which the TLS-derived (and Illgraben-specific) relationship between bed elevation change and flow depth can be applied in different settings, and to elucidate the role played by coarse debris in controlling patterns of erosion and deposition.

Seismic stratigraphy and late Quaternary shelf history, south-central Monterey Bay, California

USGS Publications Warehouse

Chin, J.L.; Clifton, H.E.; Mullins, H.T.

1988-01-01

The south-central Monterey Bay shelf is a high-energy, wave-dominated, tectonically active coastal region on the central California continental margin. A prominent feature of this shelf is a sediment lobe off the mouth of the Salinas River that has surface expression. High-resolution seismic-reflection profiles reveal that an angular unconformity (Quaternary?) underlies the entire shelf and separates undeformed strata above it from deformed strata below it. The Salinas River lobe is a convex bulge on the shelf covering an area of approximately 72 km2 in water depths from 10 to 90 m. It reaches a maximum thickness of 35 m about 2.5 km seaward of the river mouth and thins in all directions away from this point. Adjacent shelf areas are characterized by only a thin (2 to 5 m thick) and uniform veneer of sediment. Acoustic stratigraphy of the lobe is complex and is characterized by at least three unconformity-bounded depositional sequences. Acoustically, these sequences are relatively well bedded. Acoustic foresets occur within the intermediate sequence and dip seaward at 0.7?? to 2.0??. Comparison with sedimentary sequences in uplifted onshore Pleistocene marine-terrace deposits of the Monterey Bay area, which were presumably formed in a similar setting under similar processes, suggests that a general interpretation can be formulated for seismic stratigraphic patterns. Depositional sequences are interpreted to represent shallowing-upwards progradational sequences of marine to nonmarine coastal deposits formed during interglacial highstands and/or during early stages of falling sea level. Acoustic foresets within the intermediate sequence are evidence of seaward progradation. Acoustic unconformities that separate depositional sequences are interpreted as having formed largely by shoreface planation and may be the only record of the intervening transgressions. The internal stratigraphy of the Salinas River lobe thus suggests that at least several late Quaternary regressions and transgressions may be recorded under the present shelf. This record may represent the last major eustatic cycle of sea level, an interval not observed in uplifted onshore Pleistocene marine terraces. ?? 1988.

Thermodynamics of triple helix formation: spectrophotometric studies on the d(A)10.2d(T)10 and d(C+3T4C+3).d(G3A4G3).d(C3T4C3) triple helices.

PubMed Central

Pilch, D S; Brousseau, R; Shafer, R H

1990-01-01

We have stabilized the d(A)10.2d(T)10 and d(C+LT4C+3).d(G3A4G3).d(C3T4C3) triple helices with either NaCl or MgCl2 at pH 5.5. UV mixing curves demonstrate a 1:2 stoichiometry of purine to pyrimidine strands under the appropriate conditions of pH and ionic strength. Circular dichroic titrations suggest a possible sequence-independent spectral signature for triplex formation. Thermal denaturation profiles indicate the initial loss of the third strand followed by dissociation of the underlying duplex with increasing temperature. Depending on the base sequence and ionic conditions, the binding affinity of the third strand for the duplex at 25 degrees C is two to five orders of magnitude lower than that of the two strands forming the duplex. Thermodynamic parameters for triplex formation were determined for both sequences in the presence of 50 mM MgCl2 and/or 2.0 M NaCl. Hoogsteen base pairs are 0.22-0.64 kcal/mole less stable than Watson-Crick base pairs, depending on ionic conditions and base composition. C+.G and T.A Hoogsteen base pairs appear to have similar stability in the presence of Mg2+ ions at low pH. PMID:2216768

Ab initio electron propagator calculations of transverse conduction through DNA nucleotide bases in 1-nm nanopore corroborate third generation sequencing.

PubMed

Kletsov, Aleksey A; Glukhovskoy, Evgeny G; Chumakov, Aleksey S; Ortiz, Joseph V

2016-01-01

The conduction properties of DNA molecule, particularly its transverse conductance (electron transfer through nucleotide bridges), represent a point of interest for DNA chemistry community, especially for DNA sequencing. However, there is no fully developed first-principles theory for molecular conductance and current that allows one to analyze the transverse flow of electrical charge through a nucleotide base. We theoretically investigate the transverse electron transport through all four DNA nucleotide bases by implementing an unbiased ab initio theoretical approach, namely, the electron propagator theory. The electrical conductance and current through DNA nucleobases (guanine [G], cytosine [C], adenine [A] and thymine [T]) inserted into a model 1-nm Ag-Ag nanogap are calculated. The magnitudes of the calculated conductance and current are ordered in the following hierarchies: gA>gG>gC>gT and IG>IA>IT>IC correspondingly. The new distinguishing parameter for the nucleobase identification is proposed, namely, the onset bias magnitude. Nucleobases exhibit the following hierarchy with respect to this parameter: Vonset(A)

Upper Albian to Lower Turonian deposits and associated breccias along the Dahar cuestas (southeastern Tunisia): Origin and depositional environments

NASA Astrophysics Data System (ADS)

Krimi, Mabrouk; Ouaja, Mohamed; Zargouni, Fouad

2017-11-01

The carbonate Zebbag Formation of Upper Albian to Lower Turonian age which outcrops along the Dahar cuestas (south eastern Tunisia) includes several breccia intervals. The stratigraphic hierarchy of these breccia levels led to achieving a detailed sequential analysis within a spectrum of depositional environments extending from subtidal to inner to middle ramp settings. Six major transgressive/regressive sequences make up the stacking of the elementary sequences beginning with transgressive and/or storm wave breccias capped by desiccation and/or collapse breccias. The stratigraphic evolutionary history of the breccia facies are interpreted as the result of the interplay between eustatic and tectonic factors. This model is in accord with the tectonic activities common during Upper Albian-Lower Turonian responsible for the sequences onlapping.

Correcting names of bacteria deposited in National Microbial Repositories: an analysed sequence data necessary for taxonomic re-categorization of misclassified bacteria-ONE example, genus Lysinibacillus.

PubMed

Rekadwad, Bhagwan N; Gonzalez, Juan M

2017-08-01

A report on 16S rRNA gene sequence re-analysis and digitalization is presented using Lysinibacillus species (one example) deposited in National Microbial Repositories in India. Lysinibacillus species 16S rRNA gene sequences were digitalized to provide quick response (QR) codes, Chaose Game Representation (CGR) and Frequency of Chaose Game Representation (FCGR). GC percentage, phylogenetic analysis, and principal component analysis (PCA) are tools used for the differentiation and reclassification of the strains under investigation. The seven reasons supporting the statements made by us as misclassified Lysinibacillus species deposited in National Microbial Depositories are given in this paper. Based on seven reasons, bacteria deposited in National Microbial Repositories such as Lysinibacillus and many other needs reanalyses for their exact identity. Leaves of identity with type strains of related species shows difference 2 to 8 % suggesting that reclassification is needed to correctly assign species names to the analyzed Lysinibacillus strains available in National Microbial Repositories.

Language extraction from zinc sulfide

NASA Astrophysics Data System (ADS)

Varn, Dowman Parks

2001-09-01

Recent advances in the analysis of one-dimensional temporal and spacial series allow for detailed characterization of disorder and computation in physical systems. One such system that has defied theoretical understanding since its discovery in 1912 is polytypism. Polytypes are layered compounds, exhibiting crystallinity in two dimensions, yet having complicated stacking sequences in the third direction. They can show both ordered and disordered sequences, sometimes each in the same specimen. We demonstrate a method for extracting two-layer correlation information from ZnS diffraction patterns and employ a novel technique for epsilon-machine reconstruction. We solve a long-standing problem---that of determining structural information for disordered materials from their diffraction patterns---for this special class of disorder. Our solution offers the most complete possible statistical description of the disorder. Furthermore, from our reconstructed epsilon-machines we find the effective range of the interlayer interaction in these materials, as well as the configurational energy of both ordered and disordered specimens. Finally, we can determine the 'language' (in terms of the Chomsky Hierarchy) these small rocks speak, and we find that regular languages are sufficient to describe them.

Organic sedimentary deposits in Titan's dry lakebeds: Probable evaporite

USGS Publications Warehouse

Barnes, J.W.; Bow, J.; Schwartz, J.; Brown, R.H.; Soderblom, J.M.; Hayes, A.G.; Vixie, G.; Le, Mouelic S.; Rodriguez, S.; Sotin, Christophe; Jaumann, R.; Stephan, K.; Soderblom, L.A.; Clark, R.N.; Buratti, B.J.; Baines, K.H.; Nicholson, P.D.

2011-01-01

We report the discovery of organic sedimentary deposits at the bottom of dry lakebeds near Titan's north pole in observations from the Cassini Visual and Infrared Mapping Spectrometer (VIMS). We show evidence that the deposits are evaporitic, making Titan just the third known planetary body with evaporitic processes after Earth and Mars, and is the first that uses a solvent other than water. ?? 2011 Elsevier Inc.

Metastable and equilibrium phase formation in sputter-deposited Ti/Al multilayer thin films

NASA Astrophysics Data System (ADS)

Lucadamo, G.; Barmak, K.; Lavoie, C.; Cabral, C., Jr.; Michaelsen, C.

2002-06-01

The sequence and kinetics of metastable and equilibrium phase formation in sputter deposited multilayer thin films was investigated by combining in situ synchrotron x-ray diffraction (XRD) with ex situ electron diffraction and differential scanning calorimetry (DSC). The sequence included both cubic and tetragonal modifications of the equilibrium TiAl3 crystal structure. Values for the formation activation energies of the various phases in the sequence were determined using the XRD and DSC data obtained here, as well as activation energy data reported in the literature.

Evolution Of Quaternary Stream Fan Deposits At The Confluences Of Turung Khola And Bembung Khola Of Middle Teesta Basin In Sikkim-Darjeeling Himalaya,India: A Tectonic - Climate Response

NASA Astrophysics Data System (ADS)

Lukram, I. M.

2007-12-01

Tributary fan deposits are well preserved on either side of the Teesta river in the non-glaciated middle part of the Himalayan valley lying in a tectonic region bounded by the MCT and MBT. The lithofacies characteristics and assemblage patterns of these deposits bear testimony to the effects of tectonic and climatic activities on the sedimentation process in the basin. Two tributary streams, with small catchments namely Turung Khola and Bembung Khola are important in this context. Three major fan lobes (F2, F1, and F0) are preserved at Turung Khola. In contrast, two fan lobes (F1,F0) are preserved at the confluence of the Bembung Khola. Terraces, floodplains, channel bars, chute bars are associated geomorphic features in this part of the Teesta basin. Landslides cover an area of 7% and 15% in the catchment of Turung Khola and Bembung Khola, respectively. Dense forest covers 24% and 12%; open forest covers 30% and 29 %; and scrubby vegetation covers 39% and 49% of the Turung Khola and Bembung Khola, respectively. The landslides mainly occur along the margins of the dense forest where they are active in every rainy season. Tributary longitudinal profiles and Hack profiles indicate a relationship between the knick points and high SL-Index values, where fault /thrust intersections are present. Active landslides and scarps are close to the major fault/thrust planes. Sediment characteristics of these fan deposits suggest that four types of depositional flows viz. debris flows, hyperconcentrated flows, sheet flows and channel flows laid down these sequences. The channel flow deposits are dominant (32%-54 %) in the fan sequence of the Turung Khola followed by sheet flow deposits (28.5%), hyperconcentrated flow deposits (26%) and debris flow deposits (12%), respectively. Hyperconcentrated flow deposits are dominant (44%) in the F1 sequence, whereas the active channel fanlobe is dominant (80%) in the channel flow deposits. The rest of the active channel sequence is composed of sheet flow deposits (20%). On the other hand, the major part (52%) of the F1 fanlobe of Bembung Khola is built up of debris flow deposits and F0 fanlobe is composed of channel flow deposits and flood sediment. From the above analysis, an evolutionary model of the deposition and incision at the tributary stream fan confluence is proposed. The insetting of the younger fan lobes into older fan lobe surfaces is an evidence of tectonic uplift in the region. The landform and their depositional pattern are a responds to link tectonic- climatic process systems; some depositional lithofacies assemblages are responses to climatic events.

Correlating Microstructure and Optoelectronic Performance of Carbon-Based Nanomaterials

NASA Astrophysics Data System (ADS)

Rochford, Caitlin

There is a great deal of interest in carbon nanostructures such as graphene and various forms of carbon nanotubes due to their exceptional physical, electronic, and optical properties. Many technological applications have been proposed for these nanostructures, but despite the promise many carbon nanostructure-based optoelectronic devices fail to compete with their conventional counterparts. This is often due in large part to a non-optimized material or device microstructure. Factors such as crystallinity, contact quality, defect structure, and device configuration can critically affect device performance due to the high sensitivity and extreme surface to volume ratio of carbon nanostructures. In order for the exceptional intrinsic properties of the nanostructures to be exploited, a clear understanding of the microstructure and its correlation with device-relevant optoelectronic properties is needed. This dissertation presents four projects which demonstrate this principle. First, a TiO 2-coated carbon nanofiber is studied in order to optimize its structure for use in a novel dye-sensitized solar cell. Second, the electrode configuration of an individual multiwall carbon nanotube infrared sensor is investigated in order to surpass the limitations of disordered nanotube film-based infrared sensors. Third, the properties of defect structures in large area transferred graphene films grown by chemical vapor deposition are correlated with carrier diffusion in order to understand the film's low mobility compared to exfoliated graphene. Fourth, the effect of deposition conditions on graphene-metal contact was studied with the goal of achieving sufficiently transparent contacts for investigation of the superconducting proximity effect. All four projects highlight the unique properties of carbon nanostructures as well as the need to correlate their optoelectronic properties with microstructural details in order to achieve the desired device performance.

Stratigraphic Paleobiology of the Taranto Area

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

Progress in faunal correlation of Late Cenozoic fluvial sequences 2000 4: the report of the IGCP 449 biostratigraphy subgroup

NASA Astrophysics Data System (ADS)

Schreve, D. C.; Keen, D. H.; Limondin-Lozouet, N.; Auguste, P.; Santisteban, Juan I.; Ubilla, M.; Matoshko, A.; Bridgland, D. R.; Westaway, R.

2007-11-01

Vertebrate and invertebrate faunal biostratigraphy is a well-tested method for establishing relative chronologies for fluviatile sequences that has proved useful in many parts of the world. The robust bones and teeth of large mammals are commonly found in fluviatile deposits, whereas small vertebrates can be readily recovered through systematic sieving of calcareous sediments, as can molluscs, the other major faunal group that has been used for biostratigraphical analysis of fluvial sequences. Because of their rapid and quantifiable rates of evolution, extinction, body mass change and dispersal during the Late Cenozoic, mammals are especially useful for ordering the fragmentary terrestrial sequence of interglacials and glacials, and proposing correlation with the global marine climatostratigraphic record. Other groups (e.g. reptiles and amphibians, ostracods) are as yet only in the initial stages of development as a dating tool, whereas some (e.g. fish, birds) still require substantial development in order to fully explore their utility. As part of IGCP 449, vertebrate and molluscan assemblages have made important contributions to datasets from a number of areas, notably northern France, central Germany, the Czech Republic and the Ukraine. Further south, mammalian assemblages have proved useful in separating discrete periods of climatic change in Iberia and Syria. At greater distances from the core area of fluvial biostratigraphical archives, significant contributions have come from South America (Uruguay River), South Africa (Vaal) and Australia (Riverine Plain and Lake Eyre drainage basin).

Fabrication of lightweight ceramic mirrors by means of a chemical vapor deposition process

NASA Technical Reports Server (NTRS)

Goela, Jitendra S. (Inventor); Taylor, Raymond L. (Inventor)

1991-01-01

A process to fabricate lightweigth ceramic mirrors, and in particular, silicon/silicon carbide mirrors, involves three chemical vapor deposition steps: one to produce the mirror faceplate, the second to form the lightweight backstructure which is deposited integral to the faceplate, and the third and final step which results in the deposition of a layer of optical grade material, for example, silicon, onto the front surface of the faceplate. The mirror figure and finish are fabricated into this latter material.

Enhancement of nonlinear optical susceptibility of CuPc films by ITO layer

NASA Astrophysics Data System (ADS)

Ganesh, V.; Zahran, H. Y.; Yahia, I. S.; Shkir, Mohd; AlFaify, S.

2016-12-01

In the present study, the Copper Phthalocyanine (CuPc)/ITO thin film was fabricated using thermal evaporation method. The structural property was analyzed by X-ray diffraction study and confirms that the thin film has been preferentially grown along (200) plane. The atomic force microscope study was carried out on deposited film and quality of thin films is assessed by calculating the roughness of the films. The direct and indirect band gap, linear and nonlinear optical characteristics of grown films were calculated by using UV-Vis-NIR spectrometer studies. The calculated values of the first direct and indirect band gaps (Eg1(d) &Eg1(ind)) are 1.879 and 1.644 eV as a fundamental gap, while the values of second direct and indirect band gap (Eg2(d) &Eg2(ind)) are 1.660 and 1.498 eV as an onset gap for CuPc. The values of nonlinear refractive index (n2) and third order nonlinear optical susceptibility (χ3) are found to be 5 × 10-8 and 8 × 10-9 (theoretical) and 5.2 × 10-8 and 1.56 × 10-7 (experimental) respectively. The optical band and third order nonlinear properties suggest that the as-prepared films are may be applied in optoelectronic and nonlinear applications.

Fabrication and notable optical nonlinearities of ultrathin composite films derived from water-soluble Keggin-type polyoxometalates and water-insoluble phthalocyanine.

PubMed

Shehzad, Farooq Khurum; Qu, Ningning; Zhou, Yunshan; Zhang, Lijuan; Ji, Huanyao; Shi, Zonghai; Li, Jiaqi; Hassan, Sadaf Ul

2016-11-28

Composite films with the general formula (POM/CuTAPc) n derived from water-soluble Keggin-type polyoxometalates (POMs = H 5 PMo 10 V 2 O 40 , H 4 SiW 12 O 40 , H 3 PMo 12 O 40 and H 3 PW 12 O 40 ) and water-insoluble 4,9,16,23-copper tetraaminophthalocyanine (denoted CuTAPc) are successfully fabricated by a layer-by-layer self-assembly technique and systematically characterized. The structure of the polyoxometalate anions in the multilayers is kept intact; the deposition amounts of POM and CuTAPc remain constant in every adsorption cycle of the composite film assembly process. The nonlinear optical properties of the composite films were studied by a Z-scan technique at a wavelength of 532 nm and a pulse width of 7 ns. The results not only show that the composite films exhibit notable optical nonlinear self-defocusing behavior and a saturated absorption effect with the nonlinear optical absorption co-efficient β, refractive index n 2 , and third-order NLO susceptibility χ (3) of the films increasing with the increase in number of layers of the films, but also reveal importantly that the discrepancy of LUMO levels between CuTAPc and POMs is proportional to their third-order NLO response.

Microgravity Processing and Photonic Applications of Organic and Polymeric Materials

NASA Technical Reports Server (NTRS)

Frazier, Donald O.; Penn, Benjamin G.; Smith, David D.; Witherow, William K.; Paley, Mark S.; Abdeldayem, Hossin A.

1997-01-01

In recent years, a great deal of interest has been directed toward the use of organic materials in the development of high-efficiency optoelectronic and photonic devices. There is a myriad of possibilities among organics which allow flexibility in the design of unique structures with a variety of functional groups. The use of nonlinear optical (NLO) organic materials such as thin-film waveguides allows full exploitation of their desirable qualities by permitting long interaction lengths and large susceptibilities allowing modest power input. There are several methods in use to prepare thin films, such as Langmuir-Blodgett (LB) and self-assembly techniques, vapor deposition, growth from sheared solution or melt, and melt growth between glass plates. Organics have many features that make them desirable for use in optical devices such as high second- and third-order nonlinearities, flexibility of molecular design, and damage resistance to optical radiation. However, their use in devices has been hindered by processing difficulties for crystals and thin films. In this chapter, we discuss photonic and optoelectronic applications of a few organic materials and the potential role of microgravity on processing these materials. It is of interest to note how materials with second- and third-order nonlinear optical behavior may be improved in a diffusion-limited environment and ways in which convection may be detrimental to these materials.

Zn doped CdO thin films with enhanced linear and third order nonlinear optical properties for optoelectronic applications

NASA Astrophysics Data System (ADS)

Bairy, Raghavendra; Jayarama, A.; Shivakumar, G. K.; Patil, P. S.; Bhat, K. Udaya

2018-04-01

Thin films of undoped and zinc doped CdO have been deposited on glass substrate using spray pyrolysis technique with various dopant concentrations of Zn such as 1, 5 and 10%. Influence of Zn doping on CdO thin films for the structural, morphological, optical and nonlinear optical properties are reported. XRD analysis reveals that as prepared pure and Zn doped CdO films show polycrystalline nature with face centered cubic structure. Also, Zn doping does not significantly modify the crystallinity and not much increase in the crystallite size of the film. SEM images shows grains which are uniform and grain size with increase in dopant concentration. The transmittance of the prepared CdO films recorded in the UV visible spectra and it shows 50 to 60% in the visible region. The estimated optical band gap increases from 2.60 to 2.70 eV for various dopant concentrations. The nonlinear optical absorption of Zn-doped CdO films have been measured used the Z-scan technique at a wavelength 532 nm. The nonlinear optical absorption coefficient (β), nonlinear refractive index (n2) and the third order nonlinear optical susceptibility (χ(3)) of the pure and Zn doped films were determined.

Genomic sequencing in cystic fibrosis newborn screening: what works best, two-tier predefined CFTR mutation panels or second-tier CFTR panel followed by third-tier sequencing?

PubMed

Currier, Robert J; Sciortino, Stan; Liu, Ruiling; Bishop, Tracey; Alikhani Koupaei, Rasoul; Feuchtbaum, Lisa

2017-10-01

PurposeThe purpose of this study was to model the performance of several known two-tier, predefined mutation panels and three-tier algorithms for cystic fibrosis (CF) screening utilizing the ethnically diverse California population.MethodsThe cystic fibrosis transmembrane conductance regulator (CFTR) mutations identified among the 317 CF cases in California screened between 12 August 2008 and 18 December 2012 were used to compare the expected CF detection rates for several two- and three-tier screening approaches, including the current California approach, which consists of a population-specific 40-mutation panel followed by third-tier sequencing when indicated.ResultsThe data show that the strategy of using third-tier sequencing improves CF detection following an initial elevated immunoreactive trypsinogen and detection of only one mutation on a second-tier panel.ConclusionIn a diverse population, the use of a second-tier panel followed by third-tier CFTR gene sequencing provides a better detection rate for CF, compared with the use of a second-tier approach alone, and is an effective way to minimize the referrals of CF carriers for sweat testing. Restricting screening to a second-tier testing to predefined mutation panels, even broad ones, results in some missed CF cases and demonstrates the limited utility of this approach in states that have diverse multiethnic populations.

Postimpact deposition in the Chesapeake Bay impact structure: Variations in eustasy, compaction, sediment supply, and passive-aggressive tectonism

USGS Publications Warehouse

Kulpecz, A.A.; Miller, K.G.; Browning, J.V.; Edwards, L.E.; Powars, D.S.; McLaughlin, P.P.; Harris, A.D.; Feigenson, M.D.

2009-01-01

The Eyreville and Exmore, Virginia, core holes were drilled in the inner basin and annular trough, respectively, of the Chesapeake Bay impact structure, and they allow us to evaluate sequence deposition in an impact crater. We provide new high-resolution geochronologic (<1 Ma) and sequence-stratigraphic interpretations of the Exmore core, identify 12 definite (and four possible) postimpact depositional sequences, and present comparisons with similar results from Eyreville and other mid- Atlantic core holes. The concurrence of increases in ??18O with Chesapeake Bay impact structure sequence boundaries indicates a primary glacioeustatic control on deposition. However, regional comparisons show the differential preservation of sequences across the mid-Atlantic margin. We explain this distribution by the compaction of impactites, regional sediment-supply changes, and the differential movement of basement structures. Upper Eocene strata are thin or missing updip and around the crater, but they thicken into the inner basin (and offshore to the southeast) due to rapid crater infilling and concurrent impactite compaction. Oligocene sequences are generally thin and highly dissected throughout the mid-Atlantic region due to sediment starvation and tectonism, except in southeastern New Jersey. Regional tectonic uplift of the Norfolk Arch coupled with a southward decrease in sediment supply resulted in: (1) largely absent Lower Miocene sections around the Chesapeake Bay impact structure compared to thick sections in New Jersey and Delaware; (2) thick Middle Miocene sequences across the Delmarva Peninsula that thin south of the Chesapeake Bay impact structure; and (3) upper Middle Miocene sections that pinch out just north of the Chesapeake Bay impact structure. Conversely, the Upper Miocene-Pliocene section is thick across Virginia, but it is poorly represented in New Jersey because of regional variations in relative subsidence. ?? 2009 The Geological Society of America.

Coating multilayer material with improved tribological properties obtained by magnetron sputtering

NASA Astrophysics Data System (ADS)

Mateescu, A. O.; Mateescu, G.; Balasoiu, M.; Pompilian, G. O.; Lungu, M.

2017-02-01

This work is based on the Patent no. RO 128094 B1, granted by the Romanian State Office for Inventions and Trademarks. The goal of the work is to obtain for investigations tribological coatings with multilayer structure with improved tribological properties, deposited by magnetron sputtering process from three materials (sputtering targets). Starting from compound chemical materials (TiC, TiB2 and WC), as sputtering targets, by deposition in argon atmosphere on polished stainless steel, we have obtained, based on the claims of the above patent, thin films of multilayer design with promising results regarding their hardness, elastic modulus, adherence, coefficient of friction and wear resistance. The sputtering process took place in a special sequence in order to ensure better tribological properties to the coating, comparing to those of the individual component materials. The tribological properties, such as the coefficient of friction, are evaluated using the tribometer test.

11 things a geologist thinks an engineer should know about carbonate beaches

USGS Publications Warehouse

Halley, Robert B.; Magoon, Orville T.; Robbins, Lisa L.; Ewing, Lesley

2002-01-01

This is a review of the geological aspects of carbonate beaches that a geologist thinks may be useful for an engineer. Classical geologic problems of carbonate beaches, for example how ancient examples are recognized in rock sequences, are of little interest to engineers. Geologists not involved in engineering problems may find it difficult to know what an engineer should understand about carbonate beaches. Nevertheless, there are at least eleven topics that are potentially very useful for engineers to keep in mind. These eleven are chosen with as much thought going into what has been omitted as has been given to the eleven included topics. Some qualifications are in order: First, this paper does not discuss certain kinds of carbonate shorelines that are beyond the scope of engineering issues. For example, this review does not discuss very high-energy carbonate boulder beaches. These beaches are comprised of pieces of carbonate material ganging in size from ten centimeters to meters. Typically, these are high-energy storm deposits formed from pieces of either eroded carbonate rock or other large carbonate pieces such as pieces of large corals. This paper focuses on sand-sized (0.0625–2.0 mm) coastal carbonate deposits. Second, offshore beaches will not be discussed. There are many carbonate beaches that form on banks or shoals exposed at low tide, but our discussion is confined to what most people think of when they go to some tropical island and/or resort and walk out to lay on the beach. Third, this paper does not consider mixed carbonate/quartz sand beaches. While mixed beaches are common, only the end member of purely carbonate sand beaches is considered. Fourth, there will be no order of preference of the eleven topics. And lastly, these eleven topics are not consensus items. These are simply one geologist s thoughts about the aspects of carbonate beaches that would be useful for engineering colleagues to keep in mind. Where possible, general reference is made to textbooks that will lead the reader to extensive literature on carbonate sediments. Several of the topics are not so broad as to have had a large general treatment in texts, and in those cases some original literature is cited.

A time correlation function theory describing static field enhanced third order optical effects at interfaces.

PubMed

Neipert, Christine; Space, Brian

2006-12-14

Sum vibrational frequency spectroscopy, a second order optical process, is interface specific in the dipole approximation. At charged interfaces, there exists a static field, and as a direct consequence, the experimentally detected signal is a combination of enhanced second and static field induced third order contributions. There is significant evidence in the literature of the importance/relative magnitude of this third order contribution, but no previous molecularly detailed approach existed to separately calculate the second and third order contributions. Thus, for the first time, a molecularly detailed time correlation function theory is derived here that allows for the second and third order contributions to sum frequency vibrational spectra to be individually determined. Further, a practical, molecular dynamics based, implementation procedure for the derived correlation functions that describe the third order phenomenon is also presented. This approach includes a novel generalization of point atomic polarizability models to calculate the hyperpolarizability of a molecular system. The full system hyperpolarizability appears in the time correlation functions responsible for third order contributions in the presence of a static field.

Tungsten diselenide for mode-locked erbium-doped fiber lasers with short pulse duration

NASA Astrophysics Data System (ADS)

Liu, Wenjun; Liu, Mengli; OuYang, Yuyi; Hou, Huanran; Ma, Guoli; Lei, Ming; Wei, Zhiyi

2018-04-01

In this paper, a WSe2 film prepared by chemical vapor deposition (CVD) is transferred onto a tapered fiber, and a WSe2 saturable absorber (SA) is fabricated. In order to measure the third-order optical nonlinearity of the WSe2, the Z-scan technique is applied. The modulation depth of the WSe2 SA is measured as being 21.89%. Taking advantage of the remarkable nonlinear absorption characteristic of the WSe2 SA, a mode-locked erbium-doped fiber laser is demonstrated at 1557.4 nm with a bandwidth of 25.8 nm and signal to noise ratio of 96 dB. To the best of our knowledge, the pulse duration of 163.5 fs is confirmed to be the shortest compared with previous mode-locked fiber lasers based on transition-metal dichalcogenides SAs. These results indicate that WSe2 is a powerful competitor in the application of ultrashort pulse lasers.

Deposition and weathering of Asian dust in Korea

NASA Astrophysics Data System (ADS)

Jeong, G.

2013-12-01

Paleolithic stone artifacts in Korea typically occur in brown clay-silt (BCS) sequences. The origin and depositional environment of these sequences are important for reconstructing the paleoenvironment as well as for establishing chronologies of artifact-bearing stratigraphic units. We investigated four BCS-bearing sections in foothills and river and marine terraces in Korea by applying quantitative mineralogical, geochemical, microtextural, and K-Ar isotopic methods. In all four sections, the lower units are colluvial and fluvial deposits strongly influenced by diverse local lithology, whereas the upper units are characterized by BCS units. Mineralogical/geochemical compositions, grain sizes, and colors converge into common properties in the upper BCS units in all sections. These common properties are consistent with the eastward trends of increasing weathering degree and grain size fining throughout the loess-paleosol sections of the Chinese Loess Plateau (CLP). K-Ar detrital ages of the sections also converge upward into a narrow range similar to the age ranges of the loess and paleosols in the CLP. The top BCS unit in the Jeongok section, the thickest section, is underlain by an additionally weathered BCS unit, with strong red chroma indicating a change from warm to cold climate. We did not observe any clear evidence of climatic changes in other thinner sections, which may be due to a superposition of cold-stage accumulation and warm-stage deep weathering. The common properties of the BCSs in Korean sections and their relationship to the CLP loess and paleosols indicate widespread deposition of Asian dust and subsequent weathering in the late Quaternary, forming BCS sequences. In this respect, the BCS sequences investigated here are considered to be the additionally weathered equivalents of the CLP loess-paleosol sequences, having been exposed to the high annual precipitation of the Korean Peninsula. Given the wide distribution of BCS sequences at Paleolithic sites throughout the Peninsula, the findings of this study are important for the ongoing debate surrounding the depositional environments of the Paleolithic deposits, and provide a foundation for the establishment of the chronological framework of the Paleolithic artifact-bearing layers and lithic assemblages.

Deposition and weathering of Asian dust in Paleolithic sites, Korea

NASA Astrophysics Data System (ADS)

Jeong, Gi Young; Choi, Jeong-Heon; Lim, Hyoun Soo; Seong, Chuntaek; Yi, Seon Bok

2013-10-01

Paleolithic stone artifacts in Korea typically occur in brown clay-silt (BCS) sequences. The origin and depositional environment of these sequences are important for reconstructing the paleoenvironment as well as for establishing chronologies of artifact-bearing stratigraphic units. We investigated four BCS-bearing sections in foothills and river and marine terraces in Korea by applying quantitative mineralogical, geochemical, microtextural, and K-Ar isotopic methods. In all four sections, the lower units are colluvial and fluvial deposits strongly influenced by diverse local lithology, whereas the upper units are characterized by BCS units. Mineralogical/geochemical compositions, grain sizes, and colors converge into common properties in the upper BCS units in all sections. These common properties are consistent with the eastward trends of increasing weathering degree and grain size fining throughout the loess-paleosol sections of the Chinese Loess Plateau (CLP). K-Ar detrital ages of the sections also converge upward into a narrow range similar to the age ranges of the loess and paleosols in the CLP. The top BCS unit in the Jeongok section, the thickest section, is underlain by an additionally weathered BCS unit, with strong red chroma indicating a change from warm to cold climate. We did not observe any clear evidence of climatic changes in other thinner sections, which may be due to a superposition of cold-stage accumulation and warm-stage deep weathering. The common properties of the BCSs in Korean sections and their relationship to the CLP loess and paleosols indicate widespread deposition of Asian dust and subsequent weathering in the late Quaternary, forming BCS sequences. In this respect, the BCS sequences investigated here are considered to be the additionally weathered equivalents of the CLP loess-paleosol sequences, having been exposed to the high annual precipitation of the Korean Peninsula. Given the wide distribution of BCS sequences at Paleolithic sites throughout the Peninsula, the findings of this study are important for the ongoing debate surrounding the depositional environments of the Paleolithic deposits, and provide a foundation for the establishment of the chronological framework of the Paleolithic artifact-bearing layers and lithic assemblages.

The use of sequence-based SSR mining for the development of a vast collection of microsatellites in Aquilegia Formosa

Treesearch

Brandon Schlautman; Vera Pfeiffer; Juan Zalapa; Johanne Brunet

2014-01-01

Numerous microsatellite markers were developed for Aquilegia formosafrom sequences deposited within the Expressed Sequence Tag (EST), Genomic Survey Sequence (GSS), and Nucleotide databases in NCBI. Microsatellites (SSRs) were identified and primers were designed for 9 SSR containing sequences in the Nucleotide database, 3803 sequences in the EST...

Blind third-order dispersion estimation based on fractional Fourier transformation for coherent optical communication

NASA Astrophysics Data System (ADS)

Yang, Lin; Guo, Peng; Yang, Aiying; Qiao, Yaojun

2018-02-01

In this paper, we propose a blind third-order dispersion estimation method based on fractional Fourier transformation (FrFT) in optical fiber communication system. By measuring the chromatic dispersion (CD) at different wavelengths, this method can estimation dispersion slope and further calculate the third-order dispersion. The simulation results demonstrate that the estimation error is less than 2 % in 28GBaud dual polarization quadrature phase-shift keying (DP-QPSK) and 28GBaud dual polarization 16 quadrature amplitude modulation (DP-16QAM) system. Through simulations, the proposed third-order dispersion estimation method is shown to be robust against nonlinear and amplified spontaneous emission (ASE) noise. In addition, to reduce the computational complexity, searching step with coarse and fine granularity is chosen to search optimal order of FrFT. The third-order dispersion estimation method based on FrFT can be used to monitor the third-order dispersion in optical fiber system.

Third-Order Memristive Morris-Lecar Model of Barnacle Muscle Fiber

NASA Astrophysics Data System (ADS)

Rajamani, Vetriveeran; Sah, Maheshwar Pd.; Mannan, Zubaer Ibna; Kim, Hyongsuk; Chua, Leon

This paper presents a detailed analysis of various oscillatory behaviors observed in relation to the calcium and potassium ions in the third-order Morris-Lecar model of giant barnacle muscle fiber. Since, both the calcium and potassium ions exhibit all of the characteristics of memristor fingerprints, we claim that the time-varying calcium and potassium ions in the third-order Morris-Lecar model are actually time-invariant calcium and potassium memristors in the third-order memristive Morris-Lecar model. We confirmed the existence of a small unstable limit cycle oscillation in both the second-order and the third-order Morris-Lecar model by numerically calculating the basin of attraction of the asymptotically stable equilibrium point associated with two subcritical Hopf bifurcation points. We also describe a comprehensive analysis of the generation of oscillations in third-order memristive Morris-Lecar model via small-signal circuit analysis and a subcritical Hopf bifurcation phenomenon.

Rapid transport of ash and sulfate from the 2011 Puyehue-Córdon Caulle (Chile) eruption to West Antarctica

NASA Astrophysics Data System (ADS)

Dowd, E.; Koffman, B. G.; Osterberg, E. C.; Ferris, D. G.; Hartman, L.; Wheatley, S.; Kurbatov, A.; Wong, G. J.; Markle, B. R.; Dunbar, N. W.; Kreutz, K. J.; Yates, M. G.

2017-12-01

The VEI 5 eruption of the Puyehue-Cordón Caulle volcanic complex (PCC) in central Chile, which began 4 June 2011, provides a rare opportunity to assess the rapid transport and deposition of sulfate and ash from a mid-latitude volcano to the Antarctic ice sheet. We present sulfate, microparticle concentrations of fine-grained ( 5 μm diameter) tephra, and geochemistry, which document the depositional sequence of volcanic products from the PCC eruption in West Antarctic snow and shallow firn. From the depositional phasing and duration of ash and sulfate peaks, we infer that transport occurred primarily through the troposphere but that ash and sulfate transport were decoupled. We use Hysplit back-trajectory modeling to assess circulation conditions in the weeks following the eruption, and find that atmospheric conditions favored mid-to-high latitude air parcel transport during 6-14 June and 4-18 July, 2011. We suggest that two discrete pulses of cryptotephra deposition relate to these intervals, and as such, constrain the sulfate transport and deposition lifespan to the 2-3 weeks following the eruption. Finally, we compare PCC depositional patterns to those of prominent low- and high-latitude eruptions in order to improve multiparameter-based efforts to identify "unknown source" eruptions in the ice core record. Our observations suggest that mid-latitude eruptions such as PCC can be distinguished from explosive tropical eruptions by differences in ash/sulfate phasing and in the duration of sulfate deposition, and from high-latitude eruptions by differences in particle size distribution and in cryptotephra geochemical composition.

Rapid transport of ash and sulfate from the 2011 Puyehue-Cordón Caulle (Chile) eruption to West Antarctica

NASA Astrophysics Data System (ADS)

Koffman, Bess G.; Dowd, Eleanor G.; Osterberg, Erich C.; Ferris, David G.; Hartman, Laura H.; Wheatley, Sarah D.; Kurbatov, Andrei V.; Wong, Gifford J.; Markle, Bradley R.; Dunbar, Nelia W.; Kreutz, Karl J.; Yates, Martin

2017-08-01

The Volcanic Explosivity Index 5 eruption of the Puyehue-Cordón Caulle volcanic complex (PCC) in central Chile, which began 4 June 2011, provides a rare opportunity to assess the rapid transport and deposition of sulfate and ash from a midlatitude volcano to the Antarctic ice sheet. We present sulfate, microparticle concentrations of fine-grained ( 5 μm diameter) tephra, and major oxide geochemistry, which document the depositional sequence of volcanic products from the PCC eruption in West Antarctic snow and shallow firn. From the depositional phasing and duration of ash and sulfate peaks, we infer that transport occurred primarily through the troposphere but that ash and sulfate transport were decoupled. We use Hybrid Single-Particle Lagrangian Integrated Trajectory back trajectory modeling to assess atmospheric circulation conditions in the weeks following the eruption and find that conditions favored southward air parcel transport during 6-14 June and 4-18 July 2011. We suggest that two discrete pulses of cryptotephra deposition relate to these intervals, and as such, constrain the sulfate transport and deposition lifespan to the 2-3 weeks following the eruption. Finally, we compare PCC depositional patterns to those of prominent low- and high-latitude eruptions in order to improve multiparameter-based efforts to identify "unknown source" eruptions in the ice core record. Our observations suggest that midlatitude eruptions such as PCC can be distinguished from explosive tropical eruptions by differences in ash/sulfate phasing and in the duration of sulfate deposition, and from high-latitude eruptions by differences in particle size distribution and in cryptotephra geochemical composition.

Analysis of SAW properties in ZnO/AlxGa1-xN/c-Al2O3 structures.

PubMed

Chen, Ying; Emanetoglu, Nuri William; Saraf, Gaurav; Wu, Pan; Lu, Yicheng; Parekh, Aniruddh; Merai, Vinod; Udovich, Eric; Lu, Dong; Lee, Dong S; Armour, Eric A; Pophristic, Milan

2005-07-01

Piezoelectric thin films on high acoustic velocity nonpiezoelectric substrates, such as ZnO, AlN, or GaN deposited on diamond or sapphire substrates, are attractive for high frequency and low-loss surface acoustic wave devices. In this work, ZnO films are deposited on AlxGa1-xN/c-Al2O3 (0 < or = chi < or = 1) substrates using the radio frequency (RF) sputtering technique. In comparison with a single AlxGa1-xN layer deposited on c-Al2O3 with the same total film thickness, a ZnO/AlxGa1-xN/c-Al2O3 multilayer structure provides several advantages, including higher order wave modes with higher velocity and larger electromechanical coupling coefficient (K2). The surface acoustic wave (SAW) velocities and coupling coefficients of the ZnO/AlxGa1-xN/c-Al2O3 structure are tailored as a function of the Al mole percentage in AlxGa1-xN films, and as a function of the ZnO (h1) to AlxGa1-xN (h2) thickness ratio. It is found that a wide thickness-frequency product (hf) region in which coupling is close to its maximum value, K(2)max, can be obtained. The K(2)max of the second order wave mode (h1 = h2) is estimated to be 4.3% for ZnO/GaN/c-Al2O3, and 3.8% for ZnO/AlN/c-Al2O3. The bandwidth of second and third order wave modes, in which the coupling coefficient is within +/- 0.3% of K(2)max, is calculated to be 820 hf for ZnO/GaN/c-Al2O3, and 3620 hf for ZnO/AlN/c-Al2O3. Thus, the hf region in which the coupling coefficient is close to the maximum value broadens with increasing Al content, while K(2)max decreases slightly. When the thickness ratio of AlN to ZnO increases, the K(2)max and hf bandwidth of the second and third higher wave modes increases. The SAW test devices are fabricated and tested. The theoretical and experimental results of velocity dispersion in the ZnO/AlxGa1-xN/c-Al2O3 structures are found to be well matched.

Environmental, depositional and cultural changes in the upper Pleistocene and early Holocene; the Cinglera del Capello Sequence (Capellades, Spain)

USGS Publications Warehouse

Vaquero, Manuel; Allué, Ethel; Bischoff, James L.; Burjachs, Francesc; Vallverdú, Josep

2013-01-01

The correlation between environmental and cultural changes is one of the primary archeological and paleoanthropological research topics. Analysis of ice and marine cores has yielded a high-resolution record of millennial-scale changes during the Late Pleistocene and Holocene eras. However, cultural changes are documented in low-resolution continental deposits; thus, their correlation with the millennial-scale climatic sequence is often difficult. In this paper, we present a rare occurrence in which a thick archeological sequence is associated with a high-resolution environmental record. The Cinglera del Capello is a tufa-draped cliff located in the northeastern Iberian Peninsula, 50 km west of Barcelona. This cliff harbors several rock-shelters with Late Pleistocene and Early Holocene deposits. Together, the deposits of four rock-shelters span from 7000 to 70,000 years ago and provide a high-resolution record of the environmental and human dynamics during this timespan. This record allows the correlation of the cultural and environmental changes. The multiproxy approach to the Cinglera evidence indicates that the main cultural stages of the Late Pleistocene and Early Holocene (Middle Paleolithic, Upper Paleolithic and Mesolithic) are associated with significant changes in the environmental and depositional contexts.

Topographical scattering of gravity waves

NASA Astrophysics Data System (ADS)

Miles, J. W.; Chamberlain, P. G.

1998-04-01

A systematic hierarchy of partial differential equations for linear gravity waves in water of variable depth is developed through the expansion of the average Lagrangian in powers of [mid R:][nabla del, Hamilton operator][mid R:] (h=depth, [nabla del, Hamilton operator]h=slope). The first and second members of this hierarchy, the Helmholtz and conventional mild-slope equations, are second order. The third member is fourth order but may be approximated by Chamberlain & Porter's (1995) ‘modified mild-slope’ equation, which is second order and comprises terms in [nabla del, Hamilton operator]2h and ([nabla del, Hamilton operator]h)2 that are absent from the mild-slope equation. Approximate solutions of the mild-slope and modified mild-slope equations for topographical scattering are determined through an iterative sequence, starting from a geometrical-optics approximation (which neglects reflection), then a quasi-geometrical-optics approximation, and on to higher-order results. The resulting reflection coefficient for a ramp of uniform slope is compared with the results of numerical integrations of each of the mild-slope equation (Booij 1983), the modified mild-slope equation (Porter & Staziker 1995), and the full linear equations (Booij 1983). Also considered is a sequence of sinusoidal sandbars, for which Bragg resonance may yield rather strong reflection and for which the modified mild-slope approximation is in close agreement with Mei's (1985) asymptotic approximation.

The Effect of Using a Visual Representation Tool in a Teaching-Learning Sequence for Teaching Newton's Third Law

ERIC Educational Resources Information Center

Savinainen, Antti; Mäkynen, Asko; Nieminen, Pasi; Viiri, Jouni

2017-01-01

This paper presents a research-based teaching-learning sequence (TLS) that focuses on the notion of interaction in teaching Newton's third law (N3 law) which is, as earlier studies have shown, a challenging topic for students to learn. The TLS made systematic use of a visual representation tool--an interaction diagram (ID)--highlighting…

Chemistry of Living Matter, Energy Capture & Growth, Parts Three & Four of an Integrated Science Sequence, Teacher's Guide, 1973 Edition.

ERIC Educational Resources Information Center

Portland Project Committee, OR.

This teacher's guide includes parts three and four of the four-part third year Portland Project, a three-year integrated secondary science curriculum sequence. The underlying intention of the third year is to study energy and its importance to life. Energy-related concepts considered in year one and two, and the concepts related to atomic…

Sedimentology and High Resolution Sequence Stratigraphy of the Middle Jurassic Dhruma Formation Carbonates Outcrops in the Central Saudi Arabia

NASA Astrophysics Data System (ADS)

Yousif, Ibrahim; Abdullatif, Osman; Makkawi, Mohammed; Abdulghani, Waleed

2017-04-01

This study investigates the microfacies and sequence stratigraphic frame work of the Middle Jurassic Dhruma Formation in outcrops in central Saudi Arabia. The study contributes to the efforts to understand and enhance local and regional stratigraphic relationship and correlation of the Jurassic carbonate sequences and their significance to reservoir description and prediction in the subsurcae. The study describes and characterizes the sedimentology, microfacies and the stratigraphy of Dhruma Formation from outcrop sections having a total thickness of 70 m. Detailed microfacies and high-resolution stratigraphical analysis were carried out to determine microfacies, cyclicity, sequences and staking pattern. The study revealed ten lithofacies namely: oolitic grainstone,bioclastic oolitic grainstone, oolitic grapestone, bioclastic grainstone,foraminiferal packstone, echinoderm packstone, peloidal packstone to grainstone,skeletal wackestone to packstone, mudstone, and marlstone.These lithofacies were grouped into five lithofacies associations that deposited on a carbonate ramp setting. The depositional environment ranging from low energy lagoonal setting to high-energy shoals and banks to low energy outer ramp setting. Five high-resolution composite sequences have been defined and each sequence is composed at the bottom of intercalated mudstone/wackestone that passing up into grainstone lithofacies.The composite sequences range in thickness from 7 to 15 m, while the parasequences range from 0.5 to 1.5 m. The composite sequences extend laterally for a distance of more than 350 m. The overall composite section shows a shallowing upward succession of the 4th to the 5th order high-resolution sequences.The dominant lithofacies are the grainy ones, which constitute 30%, 50% and 80% of the studied sections. Furthermore, the parasequences thickness and their bio-components are increasing towards the top. The muddy lithofacies intensively affected the vertical continuity of the lower reservoir interval compared to the upper interval. Detailed examination of thin-sections reflects a clear and well-developed reservoir interval in the uppermost part of the section, which is dominated by peloidal packstone and grainstone.The findings of this high-resolution outcrop analog might help to understand and predict lithofacies, stratigraphic heirachies and correlations of Dhruma Formation within the interwell spacing. Moreover, this study might also contribute to better reservoir description and assessment of its quality and architecture in subsurface equivalent reservoirs.

Workflow and web application for annotating NCBI BioProject transcriptome data.

PubMed

Vera Alvarez, Roberto; Medeiros Vidal, Newton; Garzón-Martínez, Gina A; Barrero, Luz S; Landsman, David; Mariño-Ramírez, Leonardo

2017-01-01

The volume of transcriptome data is growing exponentially due to rapid improvement of experimental technologies. In response, large central resources such as those of the National Center for Biotechnology Information (NCBI) are continually adapting their computational infrastructure to accommodate this large influx of data. New and specialized databases, such as Transcriptome Shotgun Assembly Sequence Database (TSA) and Sequence Read Archive (SRA), have been created to aid the development and expansion of centralized repositories. Although the central resource databases are under continual development, they do not include automatic pipelines to increase annotation of newly deposited data. Therefore, third-party applications are required to achieve that aim. Here, we present an automatic workflow and web application for the annotation of transcriptome data. The workflow creates secondary data such as sequencing reads and BLAST alignments, which are available through the web application. They are based on freely available bioinformatics tools and scripts developed in-house. The interactive web application provides a search engine and several browser utilities. Graphical views of transcript alignments are available through SeqViewer, an embedded tool developed by NCBI for viewing biological sequence data. The web application is tightly integrated with other NCBI web applications and tools to extend the functionality of data processing and interconnectivity. We present a case study for the species Physalis peruviana with data generated from BioProject ID 67621. URL: http://www.ncbi.nlm.nih.gov/projects/physalis/. Published by Oxford University Press 2017. This work is written by US Government employees and is in the public domain in the US.

Submarine fan facies of Upper Cretaceous Strata, Southern San Rafael Mountains, Santa Barbara County, California

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

Toyne, C.D.

1986-04-01

A 2900-m thick Campanian-Maestrichtian(.) turbidite sequence in Upper Mono Creek Canyon is interpreted to be a progradational submarine fan complex comprised of outer fan, middle fan, inner fan, and slope facies. The basal 600 m of the section consists of thinly bedded, laterally continuous fine sandstones, siltstones, and mudstones (mainly Mutti and Ricci Lucci facies D), interpreted to be outer fan interlobe and lobe-fringe deposits. These are punctuated by infrequent medium to very thickly bedded, flat-based, fine to coarse sandstones (facies C and B), which commonly coarsen and thicken upward, and are interpreted to be depositional lobes. Overlying these depositsmore » are approximately 1400 m of middle fan deposits composed of frequent lenticular, commonly channelized and amalgamated, thickly bedded, fine to very coarse sandstones (facies C and B) organized in fining- and thinning-upward sequences, interpreted to be braided-channel deposits. These alternate with less common nonchannelized coarsening- and thickening-upward sequences suggestive of lobe-apical cycles. These multistory sand deposits are nested within thick intervals of fine sandstones, siltstones, and mudstones (facies C and D), interpreted to be levee, crevasse-splay, and interchannel deposits. Interfingered with and overlying these deposits are approximately 500 m of fining- and thinning-upward or noncyclic, erosionally based, commonly amalgamated, very thickly bedded, medium to very coarse sandstones, pebbly sandstones, and conglomerates (facies A and B), interpreted to be inner fan deposits. Intercalated within this facies, infrequent, laterally discontinuous, thin to thickly bedded, fine to coarse sandstones, siltstones, and mudstones exist, interpreted to be interchannel, levee, and possibly channel-fill deposits.« less

The transitional depositional environment and sequence stratigraphy of Chasma Boreale

NASA Astrophysics Data System (ADS)

Brothers, S. C.; Kocurek, G.

2018-07-01

The depositional system within Chasma Boreale is unique in that it contains active aeolian environments, expressed as dune fields, and active cryosphere environments, present as layered ice deposits, as well as environments that transition between these. This work presents a new analysis of the Chasma Boreale sediment system that creates an interpretative framework addressing: (a) controls on the balance between aeolian and cryospheric processes in the modern depositional system, (b) the stratigraphic architecture of related sedimentary deposits, and (c) processes of sediment accumulation and preservation. Images from Context Camera (CTX; 6 m/pixel) are used to classify and map sedimentary environments, surfaces, and deposits on the reentrant floor, to refine the established geologic map of the reentrant, and to infer the stratigraphic record of the accumulation from Chasma Boreale's depositional system. A spectrum of sedimentary environments occurring between those dominated by aeolian and by cryospheric processes are identified. Through time, the boundaries of these sedimentary environments have shifted, resulting in complex lateral changes in the configuration of sedimentary environments on the reentrant's floor. Vertically, the stratigraphic record is characterized by the punctuation of sandy aeolian deposits by icy surfaces that indicate episodes of ice growth that preserve underlying deposits, resulting in accumulation. Stabilized icy surfaces occur at multiple vertical (temporal) scales and lateral extents, suggesting the influence of both regional climate change due to allogenic forcing, as well as autogenic dynamics within the transitional system. These observations demonstrate that the Chasma Boreale accumulation can be interpreted in an aeolian sequence stratigraphic framework. This work contributes the first detailed description of the processes forming polar aeolian sequences, with an emphasis on the competing and complementary dynamics between aeolian and cryospheric systems.

Single-Molecule Electrical Random Resequencing of DNA and RNA

NASA Astrophysics Data System (ADS)

Ohshiro, Takahito; Matsubara, Kazuki; Tsutsui, Makusu; Furuhashi, Masayuki; Taniguchi, Masateru; Kawai, Tomoji

2012-07-01

Two paradigm shifts in DNA sequencing technologies--from bulk to single molecules and from optical to electrical detection--are expected to realize label-free, low-cost DNA sequencing that does not require PCR amplification. It will lead to development of high-throughput third-generation sequencing technologies for personalized medicine. Although nanopore devices have been proposed as third-generation DNA-sequencing devices, a significant milestone in these technologies has been attained by demonstrating a novel technique for resequencing DNA using electrical signals. Here we report single-molecule electrical resequencing of DNA and RNA using a hybrid method of identifying single-base molecules via tunneling currents and random sequencing. Our method reads sequences of nine types of DNA oligomers. The complete sequence of 5'-UGAGGUA-3' from the let-7 microRNA family was also identified by creating a composite of overlapping fragment sequences, which was randomly determined using tunneling current conducted by single-base molecules as they passed between a pair of nanoelectrodes.

Late Holocene stratigraphy of the Tetimpa archaeological sites, northeast flank of Popocatepetl volcano, central Mexico

USGS Publications Warehouse

Panfil, M.S.; Gardner, T.W.; Hirth, K.G.

1999-01-01

Late Holocene (240 km2 on the east side of the volcano with >25 cm of tephra. Lavas from eruptive sequence I dammed drainage in the lowland area near the town of San Nicolas and caused local upstream deposition of as much as 30 m of lacustrine silts, clays, and sands. These lacustrine deposits record an eruptive hiatus for the Tetimpa area of about 750 14C yr: between ca. 2100 and ca. 1350 yr B.P., no major tephras were deposited in the Tetimpa area. In upland areas, this time period is represented by an unconformity and by Entisols formed in the top of pumice deposits and lavas from eruptive sequence I. Artifacts, agricultural furrows, and dwellings record human reoccupation of this surface. At the end of this hiatus, several lahars were deposited above the lacustrine sequence and locally above the Entisol in upland positions adjacent to streams. Between ca. 1350 and ca. 1200 yr B.P., tephras from eruptive sequence II buried these paleosols, occupation sites, lacustrine sediments, and lahars. Andesitic (~62% SiO2) pumice lapilli deposits in the Tetimpa area record three pumice-fall eruptions directed northeast and east of the crater. The first and smallest of these (maximum Tetimpa area thickness = 12 cm; >52 km2 covered by >25 cm) took place at ca. 1350 yr B.P. and was accompanied by pyroclastic surge events preserved in the Tetimpa area by charcoal, sand waves, and cross-stratified sand-sized tephra. At ca. 1200 yr B.P., the products of two Plinian-style events and additional pyroclastic surges reached the Tetimpa area. The largest of these tephra-fall events covered the Tetimpa area with 0.5-1 m of tephra and blanketed an area of >230 km2 with a thickness of >25 cm. The Tetimpa record confirms two of the four periods of explosive volcanism recognized by studies conducted around Popocatepetl in the past 30 yr. Eruptive sequence I corresponds to the explosive period between 2100 and 2500 yr B.P., and eruptive sequence II corresponds to the period between 900 and 1400 yr B.P. The archaeology and lacustrine stratigraphy of the Tetimpa area help constrain the timing of the Plinian phase of eruptive sequence I to ca. 2100 yr B.P. and suggest that the pumice-fall eruptions of eruptive sequence II took place in at least two intervals between ca. 1350 and ca. 1200 yr B.P.

Dolni Vestonice (Czech Republic) an intermédiate loess series between Western and eastern European records

NASA Astrophysics Data System (ADS)

Rousseau, D.; Antoine, P.; Hatte, C.; Lagroix, F.; Fuchs, M.; Moine, O.; Gauthier, C.; Svoboda, J.; Lisa, L.

2010-12-01

Previous investigations on western and eastern European loess series have shown similarities at least for the main loess deposition during the last climate cycle, recording North-Atlantic abrupt climate changes, the Dansgaard-Oeschger and Heinrich events. To address the question of how such record occurred through modeling experiments (Sima et al., QSR, 2009), we need reference series located in an intermediary position between the Nussloch (Germany - Antoine et al, QI 2001, QSR, 2009; Rousseau et al, GRL 2007) and Stayky (Ukraine -Rousseau et al, Clim Past D 2010) loess series at about 50°N latitude, location of the main deposits. The key sequence of Dolni Vestonice in southern Czech Republic, had been investigated previously and described by many authors since 1961, and more especially by G Kukla and B Klima. Here we present the preliminary results of the new study of this key sequence by a multidisciplinary study, supported by ANR-ACTES project, combining the detailed stratigraphy, AMS 14C and IRSL dating, rock magnetic property, grain size, d13C and mollusks analyses. We applied the same sampling protocol than previously developed, by carefully cleaning the sequence on a vertical panel, 15m high and 5m wide in order to have parallel samples (on continuous columns) easily comparable. The results show similar patterns, high frequency variations of the different proxies in the upper part of the record corresponding to MIS 3 and 2, as observed in western and eastern European sequences supporting then our assumption of the recording of N Atlantic abrupt changes over Europe. Other interesting variations are clearly demonstrated for every proxy making these results remarkable new data for individual in deep studies. Moreover our detailed investigation also shows new data about abrupt dust events, markers, in the lower part of the sequence, and previously interpreted as strong dust events, and how they appear within sedimentary cycles linked to the cyclicity at the base of the last climate cycle.

Open resource metagenomics: a model for sharing metagenomic libraries.

PubMed

Neufeld, J D; Engel, K; Cheng, J; Moreno-Hagelsieb, G; Rose, D R; Charles, T C

2011-11-30

Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM(2)BL [1]). The CM(2)BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the academic research community and industry. This article invites the scientific community to adopt this philosophy of open resource metagenomics to extend the utility of functional metagenomics beyond initial publication, circumventing the need to start from scratch with each new research project.

Open resource metagenomics: a model for sharing metagenomic libraries

PubMed Central

Neufeld, J.D.; Engel, K.; Cheng, J.; Moreno-Hagelsieb, G.; Rose, D.R.; Charles, T.C.

2011-01-01

Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM2BL [1]). The CM2BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the academic research community and industry. This article invites the scientific community to adopt this philosophy of open resource metagenomics to extend the utility of functional metagenomics beyond initial publication, circumventing the need to start from scratch with each new research project. PMID:22180823

Spatiotemporal sedimentological and petrophysical characterization of El Gueria reservoir (Ypresian) in sFAX and Gulf of Gabes Basins (SE-Tunisia)

NASA Astrophysics Data System (ADS)

Nadhem, Kassabi; Zahra, Njahi; Ménendez, Béatriz; Salwa, Jeddi; Jamel, Touir

2017-06-01

El Gueria carbonate Formation (Ypresian) in Tunisia is a proven hydrocarbon reservoir. In the Gulf of Gabes, El Gueria reservoir consists mainly of a nummulitic limestone which is developed in an inner shelf environment. In order to characterize the depositional facies evolution and the petrophysical parameters, and to understand the origin of heterogeneity of El Gueria reservoir, we firstly conducted a sedimentological and a sequence stratigraphy study of this Formation in more than 10 wells especially in P1, then we established a detailed petrophysical study of El Gueria reservoir in P1, P3c and P7d cores. Based on lithostratigraphic and gamma ray correlations of an important number of wells in the study area, a detailed sedimentological study has been established. This latter shows that: (i): The Ypresien deposits are deposited in an inner shelf (El Gueria Formation) in the south and in an outer shelf (Boudabbous Formation) in the north of the study area with the form of horsts and grabens, (ii): 3 distinct members and 7 principal facies within El Gueria Formation have been distinguished. The coupling of data logging and data of the P1 core shows that the El Gueria deposits include 10 transgressive-regressive depositional sequences, while showing from bottom to top a broad regressive tendancy from a subtidal domain during the early Ypresian to an intertidal domain during the middle Ypresian reaching the supratidal environnement during the late Ypresian-early Lutetian. The petrophysical parameters (porosity and permeability) of El Gueria reservoir vary in time and space (laterally and vertically variation) following the deposit environment variation. Particularly, the porosity variation is controlled by eustatic cycles so that high porosities are linked with transgressive phases and low porosities with regressive phases. In addition, the vertical evolution of porosity through the El Gueria reservoir varies following the (i) deposit environments, (ii) type and morphology of nummulites such as large nummulites are more porous than small nummulites and nummilithoclastes (iii) matrix and cement such as micrite are more porous than sparite (iv) microfacies and diagenetic structures (Fractures, stylolithic seals …) such as the fractured wackstone are the most porous and permeable.

Apparatus for improved DNA sequencing

DOEpatents

Douthart, R.J.; Crowell, S.L.

1996-05-07

This invention is a means for the rapid sequencing of DNA samples. More specifically, it consists of a new design direct blotting electrophoresis unit. The DNA sequence is deposited on a membrane attached to a rotating drum. Initial data compaction is facilitated by the use of a machined multi-channeled plate called a ribbon channel plate. Each channel is an isolated mini gel system much like a gel filled capillary. The system as a whole, however, is in a slab gel like format with the advantages of uniformity and easy reusability. The system can be used in different embodiments. The drum system is unique in that after deposition the drum rotates the deposited DNA into a large non-buffer open space where processing and detection can occur. The drum can also be removed in toto to special workstations for downstream processing, multiplexing and detection. 18 figs.

Apparatus for improved DNA sequencing

DOEpatents

Douthart, Richard J.; Crowell, Shannon L.

1996-01-01

This invention is a means for the rapid sequencing of DNA samples. More specifically, it consists of a new design direct blotting electrophoresis unit. The DNA sequence is deposited on a membrane attached to a rotating drum. Initial data compaction is facilitated by the use of a machined multi-channeled plate called a ribbon channel plate. Each channel is an isolated mini gel system much like a gel filled capillary. The system as a whole, however, is in a slab gel like format with the advantages of uniformity and easy reusability. The system can be used in different embodiments. The drum system is unique in that after deposition the drum rotates the deposited DNA into a large non-buffer open space where processing and detection can occur. The drum can also be removed in toto to special workstations for downstream processing, multiplexing and detection.

Geologic map and upper Paleozoic stratigraphy of the Marble Canyon area, Cottonwood Canyon quadrangle, Death Valley National Park, Inyo County, California

USGS Publications Warehouse

Stone, Paul; Stevens, Calvin H.; Belasky, Paul; Montañez, Isabel P.; Martin, Lauren G.; Wardlaw, Bruce R.; Sandberg, Charles A.; Wan, Elmira; Olson, Holly A.; Priest, Susan S.

2014-01-01

This geologic map and pamphlet focus on the stratigraphy, depositional history, and paleogeographic significance of upper Paleozoic rocks exposed in the Marble Canyon area in Death Valley National Park, California. Bedrock exposed in this area is composed of Mississippian to lower Permian (Cisuralian) marine sedimentary rocks and the Jurassic Hunter Mountain Quartz Monzonite. These units are overlain by Tertiary and Quaternary nonmarine sedimentary deposits that include a previously unrecognized tuff to which we tentatively assign an age of late middle Miocene (~12 Ma) based on tephrochronologic analysis, in addition to the previously recognized Pliocene tuff of Mesquite Spring. Mississippian and Pennsylvanian rocks in the Marble Canyon area represent deposition on the western continental shelf of North America. Mississippian limestone units in the area (Tin Mountain, Stone Canyon, and Santa Rosa Hills Limestones) accumulated on the outer part of a broad carbonate platform that extended southwest across Nevada into east-central California. Carbonate sedimentation was interrupted by a major eustatic sea-level fall that has been interpreted to record the onset of late Paleozoic glaciation in southern Gondwana. Following a brief period of Late Mississippian clastic sedimentation (Indian Springs Formation), a rise in eustatic sea level led to establishment of a new carbonate platform that covered most of the area previously occupied by the Mississippian platform. The Pennsylvanian Bird Spring Formation at Marble Canyon makes up the outer platform component of ten third-order (1 to 5 m.y. duration) stratigraphic sequences recently defined for the regional platform succession. The regional paleogeography was fundamentally changed by major tectonic activity along the continental margin beginning in middle early Permian time. As a result, the Pennsylvanian carbonate shelf at Marble Canyon subsided and was disconformably overlain by lower Permian units (Osborne Canyon and Darwin Canyon Formations) representing part of a deep-water turbidite basin filled primarily by fine-grained siliciclastic sediment derived from cratonal sources to the east. Deformation and sedimentation along the western part of this basin continued into late Permian time. The culminating phase was part of a regionally extensive late Permian thrust system that included the Marble Canyon thrust fault just west of the present map area.

Influence of second-order bracket-archwire misalignments on loads generated during third-order archwire rotation in orthodontic treatment.

PubMed

Romanyk, Dan L; George, Andrew; Li, Yin; Heo, Giseon; Carey, Jason P; Major, Paul W

2016-05-01

To investigate the influence of a rotational second-order bracket-archwire misalignment on the loads generated during third-order torque procedures. Specifically, torque in the second- and third-order directions was considered. An orthodontic torque simulator (OTS) was used to simulate the third-order torque between Damon Q brackets and 0.019 × 0.025-inch stainless steel archwires. Second-order misalignments were introduced in 0.5° increments from a neutral position, 0.0°, up to 3.0° of misalignment. A sample size of 30 brackets was used for each misalignment. The archwire was then rotated in the OTS from its neutral position up to 30° in 3° increments and then unloaded in the same increments. At each position, all forces and torques were recorded. Repeated-measures analysis of variance was used to determine if the second-order misalignments significantly affected torque values in the second- and third-order directions. From statistical analysis of the experimental data, it was found that the only statistically significant differences in third-order torque between a misaligned state and the neutral position occurred for 2.5° and 3.0° of misalignment, with mean differences of 2.54 Nmm and 2.33 Nmm, respectively. In addition, in pairwise comparisons of second-order torque for each misalignment increment, statistical differences were observed in all comparisons except for 0.0° vs 0.5° and 1.5° vs 2.0°. The introduction of a second-order misalignment during third-order torque simulation resulted in statistically significant differences in both second- and third-order torque response; however, the former is arguably clinically insignificant.

Spherical integral transforms of second-order gravitational tensor components onto third-order gravitational tensor components

NASA Astrophysics Data System (ADS)

Šprlák, Michal; Novák, Pavel

2017-02-01

New spherical integral formulas between components of the second- and third-order gravitational tensors are formulated in this article. First, we review the nomenclature and basic properties of the second- and third-order gravitational tensors. Initial points of mathematical derivations, i.e., the second- and third-order differential operators defined in the spherical local North-oriented reference frame and the analytical solutions of the gradiometric boundary-value problem, are also summarized. Secondly, we apply the third-order differential operators to the analytical solutions of the gradiometric boundary-value problem which gives 30 new integral formulas transforming (1) vertical-vertical, (2) vertical-horizontal and (3) horizontal-horizontal second-order gravitational tensor components onto their third-order counterparts. Using spherical polar coordinates related sub-integral kernels can efficiently be decomposed into azimuthal and isotropic parts. Both spectral and closed forms of the isotropic kernels are provided and their limits are investigated. Thirdly, numerical experiments are performed to test the consistency of the new integral transforms and to investigate properties of the sub-integral kernels. The new mathematical apparatus is valid for any harmonic potential field and may be exploited, e.g., when gravitational/magnetic second- and third-order tensor components become available in the future. The new integral formulas also extend the well-known Meissl diagram and enrich the theoretical apparatus of geodesy.

Shelf-geometry response to changes in relative sea level on a mixed carbonate siliciclastic shelf in the Guyana Basin

NASA Astrophysics Data System (ADS)

Campbell, A. Ewan

2005-04-01

Differences in the shelf-margin geometry for various depositional regimes show how siliciclastic and carbonate margins respond differently to changes in accommodation space. During the Cenozoic, sequences of carbonate and siliciclastic sediment were deposited in the Guyana Basin on the passive continental margin of NE South America. Study of the sequence geometries reveal significantly different geometric responses to changes in relative sea level of intervals dominated by carbonates to intervals dominated by siliciclastics. Using the geometrical shelf break as a reference point, aggradation and progradation rates for the carbonate and siliciclastic depositional systems were measured. In siliciclastics, the lateral position of the margin remains roughly stationary with relative sea-level rises in the order of 30 m/My. At higher rates the margin retreats at lower rates it progrades. Carbonate margins remain stationary or slightly progradational even with relative sea-level rises of up to 100 m/My, the fastest rates observed in this study. This illustrates the strong tendency of carbonate platforms to stack their margins and keep up with relative rises in sea level, rather than gradually retreat landward as do siliciclastics. This observation may explain why carbonate platforms preferentially try to defend a margin prior to ultimate backstepping. The high aggradation potential of carbonate margins also gives onlap and downlap termination patterns on seismic profiles where carbonate platforms develop on sloping siliciclastic shelves. The resulting unconformities are a result of differences in sediment dispersal between the two systems and not necessarily from changes of relative sea level.

78 FR 38450 - Agency Information Collection Activities; Information Collection Renewal; Reverse Mortgage...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-26

..., internal controls, and third party risk management. \\1\\ 74 FR 66652. \\2\\ 75 FR 50801. Prior to the... DEPARTMENT OF THE TREASURY Office of the Comptroller of the Currency FEDERAL DEPOSIT INSURANCE...: Office of the Comptroller of the Currency, Treasury (OCC); Federal Deposit Insurance Corporation (FDIC...

Optimising the use of marine tephrochronology in the North Atlantic: a detailed investigation of the Faroe Marine Ash Zones II, III and IV

NASA Astrophysics Data System (ADS)

Griggs, Adam J.; Davies, Siwan M.; Abbott, Peter M.; Rasmussen, Tine L.; Palmer, Adrian P.

2014-12-01

Tephrochronology is central to the INTIMATE goals for testing the degree of climatic synchroneity during abrupt climatic events that punctuated the last glacial period. Since their identification in North Atlantic marine sequences, the Faroe Marine Ash Zone II (FMAZ II), FMAZ III and FMAZ IV have received considerable attention due to their potential for high-precision synchronisation with the Greenland ice-cores. In order to optimise the use of these horizons as isochronous markers, a detailed re-investigation of their geochemical composition, sedimentology and the processes that deposited each ash zone is presented. Shard concentration profiles, geochemical homogeneity and micro-sedimentological structures are investigated for each ash zone preserved within core JM11-19PC, retrieved from the southeastern Norwegian Sea on the central North Faroe Slope. This approach allows a thorough assessment of primary ash-fall preservation and secondary depositional features and demonstrates its value for assessing depositional integrity in the marine environment. Results indicate that the FMAZ II and IV are well-resolved primary deposits that can be used as isochrons for high-precision correlation studies. We outline key recommendations for future marine tephra studies and provide a protocol for optimising the application of tephrochronology to meet the INTIMATE synchronisation goals.

Estimating the deposition of urban atmospheric NO2 to the urban forest in Portland-Vancouver USA

NASA Astrophysics Data System (ADS)

Rao, M.; Gonzalez Abraham, R.; George, L. A.

2016-12-01

Cities are hotspots of atmospheric emissions of reactive nitrogen oxides, including nitrogen dioxide (NO2), a US EPA criteria pollutant that affects both human and environmental health. A fraction of this anthropogenic, atmospheric NO2 is deposited onto the urban forest, potentially mitigating the impact of NO2 on respiratory health within cities. However, the role of the urban forest in removal of atmospheric NO2 through deposition has not been well studied. Here, using an observationally-based statistical model, we first estimate the reduction of NO2 associated with the urban forest in Portland-Vancouver, USA, and the health benefits accruing from this reduction. In order to assess if this statistically observed reduction in NO2 associated with the urban forest is consistent with deposition, we then compare the amount of NO2 removed through deposition to the urban forest as estimated using a 4km CMAQ simulation. We further undertake a sensitivity analysis in CMAQ to estimate the range of NO2removed as a function of bulk stomatal resistance. We find that NO2 deposition estimated by CMAQ accounts for roughly one-third of the reduction in NO2 shown by the observationally-based statistical model (Figure). Our sensitivity analysis shows that a 3-10 fold increase in the bulk stomatal resistance parameter in CMAQ would align CMAQ-estimated deposition with the statistical model. The reduction of NO2 by the urban forest in the Portland-Vancouver area may yield a health benefit of at least $1.5 million USD annually, providing strong motivation to better understand the mechanism through which the urban forest may be removing air pollutants such as NO2and thus helping create healthier urban atmospheres. Figure: Comparing the amount of NO2 deposition as estimated by CMAQ and the observationally-based statistical model (LURF). Each point corresponds to a single 4 x 4km CMAQ grid cell.

Complex dynamics of small-moderate volcanic events: the example of the 2011 rhyolitic Cordón Caulle eruption, Chile

NASA Astrophysics Data System (ADS)

Pistolesi, Marco; Cioni, Raffaello; Bonadonna, Costanza; Elissondo, Manuela; Baumann, Valerie; Bertagnini, Antonella; Chiari, Laura; Gonzales, Rafael; Rosi, Mauro; Francalanci, Lorella

2015-01-01

After decades of repose, Puyehue-Cordón Caulle Volcano (Chile) erupted in June 2011 following a month of continuously increasing seismic activity. The eruption dispersed a large volume of rhyolitic tephra over a wide area and was characterized by complex dynamics. During the initial climactic phase of the eruption (24-30 h on 4-5 June), 11-14-km-high plumes dispersed most of the erupted tephra eastward towards Argentina, reaching as far as the Atlantic Ocean. This first eruptive phase was followed by activity of lower intensity, leading to the development of a complex stratigraphic sequence, mainly due to rapid shifts in wind direction and eruptive style. The resulting tephra deposits consist of 13 main layers grouped into four units. Each layer was characterized based on its dispersal direction, sedimentological features, and on the main characteristics of the juvenile fraction (texture, density, petrography, chemistry). The lowest part of the eruptive sequence (Unit I), corresponding to the tephra emitted between 4 and 5 June, is composed of alternating lapilli layers with a total estimated volume of ca. 0.75 km3; these layers record the highest intensity phase, during which a bent-over plume dispersed tephra towards the southeast-east, with negligible up-wind sedimentation. Products emitted during 5-6 June (Unit II) signaled an abrupt shift in wind direction towards the north, leading to the deposition of a coarse ash deposit in the northern sector (ca. 0.21 km3 in volume), followed by a resumption of easterly directed winds. A third phase (Unit III) began on 7 June and resulted in tephra deposits in the eastern sector and ballistic bombs around the vent area. A final phase (Unit IV) started after 15 June and was characterized by the emission of fine-grained white tephra from ash-charged plumes during low-level activity and the extrusion of a viscous lava flow. Timing and duration of the first eruptive phases were constrained based on comparison of the dispersal of the main tephra layers with satellite images, showing that most of the tephra was emitted during the first 72 h of the event. The analyzed juvenile material tightly clusters within the rhyolitic field, with negligible chemical variations through the eruptive sequence. Textural observations reveal that changes in eruption intensity (and consequently in magma ascent velocity within the conduit) and complex interactions between gas-rich and gas-depleted magma portions during ascent resulted in vesicular clasts with variable degrees of shear localization, and possibly in the large heterogeneity of the juvenile material.

Comparative genomics of Lupinus angustifolius gene-rich regions: BAC library exploration, genetic mapping and cytogenetics

PubMed Central

2013-01-01

Background The narrow-leafed lupin, Lupinus angustifolius L., is a grain legume species with a relatively compact genome. The species has 2n = 40 chromosomes and its genome size is 960 Mbp/1C. During the last decade, L. angustifolius genomic studies have achieved several milestones, such as molecular-marker development, linkage maps, and bacterial artificial chromosome (BAC) libraries. Here, these resources were integratively used to identify and sequence two gene-rich regions (GRRs) of the genome. Results The genome was screened with a probe representing the sequence of a microsatellite fragment length polymorphism (MFLP) marker linked to Phomopsis stem blight resistance. BAC clones selected by hybridization were subjected to restriction fingerprinting and contig assembly, and 232 BAC-ends were sequenced and annotated. BAC fluorescence in situ hybridization (BAC-FISH) identified eight single-locus clones. Based on physical mapping, cytogenetic localization, and BAC-end annotation, five clones were chosen for sequencing. Within the sequences of clones that hybridized in FISH to a single-locus, two large GRRs were identified. The GRRs showed strong and conserved synteny to Glycine max duplicated genome regions, illustrated by both identical gene order and parallel orientation. In contrast, in the clones with dispersed FISH signals, more than one-third of sequences were transposable elements. Sequenced, single-locus clones were used to develop 12 genetic markers, increasing the number of L. angustifolius chromosomes linked to appropriate linkage groups by five pairs. Conclusions In general, probes originating from MFLP sequences can assist genome screening and gene discovery. However, such probes are not useful for positional cloning, because they tend to hybridize to numerous loci. GRRs identified in L. angustifolius contained a low number of interspersed repeats and had a high level of synteny to the genome of the model legume G. max. Our results showed that not only was the gene nucleotide sequence conserved between soybean and lupin GRRs, but the order and orientation of particular genes in syntenic blocks was homologous, as well. These findings will be valuable to the forthcoming sequencing of the lupin genome. PMID:23379841

Mg/Ti multilayers: Structural and hydrogen absorption properties

NASA Astrophysics Data System (ADS)

Baldi, A.; Pálsson, G. K.; Gonzalez-Silveira, M.; Schreuders, H.; Slaman, M.; Rector, J. H.; Krishnan, G.; Kooi, B. J.; Walker, G. S.; Fay, M. W.; Hjörvarsson, B.; Wijngaarden, R. J.; Dam, B.; Griessen, R.

2010-06-01

Mg-Ti alloys have uncommon optical and hydrogen absorbing properties, originating from a “spinodal-like” microstructure with a small degree of chemical short-range order in the atomic distribution. In the present study we artificially engineer short-range order by depositing Pd-capped Mg/Ti multilayers with different periodicities. Notwithstanding the large lattice mismatch between Mg and Ti, the as-deposited metallic multilayers show good structural coherence. On exposure to H2 gas a two-step hydrogenation process occurs with the Ti layers forming the hydride before Mg. From in situ measurements of the bilayer thickness Λ at different hydrogen pressures, we observe large out-of-plane expansions of Mg and Ti layers on hydrogenation, indicating strong plastic deformations in the films and a consequent shortening of the coherence length. On unloading at room temperature in air, hydrogen atoms remain trapped in the Ti layers due to kinetic constraints. Such loading/unloading sequence can be explained in terms of the different thermodynamic properties of hydrogen in Mg and Ti, as shown by diffusion calculations on a model multilayered systems. Absorption isotherms measured by hydrogenography can be interpreted as a result of the elastic clamping arising from strongly bonded Mg/Pd and broken Mg/Ti interfaces.

Late Neogene sedimentary facies and sequences in the Pannonian Basin, Hungary

USGS Publications Warehouse

Juhasz, E.; Phillips, L.; Muller, P.; Ricketts, B.; Toth-Makk, A.; Lantos, M.; Kovacs, L.O.

1999-01-01

This paper is part of the special publication No.156, The Mediterranean basins: Tertiary extension within the Alpine Orogen. (eds B.Durand, L. Jolivet, F.Horvath and M.Seranne). Detailed sedimentological, facies and numerical cycle analysis, combined with magnetostratigraphy, have been made in a number of boreholes in the Pannonian Basin, in order to study the causes of relative water-level changes and the history of the basin subsidence. Subsidence and infilling of the Pannonian Basin, which was an isolated lake at that time occurred mainly during the Late Miocene and Pliocene. The subsidence history was remarkably different in the individual sub-basins: early thermal subsidence was interrupted in the southern part of the basin, while high sedimentation rate and continuous subsidence was detected in the northeastern sub-basin. Three regional unconformities were detected in the Late Neogene Pannonian Basin fill, which represent 0.5 and 7.5 Ma time spans corresponding to single and composite unconformities. Consequently two main sequences build up the Late Neogene Pannonian Basin fill: a Late Miocene and a Pliocene one. Within the Late Miocene sequence there are smaller sedimentary cycles most probably corresponding to climatically driven relative lake-level changes in the Milankovitch frequency band. Considering the periods, the estimated values for precession and eccentricity in this study (19 and 370 ka) are close to the usually cited ones. In the case of obliquity the calculated period (71 ka) slightly deviates from the generally accepted number. Based on the relative amplitudes of oscillations, precession (sixth order) and obliquity (fifth order) cycles had the most significant impact on the sedimentation. Eccentricity caused cycles (fourth order) are poorly detectable in the sediments. The longer term (third order) cycles had very slight influence on the sedimentation pattern. Progradation, recorded in the Late Miocene sequence, correlates poorly in time within the basin. The dominant controls of this process probably were changes of basin subsidence rate and the very high sedimentation rate. The slow, upward trend of silt and sand bed thickness as well as that of the grain size also reflects the local progradation.

Molecular evolution of ependymin and the phylogenetic resolution of early divergences among euteleost fishes.

PubMed

Ortí, G; Meyer, A

1996-04-01

The rate and pattern of DNA evolution of ependymin, a single-copy gene coding for a highly expressed glycoprotein in the brain matrix of teleost fishes, is characterized and its phylogenetic utility for fish systematics is assessed. DNA sequences were determined from catfish, electric fish, and characiforms and compared with published ependymin sequences from cyprinids, salmon, pike, and herring. Among these groups, ependymin amino acid sequences were highly divergent (up to 60% sequence difference), but had surprisingly similar hydropathy profiles and invariant glycosylation sites, suggesting that functional properties of the proteins are conserved. Comparison of base composition at third codon positions and introns revealed AT-rich introns and GC-rich third codon positions, suggesting that the biased codon usage observed might not be due to mutational bias. Phylogenetic information content of third codon positions was surprisingly high and sufficient to recover the most basal nodes of the tree, in spite of the observation that pairwise distances (at third codon positions) were well above the presumed saturation level. This finding can be explained by the high proportion of phylogenetically informative nonsynonymous changes at third codon positions among these highly divergent proteins. Ependymin DNA sequences have established the first molecular evidence for the monophyly of a group containing salmonids and esociforms. In addition, ependymin suggests a sister group relationship of electric fish (Gymnotiformes) and Characiformes, constituting a significant departure from currently accepted classifications. However, relationships among characiform lineages were not completely resolved by ependymin sequences in spite of seemingly appropriate levels of variation among taxa and considerably low levels of homoplasy in the data (consistency index = 0.7). If the diversification of Characiformes took place in an "explosive" manner, over a relatively short period of time this pattern should also be observed using other phylogenetic markers. Poor conservation of ependymin's primary structure hinders the design of efficient primers for PCR that could be used in wide-ranging fish systematic studies. However, alternative methods like PCR amplification from cDNA used here should provide promising comparative sequence data for the resolution of phylogenetic relationships among other basal lineages of teleost fishes.

Lateral trends and vertical sequences in estuarine sediments, Willapa Bay, Washington

USGS Publications Warehouse

Clifton, H. Edward; Phillips, L.

1980-01-01

Willapa Bay is a sizable estuary on the southern coast of Washington- Relatively unmodified in a geologic sense by human activity the bay provides an excellent example of modern depositional facies in an estuarine setting. Studies of these deposits indicate that consistent lateral trends exist in sediment texture and sedimentary structures. The texture changes from sandy at the mouth of the bay to muddy in its upper parts. In any part of the bay , sediment is coarsest in the channel bottoms, where lag deposits accumulate. The sediment tends to fine in an upslope direction and is finest in supratidal flat deposits of silt and clay. The nature of sedimentary structures depends on the combination of physical and biological processes and sediment textures. Bedforms exist wherever the bed is sandy. In the main tidal channels sandwaves and dunes up to 4 meters high occur. In tributary channels and at the margins of the main channel, at shallower depths and under less intense currents , the structures are generally less than a meter high. Current ripples occur in t he sandy bed of all of the tidal channels and in runoff channels cross the tidal flat. Symmetric long-crested ripples are produced by wave action over the sandy intertidal flat. Internal structures in the bay's sediment depend not only on the nature of the bedform but also on the rate of bioturbation relative to physical processes. Under fields of large sandwaves or dunes, medium- to large-scale tabular and trough crossbedding predominates. This crossbedding generally is unidirectional, reflecting the locally dominant current (ebb or flood). Ripple bedding predominates elsewhere in sandy sediment within the channels. Where sand transport is diminished, as on the floor of the upper tributary channels, bioturbation exceeds the rate of production of physical structures and bedding is destroyed. The depositional banks in such areas tend to be sites of rapid sediment accumulation and bedding in the form of interlayered sand (commonly ripple bedded) and mud persists. On intertidal flats the sediment accumulates slowly and bioturbation erases nearly all physical structures. Bedding is preserved only where deposition is locally rapid , as in topographic depressions or on the depositional banks of runoff channels, or where faunal activity is inhibited, as beneath mounds of blue-green algae. The rate of sedimentation is slower still on the supratidal flats, but the general paucity of faunal activity allows the preservation of thin alternations of fine sand , silt or clay. The lateral migration of the tidal channels produces vertical sequences in which topographically higher facies are superposed on one another. Near the mouth of the estuary the upward sequence: lag deposit — crossbedded sand — ripple or planar-bedded sand is typical. The crossbedding shows a general upward decrease in thickness and a progression from trough to tabular units. In the main tidal channel - in the central estuary and in sandy tributary channels, the typical vertical sequence resembles that near the mouth , with the exception that the sequence is capped by bioturbated sandy or muddy tide flat deposits. In the upper estuary , where muddy sediment predominates, a typical sequence shows the progression-. bioturbated lag deposit — gently dipping interlaminated sand and mud layers of the accretionary bank — bioturbated mud flat deposits — thinly laminated fine supratidal deposits.

Paleogeographic implications of an erosional remnant of Paleogene rocks southwest of the Sur-Nacimiento Fault Zone, southern Coast Ranges, California

USGS Publications Warehouse

Vedder, J.G.; McLean, H.; Stanley, R.G.; Wiley, T.J.

1991-01-01

A small tract of heretofore-unrecognized Paleogene rocks lies about 30 km northeast of Santa Maria and 1 km southwest of the Sur-Nacimiento fault zone near upper Pine Creek. This poorly exposed assemblage of rocks is less than 50 m thick, lies unconformably on regionally distributed Upper Cretaceous submarine-fan deposits, and consists of three units: fossiliferous lower Eocene mudstone, Oligocene(?) conglomerate, and basaltic andesite that has a radiometric age of 26.6 ?? 0.5 Ma. Both the sedimentary and igneous constituents in the Paleogene sequence are unlike those of known sequences on either side of the Sur-Nacimiento fault zone. The Paleogene sedimentary rocks near upper Pine Creek presumably are remnants of formerly widespread early Eocene bathyal deposits and locally distributed Oligocene(?) fluvial deposits southwest of the fault zone. The 26.6 Ma basaltic andesite, however, may not have extended much beyond its present outcrops. An episode of Oligocene(?) displacement is required by the contrast in thicknesses, depositional patterns, and paleobathymetry of the juxtaposed rock sequences. -from Authors

Improved synthesis of carbon-clad silica stationary phases.

PubMed

Haidar Ahmad, Imad A; Carr, Peter W

2013-12-17

Previously, we described a novel method for cladding elemental carbon onto the surface of catalytically activated silica by a chemical vapor deposition (CVD) method using hexane as the carbon source and its use as a substitute for carbon-clad zirconia.1,2 In that method, we showed that very close to exactly one uniform monolayer of Al (III) was deposited on the silica by a process analogous to precipitation from homogeneous solution in order to preclude pore blockage. The purpose of the Al(III) monolayer is to activate the surface for subsequent CVD of carbon. In this work, we present an improved procedure for preparing the carbon-clad silica (denoted CCSi) phases along with a new column packing process. The new method yields CCSi phases having better efficiency, peak symmetry, and higher retentivity compared to carbon-clad zirconia. The enhancements were achieved by modifying the original procedure in three ways: First, the kinetics of the deposition of Al(III) were more stringently controlled. Second, the CVD chamber was flushed with a mixture of hydrogen and nitrogen gas during the carbon cladding process to minimize generation of polar sites by oxygen incorporation. Third, the fine particles generated during the CVD process were exhaustively removed by flotation in an appropriate solvent.

An image-based model of brain volume biomarker changes in Huntington's disease.

PubMed

Wijeratne, Peter A; Young, Alexandra L; Oxtoby, Neil P; Marinescu, Razvan V; Firth, Nicholas C; Johnson, Eileanoir B; Mohan, Amrita; Sampaio, Cristina; Scahill, Rachael I; Tabrizi, Sarah J; Alexander, Daniel C

2018-05-01

Determining the sequence in which Huntington's disease biomarkers become abnormal can provide important insights into the disease progression and a quantitative tool for patient stratification. Here, we construct and present a uniquely fine-grained model of temporal progression of Huntington's disease from premanifest through to manifest stages. We employ a probabilistic event-based model to determine the sequence of appearance of atrophy in brain volumes, learned from structural MRI in the Track-HD study, as well as to estimate the uncertainty in the ordering. We use longitudinal and phenotypic data to demonstrate the utility of the patient staging system that the resulting model provides. The model recovers the following order of detectable changes in brain region volumes: putamen, caudate, pallidum, insula white matter, nonventricular cerebrospinal fluid, amygdala, optic chiasm, third ventricle, posterior insula, and basal forebrain. This ordering is mostly preserved even under cross-validation of the uncertainty in the event sequence. Longitudinal analysis performed using 6 years of follow-up data from baseline confirms efficacy of the model, as subjects consistently move to later stages with time, and significant correlations are observed between the estimated stages and nonimaging phenotypic markers. We used a data-driven method to provide new insight into Huntington's disease progression as well as new power to stage and predict conversion. Our results highlight the potential of disease progression models, such as the event-based model, to provide new insight into Huntington's disease progression and to support fine-grained patient stratification for future precision medicine in Huntington's disease.

A composite foraminiferal biostratigraphic sequence for the Lower Miocene deposits in the type area of the Qom Formation, central Iran, developed by constrained optimization (CONOP)

NASA Astrophysics Data System (ADS)

Daneshian, Jahanbakhsh; Ramezani Dana, Leila; Sadler, Peter

2017-01-01

Benthic foraminifera species commonly outnumber planktic species in the type area of the Lower Miocene Qom Formation, in north central Iran, where it records the Tethyan link between the eastern Mediterranean and Indo- Pacific provinces. Because measured sections preserve very different sequences of first and last occurrences of these species, no single section provides a completely suitable baseline for correlation. To resolve this problem, we combined bioevents from three stratigraphic sections into a single composite sequence by constrained optimization (CONOP). The composite section arranges the first and last appearance events (FAD and LAD) of 242 foraminifera in an optimal order that minimizes the implied diachronism between sections. The composite stratigraphic ranges of the planktic foraminifera support a practical biozonation which reveals substantial local changes of accumulation rate during Aquitanian to Burdigalian times. Traditional biozone boundaries emerge little changed but an order of magnitude more correlations can be interpolated. The top of the section at Dobaradar is younger than previously thought and younger than sections at Dochah and Tigheh Reza-Abad. The latter two sections probably extend older into the Aquitanian than the Dobaradar section, but likely include a hiatus near the base of the Burdigalian. The bounding contacts with the Upper Red and Lower Red Formations are shown to be diachronous.

The influence of sequence of precursor films on CZTSe thin films prepared by ion-beam sputtering deposition

NASA Astrophysics Data System (ADS)

Zhao, Jun; Liang, Guangxing; Zeng, Yang; Fan, Ping; Hu, Juguang; Luo, Jingting; Zhang, Dongping

2017-02-01

The CuZnSn (CZT) precursor thin films are grown by ion-beam sputtering Cu, Zn, Sn targets with different orders and then sputtering Se target to fabricate Cu2ZnSnSe4 (CZTSe) absorber thin films on molybdenum substrates. They are annealed in the same vacuum chamber at 400 °C. The characterization methods of CZTSe thin films include X-ray diffraction (XRD), energy dispersive spectroscopy (EDS), scanning electron microscopy (SEM), and X-ray photoelectron spectra (XPS) in order to study the crystallographic properties, composition, surface morphology, electrical properties and so on. The results display that the CZTSe thin films got the strongest diffraction peak intensity and were with good crystalline quality and its morphology appeared smooth and compact with a sequence of Cu/Zn/Sn/Se, which reveals that the expected states for CZTSe are Cu1+, Zn2+, Sn4+, Se2+. With the good crystalline quality and close to ideal stoichiometric ratio the resistivity of the CZTSe film with the sequence of Cu/Zn/Sn/Se is lower, whose optical band gap is about 1.50 eV. Project supported by the National Natural Science Foundation of China (No. 61404086), the Basical Research Program of Shenzhen (Nos. JCYJ20150324140036866, JCYJ20150324141711581), and the Natural Science Foundation of SZU (No. 2014017).

Evaluating order in vertical successions of deltaic Holocene sediments on the Ganges-Brahmaputra-Meghna delta

NASA Astrophysics Data System (ADS)

Sincavage, R.; Goodbred, S. L., Jr.

2017-12-01

Most stratigraphic models are predicated on the presence of cyclicity or some form of order in vertical successions of strata. In spite of this a priori assumption of ordered stratigraphy, rarely are statistical metrics employed to quantify cyclicity in sedimentary packages. The presence or absence of preserved order in vertical sedimentary successions has important implications for the nature of environmental signals that are transmitted into the rock record. We interrogate the Holocene sedimentary archive of the Ganges-Brahmaputra-Meghna delta (GBMD) in an effort to explore to what extent fluvio-deltaic deposits exhibit recognizable order. Specifically, we focus on grain size data to evaluate 1.) if stratigraphic order in vertical sedimentary successions can be identified and quantified, and 2.) if there are spatial patterns of stratigraphic order across the GBMD. A runs order metric r is used to identify sequences of coarsening and fining within an extensive borehole network. Observed grain size data are shuffled enough times to generate synthetic "random" stratigraphy, and a Monte Carlo simulation generates 5000 realizations. The distribution of r values from the Monte Carlo are compared to the r metric calculated from observed data to determine how likely the observed metric could be generated by chance. The spatial distribution of order metrics indicates a relationship between areas of enhanced mass extraction and preservation of fluvial successions that scale with modern bar deposits on the Jamuna River. Similarly, probability metrics indicate that vertical successions of grain size data unlikely to have been generated by chance are more likely to be found on distal areas of the delta where 60% of the input mass has been extracted. Combining a mass balance framework with simple statistical metrics has the potential of improving predictions of the stratigraphic architecture and the preservation of ordered vs. disordered signals in the sedimentary record.

A note on coarse-grained gravity-flow deposits within proterozoic lacustrine sedimentary rocks, Transvaal sequence, South Africa

NASA Astrophysics Data System (ADS)

Eriksson, P. G.

A widely developed, thin, coarse-matrix conglomerate occurs within early Proterozoic lacustrine mudrocks in the Transvaal Sequence, South Africa. The poorly sorted tabular chert clasts, alternation of a planar clast fabric with disorientated zones, plus normal and inverse grading in the former rock type suggest deposition by density-modified grain-flow and high density turbidity currents. The lower fan-delta slope palæenvironment inferred for the conglomerate is consistent with the lacustrine interpretation for the enclosing mudrock facies. This intracratonic setting contrasts with the marine environment generally associated with density-modified grain-flow deposits.

Recent "omics" advances in Helicobacter pylori.

PubMed

Berthenet, Elvire; Sheppard, Sam; Vale, Filipa F

2016-09-01

The development of high-throughput whole genome sequencing (WGS) technologies is changing the face of microbiology, facilitating the comparison of large numbers of genomes from different lineages of a same organism. Our aim was to review the main advances on Helicobacter pylori "omics" and to understand how this is improving our knowledge of the biology, diversity and pathogenesis of H. pylori. Since the first H. pylori isolate was sequenced in 1997, 510 genomes have been deposited in the NCBI archive, providing a basis for improved understanding of the epidemiology and evolution of this important pathogen. This review focuses on works published between April 2015 and March 2016. Helicobacter "omics" is already making an impact and is a growing research field. Ultimately these advances will be translated into a routine clinical laboratory setting in order to improve public health. © 2016 John Wiley & Sons Ltd.

Early Pleistocene 40Ar/39Ar ages for Bapang Formation hominins, Central Jawa, Indonesia

PubMed Central

Larick, Roy; Ciochon, Russell L.; Zaim, Yahdi; Sudijono; Suminto; Rizal, Yan; Aziz, Fachroel; Reagan, Mark; Heizler, Matthew

2001-01-01

The Sangiran dome is the primary stratigraphic window for the Plio-Pleistocene deposits of the Solo basin of Central Jawa. The dome has yielded nearly 80 Homo erectus fossils, around 50 of which have known findspots. With a hornblende 40Ar/39Ar plateau age of 1.66 ± 0.04 mega-annum (Ma) reportedly associated with two fossils [Swisher, C.C., III, Curtis, G. H., Jacob, T., Getty, A. G., Suprijo, A. & Widiasmoro (1994) Science 263, 1118–1121), the dome offers evidence that early Homo dispersed to East Asia during the earliest Pleistocene. Unfortunately, the hornblende pumice was sampled at Jokotingkir Hill, a central locality with complex lithostratigraphic deformation and dubious specimen provenance. To address the antiquity of Sangiran H. erectus more systematically, we investigate the sedimentary framework and hornblende 40Ar/39Ar age for volcanic deposits in the southeast quadrant of the dome. In this sector, Bapang (Kabuh) sediments have their largest exposure, least deformation, and most complete tephrostratigraphy. At five locations, we identify a sequence of sedimentary cycles in which H. erectus fossils are associated with epiclastic pumice. From sampled pumice, eight hornblende separates produced 40Ar/39Ar plateau ages ranging from 1.51 ± 0.08 Ma at the Bapang/Sangiran Formation contact, to 1.02 ± 0.06 Ma, at a point above the hominin-bearing sequence. The chronological sequence of 40Ar/39Ar ages follows stratigraphic order across the southeast quadrant. An intermediate level yielding four nearly complete crania has an age of about 1.25 Ma. PMID:11309488

Microbial Composition of Near-Boiling Silica-Depositing Thermal Springs throughout Yellowstone National Park

PubMed Central

Blank, Carrine E.; Cady, Sherry L.; Pace, Norman R.

2002-01-01

The extent of hyperthermophilic microbial diversity associated with siliceous sinter (geyserite) was characterized in seven near-boiling silica-depositing springs throughout Yellowstone National Park using environmental PCR amplification of small-subunit rRNA genes (SSU rDNA), large-subunit rDNA, and the internal transcribed spacer (ITS). We found that Thermocrinis ruber, a member of the order Aquificales, is ubiquitous, an indication that primary production in these springs is driven by hydrogen oxidation. Several other lineages with no known close relatives were identified that branch among the hyperthermophilic bacteria. Although they all branch deep in the bacterial tree, the precise phylogenetic placement of many of these lineages is unresolved at this time. While some springs contained a fair amount of phylogenetic diversity, others did not. Within the same spring, communities in the subaqueous environment were not appreciably different than those in the splash zone at the edge of the pool, although a greater number of phylotypes was found along the pool's edge. Also, microbial community composition appeared to have little correlation with the type of sinter morphology. The number of cell morphotypes identified by fluorescence in situ hybridization and scanning electron microscopy was greater than the number of phylotypes in SSU clone libraries. Despite little variation in Thermocrinis ruber SSU sequences, abundant variation was found in the hypervariable ITS region. The distribution of ITS sequence types appeared to be correlated with distinct morphotypes of Thermocrinis ruber in different pools. Therefore, species- or subspecies-level divergences are present but not detectable in highly conserved SSU sequences. PMID:12324363

Early Pleistocene 40Ar/39Ar ages for Bapang Formation hominins, Central Jawa, Indonesia.

PubMed

Larick, R; Ciochon, R L; Zaim, Y; Sudijono; Suminto; Rizal, Y; Aziz, F; Reagan, M; Heizler, M

2001-04-24

The Sangiran dome is the primary stratigraphic window for the Plio-Pleistocene deposits of the Solo basin of Central Jawa. The dome has yielded nearly 80 Homo erectus fossils, around 50 of which have known findspots. With a hornblende (40)Ar/(39)Ar plateau age of 1.66 +/- 0.04 mega-annum (Ma) reportedly associated with two fossils [Swisher, C.C., III, Curtis, G. H., Jacob, T., Getty, A. G., Suprijo, A. & Widiasmoro (1994) Science 263, 1118-1121), the dome offers evidence that early Homo dispersed to East Asia during the earliest Pleistocene. Unfortunately, the hornblende pumice was sampled at Jokotingkir Hill, a central locality with complex lithostratigraphic deformation and dubious specimen provenance. To address the antiquity of Sangiran H. erectus more systematically, we investigate the sedimentary framework and hornblende (40)Ar/(39)Ar age for volcanic deposits in the southeast quadrant of the dome. In this sector, Bapang (Kabuh) sediments have their largest exposure, least deformation, and most complete tephrostratigraphy. At five locations, we identify a sequence of sedimentary cycles in which H. erectus fossils are associated with epiclastic pumice. From sampled pumice, eight hornblende separates produced (40)Ar/(39)Ar plateau ages ranging from 1.51 +/- 0.08 Ma at the Bapang/Sangiran Formation contact, to 1.02 +/- 0.06 Ma, at a point above the hominin-bearing sequence. The chronological sequence of (40)Ar/(39)Ar ages follows stratigraphic order across the southeast quadrant. An intermediate level yielding four nearly complete crania has an age of about 1.25 Ma.

Sedimentary record of erg migration

NASA Astrophysics Data System (ADS)

Porter, M. L.

1986-06-01

The sedimentary record of erg (eolian sand sea) migration consists of an idealized threefold division of sand-sea facies sequences. The basal division, here termed the fore-erg, is composed of a hierarchy of eolian sand bodies contained within sediments of the flanking depositional environment. These sand bodies consist of eolian strata deposited by small dune complexes, zibars, and sand sheets. The fore-erg represents the downwind, leading edge of the erg and records the onset of eolian sedimentation. Basin subsidence coupled with erg migration places the medial division, termed the central erg, over the fore-erg strata. The central erg, represented by a thick accumulation of large-scale, cross-stratified sandstone, is the product of large draa complexes. Eolian influence on regional sedimentation patterns is greatest in the central erg, and most of the sand transported and deposited in the erg is contained within this region. Reduction in sand supply and continued erg migration will cover the central-erg deposits with a veneer of back-erg deposits. This upper division of the erg facies sequence resembles closely the fore-erg region. Similar types of eolian strata are present and organized in sand bodies encased in sediments of the upwind flanking depositional environment(s). Back-erg deposits may be thin due to limited eolian influence on sedimentation or incomplete erg migration, or they may be completely absent because of great susceptibility to postdepositional erosion. Tectonic, climatic, and eustatic influences on sand-sea deposition will produce distinctive variations or modifications of the idealized erg facies sequence. The resulting variants in the sedimentary record of erg migration are illustrated with ancient examples from western North America, Europe, southern Africa, and South America.

Depositional environments and paleogeography of the Upper Miocene Wassuk Group, west-central Nevada

USGS Publications Warehouse

Golia, R.T.; Stewart, John H.

1984-01-01

Fluvial and lacustrine deposits of the Miocene Wassuk Group, exposed in Coal Valley, west-central Nevada, are divided into five lithofacies: (1) diatomite, claystone, siltstone, and carbonaceous siltstone deposited in a lake with paludal conditions at the margin; (2) upward-coarsening sequences of sandstone deposited on a delta and fan-delta; (3) channel-form sandstone deposited on a distal braided alluvial plain; (4) clast-supported conglomerate deposited on a proxial braided alluvial plain or distal alluvial fan; and (5) matrix-supported conglomerate deposited on a distal to middle alluvial fan. Petrographic analysis records an upsection change from a predominantly andesitic to a predominantly plutonic provenance. This change, combined with the overall upward-coarsening of the Wassuk Group and the great thickness (2400 m) of the sequence, suggests active uplift and rapid subsidence during deposition of the group. Facies relationships and paleocurrent directions indicate source areas to the south, southeast and west of Coal Valley. The Miocene Wassuk Group was deposited in an intra-arc basin with penecontemporaneous volcanism and tectonic activity. Syndepositional faulting at the southern margin of Coal Valley between 13 and 11 m.y. ago suggests an early episode of northeast-southwest extension prior to the onset of east-west basin and range extension. ?? 1984.

Optical resonance imaging: An optical analog to MRI with sub-diffraction-limited capabilities.

PubMed

Allodi, Marco A; Dahlberg, Peter D; Mazuski, Richard J; Davis, Hunter C; Otto, John P; Engel, Gregory S

2016-12-21

We propose here optical resonance imaging (ORI), a direct optical analog to magnetic resonance imaging (MRI). The proposed pulse sequence for ORI maps space to time and recovers an image from a heterodyne-detected third-order nonlinear photon echo measurement. As opposed to traditional photon echo measurements, the third pulse in the ORI pulse sequence has significant pulse-front tilt that acts as a temporal gradient. This gradient couples space to time by stimulating the emission of a photon echo signal from different lateral spatial locations of a sample at different times, providing a widefield ultrafast microscopy. We circumvent the diffraction limit of the optics by mapping the lateral spatial coordinate of the sample with the emission time of the signal, which can be measured to high precision using interferometric heterodyne detection. This technique is thus an optical analog of MRI, where magnetic-field gradients are used to localize the spin-echo emission to a point below the diffraction limit of the radio-frequency wave used. We calculate the expected ORI signal using 15 fs pulses and 87° of pulse-front tilt, collected using f /2 optics and find a two-point resolution 275 nm using 800 nm light that satisfies the Rayleigh criterion. We also derive a general equation for resolution in optical resonance imaging that indicates that there is a possibility of superresolution imaging using this technique. The photon echo sequence also enables spectroscopic determination of the input and output energy. The technique thus correlates the input energy with the final position and energy of the exciton.

The actual scaling of a nominally third-order Reynolds stress

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

Krommes, J. A., E-mail: krommes@princeton.edu; Hammett, G. W., E-mail: hammett@princeton.edu

2014-05-15

It is shown that a particular higher-order Reynolds stress arising from a term in the third-order gyrokinetic Hamiltonian is smaller than it nominally appears to be. However, it does not follow that all third-order terms are unimportant. The discussion is relevant to the ongoing debate about the importance of higher-order terms in the gyrokinetic theory of momentum transport.

Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 Mb region of pig chromosome 17

PubMed Central

Hart, Elizabeth A; Caccamo, Mario; Harrow, Jennifer L; Humphray, Sean J; Gilbert, James GR; Trevanion, Steve; Hubbard, Tim; Rogers, Jane; Rothschild, Max F

2007-01-01

Background We describe here the sequencing, annotation and comparative analysis of an 8 Mb region of pig chromosome 17, which provides a useful test region to assess coverage and quality for the pig genome sequencing project. We report our findings comparing the annotation of draft sequence assembled at different depths of coverage. Results Within this region we annotated 71 loci, of which 53 are orthologous to human known coding genes. When compared to the syntenic regions in human (20q13.13-q13.33) and mouse (chromosome 2, 167.5 Mb-178.3 Mb), this region was found to be highly conserved with respect to gene order. The most notable difference between the three species is the presence of a large expansion of zinc finger coding genes and pseudogenes on mouse chromosome 2 between Edn3 and Phactr3 that is absent from pig and human. All of our annotation has been made publicly available in the Vertebrate Genome Annotation browser, VEGA. We assessed the impact of coverage on sequence assembly across this region and found, as expected, that increased sequence depth resulted in fewer, longer contigs. One-third of our annotated loci could not be fully re-aligned back to the low coverage version of the sequence, principally because the transcripts are fragmented over several contigs. Conclusion We have demonstrated the considerable advantages of sequencing at increased read depths and discuss the implications that lower coverage sequence may have on subsequent comparative and functional studies, particularly those involving complex loci such as GNAS. PMID:17705864

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.

Significance of a near-source tephra-stratigraphic sequence to the eruptive history of Hayes Volcano, south-central Alaska

USGS Publications Warehouse

Wallace, Kristi; Coombs, Michelle L.; Hayden, Leslie A.; Waythomas, Christopher F.

2014-01-01

Bluffs along the Hayes River valley, 31 km northeast and 40 km downstream from Hayes Volcano, reveal volcanic deposits that shed new light on its eruptive history. Three thick (>10 cm) and five thin (<10 cm) tephra-fall deposits are dacitic in whole rock composition and contain high proportions of amphibole to pyroxene and minor biotite and broadly correlate to Hayes tephra set H defined by earlier investigators. Two basal ages for the tephra-fall sequence of 3,690±30 and 3,750±30 14C yr B.P. are also consistent with the Hayes tephra set H timeframe. Distinguishing among Hayes tephra set H units is critical because the set is an important time-stratigraphic marker in south-central Alaska and this section provides a new reference section for Hayes tephra set H. Analysis of Fe-Ti oxide grains in the tephras shows promise for identifying individual Hayes deposits. Beneath the dacitic tephra sequence lies an older, poorly sorted tephra (tephra A) that contains dacite and rhyolite lapilli and whose basal age is 4,450±30 14C yr B.P. Immediately below the tephra-fall sequence (Unit III) lies a series of mass-flow deposits that are rich in rhyodacitic clasts (Unit II). Below Unit II and possibly coeval with it, is a 20–30 m thick pumiceous pyroclastic-flow deposit (Unit I) that extends to the valley floor. Here informally named the Hayes River ignimbrite, this deposit contains pumice clasts of rhyolite with quartz, sanidine, plagioclase, and biotite phenocrysts, an assemblage that is unique among known Quaternary volcanic products of Hayes and other Alaskan volcanoes. Units I, II, and tephra A of Unit III represent at least two previously unrecognized eruptions of Hayes Volcano that occurred prior to ~3,700 yr B.P. No compositionally equivalent distal tephra deposits correlative with Hayes Volcano rhyodacites or rhyolites have yet been identified, perhaps indicating that some of these deposits are pre-Holocene, and were largely removed by glacial ice during the last ice age. More field and analytical work is needed to further refine the eruptive history of Hayes Volcano.

Sequence-Stratigraphic Analysis of the Regional Observation Monitoring Program (ROMP) 29A Test Corehole and Its Relation to Carbonate Porosity and Regional Transmissivity in the Floridan Aquifer System, Highlands County, Florida

USGS Publications Warehouse

Ward, W. C.; Cunningham, K.J.; Renken, R.A.; Wacker, M.A.; Carlson, J.I.

2003-01-01

An analysis was made to describe and interpret the lithology of a part of the Upper Floridan aquifer penetrated by the Regional Observation Monitoring Program (ROMP) 29A test corehole in Highlands County, Florida. This information was integrated into a one-dimensional hydrostratigraphic model that delineates candidate flow zones and confining units in the context of sequence stratigraphy. Results from this test corehole will serve as a starting point to build a robust three-dimensional sequence-stratigraphic framework of the Floridan aquifer system. The ROMP 29A test corehole penetrated the Avon Park Formation, Ocala Limestone, Suwannee Limestone, and Hawthorn Group of middle Eocene to Pliocene age. The part of the Avon Park Formation penetrated in the ROMP 29A test corehole contains two composite depositional sequences. A transgressive systems tract and a highstand systems tract were interpreted for the upper composite sequence; however, only a highstand systems tract was interpreted for the lower composite sequence of the deeper Avon Park stratigraphic section. The composite depositional sequences are composed of at least five high-frequency depositional sequences. These sequences contain high-frequency cycle sets that are an amalgamation of vertically stacked high-frequency cycles. Three types of high-frequency cycles have been identified in the Avon Park Formation: peritidal, shallow subtidal, and deeper subtidal high-frequency cycles. The vertical distribution of carbonate-rock diffuse flow zones within the Avon Park Formation is heterogeneous. Porous vuggy intervals are less than 10 feet, and most are much thinner. The volumetric arrangement of the diffuse flow zones shows that most occur in the highstand systems tract of the lower composite sequence of the Avon Park Formation as compared to the upper composite sequence, which contains both a backstepping transgressive systems tract and a prograding highstand systems tract. Although the porous and permeable layers are not thick, some intervals may exhibit lateral continuity because of their deposition on a broad low-relief ramp. A thick interval of thin vuggy zones and open faults forms thin conduit flow zones mixed with relatively thicker carbonate-rock diffuse flow zones between a depth of 1,070 and 1,244 feet below land surface (bottom of the test corehole). This interval is the most transmissive part of the Avon Park Formation penetrated in the ROMP 29A test corehole and is included in the highstand systems tract of the lower composite sequence. The Ocala Limestone is considered to be a semiconfining unit and contains three depositional sequences penetrated by the ROMP 29A test corehole. Deposited within deeper subtidal depositional cycles, no zones of enhanced porosity and permeability are expected in the Ocala Limestone. A thin erosional remnant of the shallow marine Suwannee Limestone overlies the Ocala Limestone, and permeability seems to be comparatively low because moldic porosity is poorly connected. Rocks that comprise the lower Hawthorn Group, Suwannee Limestone, and Ocala Limestone form a permeable upper zone of the Upper Floridan aquifer, and rocks of the lower Ocala Limestone and Avon Park Formation form a permeable lower zone of the Upper Floridan aquifer. On the basis of a preliminary analysis of transmissivity estimates for wells located north of Lake Okeechobee, spatial relations among groups of relatively high and low transmissivity values within the upper zone are evident. Upper zone transmissivity is generally less than 10,000 feet squared per day in areas located south of a line that extends through Charlotte, Sarasota, DeSoto, Highlands, Polk, Osceola, Okeechobee, and St. Lucie Counties. Transmissivity patterns within the lower zone of the Avon Park Formation cannot be regionally assessed because insufficient data over a wide areal extent have not been compiled.

Diamondlike carbon protective coatings for IR materials

NASA Technical Reports Server (NTRS)

Mirtich, M. J.; Nir, D.; Swec, D. M.; Banks, B. A.

1985-01-01

Diamondlike carbon (DLC) films have the potential to protect optical windows in applications where it is important to maintain the integrity of the specular transmittance of these films on ZnS and ZnSe infrared transmitting windows. The films must be adherent and durable such that they protect the windows from rain and particle erosion as well as chemical attack. In order to optimize the performance of these films, 0.1 micro m thick diamondlike carbon films were deposited on fused silica and silicon wafers, using three different methods of ion beam deposition. One method was sputter deposition from a carbon target using an 8 cm ion source. The merits of hydrogen addition were experimentally evaluated in conjunction with this method. The second method used a 30 cm hollow cathode ion source with hydrocarbon/Argon gases to deposit diamondlike carbon films from the primary beam at 90 to 250 eV. The third method used a dual beam system employing a hydrocarbon/Argon 30 cm ion source and an 8 cm ion source. Films were evaluated for adherence, intrinsic stress, infrared transmittance between 2.5 and 50 micro m, and protection from particle erosion. An erosion test using a sandblaster was used to give quantitative values of the protection afforded to the fused silica by the diamondlike carbon films. The fused silica surfaces protected by diamondlike carbon films were exposed to 100 micro m diameter SiO particles at 60 mi/hr (26.8/sec) in the sandblaster.

The Olympic Dam copper-uranium-gold deposit, Roxby Downs, South Australia

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

Roberts, D.E.; Hudson, G.R.T.

1983-08-01

The Olympic Dam copper-uranium-gold deposit appears to be a new type of strata-bound sediment-hosted ore deposit. It is located 650 km north-northwest of Adelaide in South Australia and was discovered in 1975. It has an areal extent exceeding 20 km/sup 2/ with vertical thicknesses of mineralization up to 350 m. The deposit is estimated to contain in excess of 2,000 million metric tons of mineralized material with an average grade of 1.6 percent copper, 0.06 percent uranium oxide, and 0.6 g/metric ton gold. The deposit occurs in the basement beneath 350 m of unmineralized, flat-lying Adelaidean (late Proterozoic) to Cambrianmore » sediments in the Stuart shelf region of South Australia. The host rocks of the deposit are unmetamorphosed and are probably younger than 1,580 m.y. The deposit is spatially related to coincident gravity and magnetic anomalies and the intersection of west-northwest- and north-northwest-trending lineaments. The Proterozoic sediments comprising the local basement sequence are predominantly sedimentary breccias ranging from matrix-poor granite breccias to matrix-rich polymict breccias containing clasts of a variety of rock types. This sequence is over 1 km thick and has been divided into two main units--the Olympic Dam Formation and the Greenfield Formation. The Olympic Dam Formation has five members, three of which are matrix rich. The Greenfield Formation has three members, the lower two being very hematite rich while the upper has a significant volcanic component. Pervasive hematite, chlorite, and sericite alteration of varying intensity affects all the basement sequence.« less

Glacial origin for cave rhythmite during MIS 5d-c in a glaciokarst landscape, Picos de Europa (Spain)

NASA Astrophysics Data System (ADS)

Ballesteros, Daniel; Jiménez-Sánchez, Montserrat; Giralt, Santiago; DeFelipe, Irene; García-Sansegundo, Joaquín

2017-06-01

Laminated slackwater deposits have been identified in many karst caves related to fluvial and lacustrine sedimentation. However, sedimentological evidence rarely supports a glacial origin for these deposits, which was proposed by previous studies. The Torca La Texa shaft is located in a glaciokarst area that comprises numerous slackwater-type deposits, piled up in fining-upward sequences. A basal sandy erosive layer and millimeter-sized laminated rhythmite with interbedded flowstone characterize these sequences. Fining-upward layers of carbonate silt, clay, and minor quartz sand deposited in flooded conduits define the rhythmite lamination. The presence of allochthonous minerals indicates that the rhythmite sediment comes from the glacial erosion of nearby carbonate mountains. Two 234U/230Th radiometric ages dated the rhythmite deposits around 109 and 95 ka, coinciding with relative cold periods included in the MIS 5d-c. These cold periods were marked by a high annual seasonality, immediately after the glacial local maximum extension, in agreement with a varve-type deposit. The combination of these sedimentological mineralogical, geomorphological and paleoclimate information indicates that the rhythmite should be introduced into the studied cave during the summer melting of the glaciers, which produced the recharge of the karst aquifer, triggering cave floods. In addition, punctual glacier collapses would also have their imprint in the slackwater sequences with thicker, coarser and erosive sand deposits and the spring blocking by glaciers may have promoted floods inside the cave. Therefore, the studied rhythmite can be interpreted as glacial varves decanted during the relatively cold climate conditions.

Distribution and tectonic implications of Cretaceous-Quaternary sedimentary facies in Solomon Islands

NASA Astrophysics Data System (ADS)

Turner, C. C.; Hughes, G. W.

1982-08-01

Sedimentary rocks of the Solomon Islands-Bougainville Arc are described in terms of nine widespread facies. Four facies associations are recognised by grouping facies which developed in broadly similar sedimentary environments. A marine pelagic association of Early Cretaceous to Miocene rocks comprises three facies. Facies Al: Early Cretaceous siliceous mudstone, found only on Malaita, is interpreted as deep marine siliceous ooze. Facies A2: Early Cretaceous to Eocene limestone with chert, overlies the siliceous mudstone facies, and is widespread in the central and eastern Solomons. It represents lithified calcareous ooze. Facies A3: Oligocene to Miocene calcisiltite with thin tuffaceous beds, overlies Facies A2 in most areas, and also occurs in the western Solomons. This represents similar, but less lithified calcareous ooze, and the deposits of periodic andesitic volcanism. An open marine detrital association of Oligocene to Recent age occurs throughout the Solomons. This comprises two facies. Facies B1 is variably calcareous siltstone, of hemipelagic origin; and Facies B2 consists of volcanogenic clastic deposits, laid down from submarine mass flows. A third association, of shallow marine carbonates, ranges in age from Late Oligocene to Recent. Facies C1 is biohermal limestone, and Facies C2 is biostromal calcarenite. The fourth association comprises areally restricted Pliocene to Recent paralic detrital deposits. Facies D1 includes nearshore clastic sediments, and Facies D2 comprises alluvial sands and gravels. Pre-Oligocene pelagic sediments were deposited contemporaneously with, and subsequent to, the extrusion of oceanic tholeiite. Island arc volcanism commenced along the length of the Solomons during the Oligocene, and greatly influenced sedimentation. Thick volcaniclastic sequences were deposited from submarine mass flows, and shallow marine carbonates accumulated locally. Fine grained graded tuffaceous beds within the marine pelagic association are interpreted as products of this volcanism, suggesting that the Santa Isabel-Malaita-Ulawa area, where these beds are prevalent, was relatively close to the main Solomons chain at this time. A subduction zone may have dipped towards the northeast beneath this volcanic chain. Pliocene to Pleistocene calcalkaline volcanism and tectonism resulted in the emergence of all large islands and led to deposition of clastic and carbonate facies in paralic, shallow and deep marine environments.

Constraining Depositional Slope From Sedimentary Structures in Sandy Braided Streams

NASA Astrophysics Data System (ADS)

Lynds, R. M.; Mohrig, D.; Heller, P. L.

2003-12-01

Determination of paleoslopes in ancient fluvial systems has potentially broad application to quantitatively constraining the history of tectonics and paleoclimate in continental sequences. Our method for calculating paleoslopes for sandy braided streams is based upon a simple physical model that establishes depositional skin-frictional shear stresses from assemblages of sedimentary structures and their associated grain size distributions. The addition of a skin-frictional shear stress, with a geometrically determined form-drag shear stress results in a total boundary shear stress which is directly related to water-surface slope averaged over an appropriate spatial scale. In order to apply this model to ancient fluvial systems, it is necessary to measure the following: coarsest suspended sediment size, finest grain size carried in bed load, flow depth, dune height, and dune length. In the rock record, suspended load and bed load can be accurately assessed by well-preserved suspended load deposits ("low-energy" ripples) and bed load deposits (dune foresets). This model predicts an average slope for the North Loup River near Taylor, Nebraska (modern case study) of 2.7 x 10-3. The measured reach-averaged water surface slope for the same reach of the river is 1.37 x 10-3. We suggest that it is possible to calculate the depositional slope of a sandy fluvial system by a factor of approximately two. Additionally, preliminary application of this model to the Lower Jurassic Kayenta Formation throughout the Colorado Plateau provides a promising and consistent evaluation of paleoslope in an ancient and well-preserved, sandy braided stream deposit.

Sedimentary Basin Structure of the Hadar Formation's Lacustrine-Dominated Depocenter (Ledi-Geraru, Afar, Ethiopia) and its Relevance for Investigating Hominin Paleoenvironments

NASA Astrophysics Data System (ADS)

Dimaggio, E. N.; Campisano, C. J.; Arrowsmith, J. R.; Dupont-Nivet, G.; Johnson, R. A.; Warren, M. B.

2008-12-01

Sedimentary sequences preserved in East African rift basins record the long-term response of past depositional environments to climatic and tectonic forcing. Motivations for recent field investigations at the Ledi-Geraru site, part of the greater Hadar sedimentary basin in the Afar region of Ethiopia, stem from a need to characterize local basin structure and expand and refine interpretations of the complex mid-late Pliocene history of local and regional-scale landscape change during a time of critical importance for understanding hominin evolution. Detailed geologic mapping (1:7,000), measured stratigraphic sections, and seismic reflection surveys provide the datasets necessary for basin evaluation. The Ledi-Geraru sedimentary sequence (>250m thick) exposes nearly the entirety of the hominin-bearing Hadar Formation of west- central Afar. Both primary unmodified lake deposits and intervals modified by subsequent subaerial exposure and pedogenesis are well-exposed. The lacustrine-dominated signature is indicated by the prevalence of laminated silty clays that contain leaf impressions, fish scales, and gastropod shells, undisturbed laminated diatomite and clays, and pedogenically modified diatomaceous silts. The sequence is generally flat lying, with low bedding dips ranging from 0-2° NNW to <1° NNE and minor NNW trending faults with <5 m vertical offset. Whereas coeval fluvio-lacustrine sediments associated with hominin and archaeological sites west of Ledi-Geraru (e.g., Hadar and Gona) are marked by comparatively slow and episodic sedimentation, sedimentation rates in the Ledi-Geraru sequence are extremely high and consistent, on the order of ~0.9-1.0mm/yr. Laterally extensive tephra marker beds and paleomagnetic records provide excellent age control for sedimentation rate estimates and correlation to nearby fossil-rich sequences. As the Hadar basin sediments preserve a rich paleoanthropologic and archaeological record, this work provides the geologic framework necessary for a proposed (2011) continental drilling effort to obtain a near-continuous, ultra-high resolution terrestrial record of past climate variability from multiple paleo-lake basins in East Africa, including the Ledi-Geraru. A seismic reflection survey was completed there in spring 2008, below the planned drilling site. Gently east-dipping coherent reflections interpreted to be from the Ledi-Geraru sedimentary sequence are imaged in the seismic data to at least 0.2 to 0.3 s (two-way travel time). Preliminary average velocities of about 2000 m/s suggest a sequence thickness of 200-300 m. Furthermore, there is no indication of large-offset faults or of buried basalt ridges that would disrupt or reduce the stratigraphic column available for coring. The anticipated cores from Ledi-Geraru should yield a high-resolution chronostratigraphic framework and paleoenvironmental record from >3.5 to 2.9Ma. Combined geologic and seismic evaluations of depositional sequences are central for evaluating the geometry, tectonic evolution, and stratigraphic history of basins and facilitate interpretations of the space-time progression of evolving paleosurfaces.

Tephro- and chemo-stratigraphy of the Vulcanello Peninsula (Vulcano, Aeolian Islands)

NASA Astrophysics Data System (ADS)

Rosi, M.; Fusillo, R.; di Traglia, F.; Pistolesi, M.; Todman, A.; Menzies, M. A.

2009-12-01

New stratigraphic studies of the Vulcanello Peninsula have been used to better define the small-scale evolution of this young (1000 AD and 325±100 BP) volcanic center and to re-investigate the last 1000 years of volcanic history for the Island of Vulcano (Aeolian Islands, Southern Italy). Vulcanello Peninsula is the northern-most part of the Island of Vulcano. It comprises a shoshonitic lava platform and a volcanic edifice made up of three overlying cones, which are shoshonitic to trachytic in composition. Volcanic activity in this area was coeval with the recent eruptions of the La Fossa Cone, the present-day active center of the island. Our goal is to constrain the recent volcanic development of this mafic volcano and to focus on the historic eruptive activity of the two other recent or active centres in the southern Aeolian Islands, Mt. Pilato (Island of Lipari) and La Fossa Cone. In order to do so, we reconstructed the stratigraphical setting of the proximal deposits of the three Vulcanello cones, through the investigation of 25 outcrops. We analyzed the stratigraphy of the tephra blankets deposited on the lava platform, studying 10 trenches. Our intention is to integrate morphological, textural and chemical data in order to correlate these deposits with the Vulcanello, La Fossa Cone or Mt Pilato. LA-MC-ICPMS (RHUL) analysis of juvenile clasts is underway in order to investigate the evolution of the Vulcanello juvenile clasts. In addition 14C dating is planned on selected organic matter from the volcanostratigraphic sections. Our preliminary data for the Vulcanello proximal deposits suggest that each of the three cones experienced several eruptions, with a wide spectrum of eruptive styles and a diversity of chemistry. The oldest cone (Vulcanello I) is characterised by four different eruptions separated by minor unconformities or reworking material indicative of little or not time breaks in the eruptive cycle. The eruptions shift from Violent Strombolian to Hawaiian in style, testifying to a reduction in fragmentation and dispersal. The second cone (Vulcanello II), contains volcanic deposits from Strombolian eruptions only. The third cone (Vulcanello III), displays a complex evolution with an initial effusive episode of a trachytic lava flow, followed by phreatic explosions, evident as altered fine ash layers. These deposits are interbedded with scoriaceous fall deposits, attesting the occurrence of some mild explosive activity during this eruptive phase. This detailed study of the effusive and explosive products from Vulcanello reveals rapid evolution of Vulcanello during the initial phases (1000 AD to 1200 AD) with voluminous mafic eruptions, both effusive and explosive. A progressive reduction in emitted volume is apparent. The presence of abundant explosive deposits related to phreatic explosions during the Vulcanello III phase, is related to the presence of water, a reduction in magma volume and the presence of intense hydrothermal activity in the latter stage of the evolution of Vulcanello evolution until 1878. This may indicate the presence of a stable shallow thermal anomaly.

Sedimentary facies and Holocene progradation rates of the Changjiang (Yangtze) delta, China

NASA Astrophysics Data System (ADS)

Hori, Kazuaki; Saito, Yoshiki; Zhao, Quanhong; Cheng, Xinrong; Wang, Pinxian; Sato, Yoshio; Li, Congxian

2001-11-01

The Changjiang (Yangtze) River, one of the largest rivers in the world, has formed a broad tide-dominated delta at its mouth during the Holocene sea-level highstand. Three boreholes (CM97, JS98, and HQ98) were obtained from the Changjiang delta plain in 1997-1998 to clarify the characteristics of tide-dominated delta sediments and architecture. Based on sediment composition and texture, and faunal content, core sediments were divided into six depositional units. In ascending order, they were interpreted as tidal sand ridge, prodelta, delta-front, subtidal to lower intertidal flat, upper intertidal flat, and surface soil deposits. The deltaic sequence from the prodelta deposits to the delta front deposits showed an upward-coarsening succession, overlain by an upward-fining succession from the uppermost part of the delta front deposits to the surface soil. Thinly interlaminated to thinly interbedded sand and mud (sand-mud couplets), and bidirectional cross laminations in these deposits show that tide is the key factor affecting the formation of Changjiang deltaic facies. Sediment facies and their succession combined with AMS 14C dating revealed that isochron lines cross unit boundaries clearly, and delta progradation has occurred since about 6000 to 7000 years BP, when the rising sea level neared or reached its present position. The average progradation rate of the delta front was approximately 50 km/kyear over the last 5000 years. The progradation rate, however, increased abruptly ca. 2000 years BP, going from 38 to 80 km/kyear. The possible causes for this active progradation could have been an increase in sediment production in the drainage basin due to widespread human interference and/or decrease in deposition in the middle reaches related to the channel stability caused by human activity and climatic cooling after the mid-Holocene.

Coupling molecules and morphology to discover new clades of ciliates.

NASA Astrophysics Data System (ADS)

Grattepanche, J. D.; Maurer-Alcalá, X. X.; Tucker, S. J.; McManus, G. B.; Katz, L. A.

2016-02-01

In a previous study using high-throughput sequencing (Grattepanche et al submitted, oral presentation?), we observe the presence of two clades of spirotrich ciliates mainly present in marine deep-water along the New England coast. These clades, clusters X1 and X2, are characterized by several deletions in their SSU-rDNA and have been observed elsewhere as both identical and similar sequences have been deposited on GenBank from other environmental studies, but lack morphological description. In order to link molecules (SSU-rDNA sequence) to their morphology, we sample below the photic zone (between 60 to 400m of depth) in the New England coast (Northeast Atlantic) in a transect crossing the continental shelf. We designed an oligonucleotide probe specific for choreotrich and oligotrich ciliates and another specific to clusters X1 and X2 to describe these clades through a combination of Fluorescence In Situ Hybridization (FISH) and light microscopy. Our aim is to increase our knowledge on the morphology of these `unknown' clades of ciliates, which will allow for future ecological studies.

Sedimentology and geochemistry of lacustrine sequences of the upper Pleistocene and holocene in intertropical area (Lake Magadi and Green crater lake): paleoclimatic implications

NASA Astrophysics Data System (ADS)

Damnati, B.

1993-05-01

Sedimentological and geochemical analyses have been carried out on lacustrine deposits of East Africa, at Lake Magadi (2°S, 36°E, Kenya) and at Green Crater Lake (0°S, 36°E, Kenya), to determine the parameters controlling climatic and environmental dynamics during late Pleistocene and Holocene. These sedimentary sequences were collected with a stationary piston corer. At Lake Magadi (Fig. 1), sedimentary and geochemical control show three phases of lake level variation which corresponds to climatic change occurring during the last 40 thousand years. These phases were defined by three lithostratigraphic units. Laminated deposits of Lake Magadi were formed during a wet period. Analysis of these laminae define two microfacies: a dark lamina, characterised by lacustrine organic matter and a light lamina enriched in detritus, carbonates (CaCO 3) and magadiite (NaSi 7O 13(OH) 3, 3H 2O). The formation and preservation of each couplet was favoured by climatic contrast, lake stratification and various origin of the sediments (autochthon and allochthon) in the drainage basin. Therefore a relative chronology can be derived from laminae counting and the duration of deposition of each couplet. Spectral analysis applied on variation of the laminae thickness, shows the existence of three main periods, 4-7 years, 8-14 years and 18-30 years, respectively (Fig. 2). These cyclicites of the lacustrine environment precise former determinations established on more recent lacustrine sequences from East Africa. They are related to the global climatic cycle (quasi-biannual oscillations, El Nino Southern Oscillations and the sun spot cycles). At Green Crater Lake, the study of the sedimentary sequence was completed by physico-chemical analysis of the waters and interface sediments which demonstrate the carbonate, sodium, bicarbonate composition and the thermal and chemical stratification of the modern lake. The sedimentary sequence is characterized by volcanic deposits overlain by physico-chemical analysis of the lake waters and interface sediments which demonstrate the carbonate, sodium, bicarbonate composition and the thermal and chemical stratification of the modern lake. The sedimentary sequence is characterized by volcanic deposits overlain by silt and clays deposited before 7400 years B.P., followed by loweing of the lake level at 3000 years B. P. Results from lake Magadi document the occurrence of a wet period starting at about 12,000 years B. P. The methodology applied on modern Green Crater lake provides base of interpretative models for other Holocene sequence lacustrine systems of intertropical zones.

Basin evolution of the Paleoproterozoic Karelian Supergroup of the Fennoscandian (Baltic) Shield

NASA Astrophysics Data System (ADS)

Ojakangas, Richard W.; Marmo, Jukka S.; Heiskanen, Kim I.

2001-06-01

The peneplaned Archean craton of the Fennoscandian Shield served as a platform upon which a continental margin assemblage, the Karelian Supergroup, was deposited between ˜2.45 and ˜1.9 Ga. Major subaerial unconformities separate five sedimentary-volcanic groups of the supergroup — the Sumian, Sariolian, Jatulian (Lower and Upper), Ludicovian, and Kalevian. Second-order depositional sequences are implied. Early extension (˜2.45 Ga) resulted in localized rifts that were likely areas of later subsidence as well; they received thicker accumulations of sediments and volcanic rocks than did the adjacent platform. It is in these rifts and perhaps other downwarped areas that the sediments that were once more widespread were preserved, leading to interpretations of separate depositional basins by some workers. Seas transgressed onto the craton at least three times — in Sariolian time as evidenced by interpreted glaciomarine deposits, in Jatulian time as evidenced by widespread orthoquartzites (including tidalites) and stromatolitic carbonates, and in Ludicovian time as evidenced by organic-rich shales and turbidites. The tectonic-magmatic history is complex. Three episodes of mafic volcanism were widespread at 2.45, 2.2, and 2.1 Ga. Island arcs formed to the south of the craton and collided at ˜1.9-1.85 Ga (the Svecofennian orogeny). This collision resulted in northeastward thrusting (e.g. the Outokumpu nappe) and folding and metamorphism of the Karelian Supergroup. The primary paleoclimatic indicators are (1) glaciogenic rocks near the base of the Paleoproterozoic succession indicating ice-house conditions; (2) remnants of a major paleosol on the glaciogenic rocks, indicative of deep weathering under greenhouse conditions (subtropical or tropical?); and (3) carbonate pseudomorphs after evaporite minerals in stromatolitic dolomites, perhaps indicative of aridity. Similarities in magmatism, tectonics, sedimentary rock types and sequences, and paleoclimatic indicators have led to hypotheses that the Fennoscandian Shield and North America may have been part of the same supercontinent during Neoarchean and Paleoproterozoic time.

Geology, ore facies and sulfur isotopes geochemistry of the Nudeh Besshi-type volcanogenic massive sulfide deposit, southwest Sabzevar basin, Iran

NASA Astrophysics Data System (ADS)

Maghfouri, Sajjad; Rastad, Ebrahim; Mousivand, Fardin; Lin, Ye; Zaw, Khin

2016-08-01

The southwest Sabzevar basin is placed in the southwestern part of a crustal domain known as the Sabzevar zone, at the north of Central Iranian microcontinent. This basin hosts abundant mineral deposits; particularly of the Mn exhalative and Cu-Zn volcanogenic massive sulfide (VMS) types. The evolution of this basin is governed by the Neo-tethys oceanic crust subduction beneath the Central Iranian microcontinent and by the resulting continental arc (Sanandaj-Sirjan) and back-arc (Sabzevar-Naien). This evolution followed two major sequences: (I) Lower Late Cretaceous Volcano-Sedimentary Sequence (LLCVSS), which is indicated by fine-grained siliciclastic sediments, gray basic coarse-grained different pyroclastic rocks and bimodal volcanism. During this stage, tuff-hosted stratiform, exhalative Mn deposits (Nudeh, Benesbourd, Ferizy and Goft), oxide Cu deposits (Garab and Ferizy) and Cu-Zn VMS (Nudeh, Chun and Lala) deposits formed. (II) Upper Late Cretaceous Sedimentary Dominated Sequence (ULCSS), including pelagic limestone, marly tuff, silty limestone and marl with minor andesitic tuff rocks. The economically most important Mn (Zakeri and Cheshmeh-sefid) deposits of Sabzevar zone occur within the marly tuff of this sequence. The Nudeh Cu-Zn volcanogenic massive sulfide (VMS) deposit is situated in the LLCVSS. The host-rock of deposits consists of alkali olivine basalt flow and tuffaceous silty sandstone. Mineralization occurs as stratiform blanket-like and tabular orebodies. Based on ore body structure, mineralogy, and ore fabric, we recognize three different ore facies in the Nudeh deposit: (1) a stringer zone, consisting of a discordant mineralization of sulfides forming a stockwork of sulfide-bearing quartz veins cutting the footwall volcano-sedimentary rocks; (2) a massive ore, consisting of massive replacement pyrite, chalcopyrite, sphalerite and Friedrichite with magnetite; (3) bedded ore, with laminated to disseminated pyrite, and chalcopyrite. Chloritization, silicification, sericitization and epidotization are the main wall-rock alterations; alteration intensity increases towards the stringer zone. The δ34S composition of the sulfides ranges from -1.5‰ to +3.69‰ with a general increase of δ34S ratios of massive ore facies to stockwork zone. The heavier values indicate that some of the sulfur was derived from seawater sulfate that was ultimately thermochemically reduced in deep hydrothermal reaction zones. Sulfur isotopes, along with sedimentological, textural, petrological, mineralogical, and geochemical evidences, suggest that this deposit should be classified as a Besshi-type VMS ore deposit.

Third-order dissipative hydrodynamics from the entropy principle

NASA Astrophysics Data System (ADS)

El, Andrej; Xu, Zhe; Greiner, Carsten

2010-06-01

We review the entropy based derivation of third-order hydrodynamic equations and compare their solutions in one-dimensional boost-invariant geometry with calculations by the partonic cascade BAMPS. We demonstrate that Grad's approximation, which underlies the derivation of both Israel-Stewart and third-order equations, describes the transverse spectra from BAMPS with high accuracy. At the same time solutions of third-order equations are much closer to BAMPS results than solutions of Israel-Stewart equations. Introducing a resummation scheme for all higher-oder corrections to one-dimensional hydrodynamic equation we demonstrate the importance of higher-order terms if the Knudsen number is large.

Early Miocene sequence development across the New Jersey margin

USGS Publications Warehouse

Monteverde, D.H.; Mountain, Gregory S.; Miller, K.G.

2008-01-01

Sequence stratigraphy provides an understanding of the interplay between eustasy, sediment supply and accommodation in the sedimentary construction of passive margins. We used this approach to follow the early to middle Miocene growth of the New Jersey margin and analyse the connection between relative changes of sea level and variable sediment supply. Eleven candidate sequence boundaries were traced in high-resolution multi-channel seismic profiles across the inner margin and matched to geophysical log signatures and lithologic changes in ODP Leg 150X onshore coreholes. Chronologies at these drill sites were then used to assign ages to the intervening seismic sequences. We conclude that the regional and global correlation of early Miocene sequences suggests a dominant role of global sea-level change but margin progradation was controlled by localized sediment contribution and that local conditions played a large role in sequence formation and preservation. Lowstand deposits were regionally restricted and their locations point to both single and multiple sediment sources. The distribution of highstand deposits, by contrast, documents redistribution by along shelf currents. We find no evidence that sea level fell below the elevation of the clinoform rollover, and the existence of extensive lowstand deposits seaward of this inflection point indicates efficient cross-shelf sediment transport mechanisms despite the apparent lack of well-developed fluvial drainage. ?? 2008 The Authors. Journal compilation ?? 2008 Blackwell Publishing.

Molecular phylogeny of Systellognatha (Plecoptera: Arctoperlaria) inferred from mitochondrial genome sequences.

PubMed

Chen, Zhi-Teng; Zhao, Meng-Yuan; Xu, Cheng; Du, Yu-Zhou

2018-05-01

The infraorder Systellognatha is the most species-rich clade in the insect order Plecoptera and includes six families in two superfamilies: Pteronarcyoidea (Pteronarcyidae, Peltoperlidae, and Styloperlidae) and Perloidea (Perlidae, Perlodidae, and Chloroperlidae). To resolve the debatable phylogeny of Systellognatha, we carried out the first mitochondrial phylogenetic analysis covering all the six families, including three newly sequenced mitogenomes from two families (Perlodidae and Peltoperlidae) and 15 published mitogenomes. The three newly reported mitogenomes share conserved mitogenomic features with other sequenced stoneflies. For phylogenetic analyses, we assembled five datasets with two inference methods to assess their influence on topology and nodal support within Systellognatha. The results indicated that inclusion of the third codon positions of PCGs, exclusion of rRNA genes, the use of nucleotide datasets and Bayesian inference could improve the phylogenetic reconstruction of Systellognatha. The monophyly of Perloidea was supported in the mitochondrial phylogeny, but Pteronarcyoidea was recovered as paraphyletic and remained controversial. In this mitochondrial phylogenetic study, the relationships within Systellognatha were recovered as (((Perlidae + (Perlodidae + Chloroperlidae)) + (Pteronarcyidae + Styloperlidae)) + Peltoperlidae). Copyright © 2018 Elsevier B.V. All rights reserved.

Export of FepA::PhoA fusion proteins to the outer membrane of Escherichia coli K-12.

PubMed

Murphy, C K; Klebba, P E

1989-11-01

A library of fepA::phoA gene fusions was generated in order to study the structure and secretion of the Escherichia coli K-12 ferric enterobactin receptor, FepA. All of the fusion proteins contained various lengths of the amino-terminal portion of FepA fused in frame to the catalytic portion of bacterial alkaline phosphatase. Localization of FepA::PhoA fusion proteins in the cell envelope was dependent on the number of residues of mature FepA present at the amino terminus. Hybrids containing up to one-third of the amino-terminal portion of FepA fractionated with their periplasm, while those containing longer sequences of mature FepA were exported to the outer membrane. Outer membrane-localized fusion proteins expressed FepA sequences on the external face of the outer membrane and alkaline phosphatase moieties in the periplasmic space. From sequence determinations of the fepA::phoA fusion joints, residues within FepA which may be exposed on the periplasmic side of the outer membrane were identified.

Azimuthal-angle dependence of charged-pion-interferometry measurements with respect to second- and third-order event planes in Au+Au collisions at √[S(NN)]=200  GeV.

PubMed

Adare, A; Afanasiev, S; Aidala, C; Ajitanand, N N; Akiba, Y; Al-Bataineh, H; Alexander, J; Aoki, K; Aramaki, Y; Atomssa, E T; Averbeck, R; Awes, T C; Azmoun, B; Babintsev, V; Bai, M; Baksay, G; Baksay, L; Barish, K N; Bassalleck, B; Basye, A T; Bathe, S; Baublis, V; Baumann, C; Bazilevsky, A; Belikov, S; Belmont, R; Bennett, R; Berdnikov, A; Berdnikov, Y; Bickley, A A; Bok, J S; Boyle, K; Brooks, M L; Buesching, H; Bumazhnov, V; Bunce, G; Butsyk, S; Camacho, C M; Campbell, S; Chen, C-H; Chi, C Y; Chiu, M; Choi, I J; Choudhury, R K; Christiansen, P; Chujo, T; Chung, P; Chvala, O; Cianciolo, V; Citron, Z; Cole, B A; Connors, M; Constantin, P; Csanád, M; Csörgő, T; Dahms, T; Dairaku, S; Danchev, I; Das, K; Datta, A; David, G; Denisov, A; Deshpande, A; Desmond, E J; Dietzsch, O; Dion, A; Donadelli, M; Drapier, O; Drees, A; Drees, K A; Durham, J M; Durum, A; Dutta, D; Edwards, S; Efremenko, Y V; Ellinghaus, F; Engelmore, T; Enokizono, A; En'yo, H; Esumi, S; Fadem, B; Fields, D E; Finger, M; Finger, M; Fleuret, F; Fokin, S L; Fraenkel, Z; Frantz, J E; Franz, A; Frawley, A D; Fujiwara, K; Fukao, Y; Fusayasu, T; Garishvili, I; Glenn, A; Gong, H; Gonin, M; Goto, Y; Granier de Cassagnac, R; Grau, N; Greene, S V; Grosse Perdekamp, M; Gunji, T; Gustafsson, H-Å; Haggerty, J S; Hahn, K I; Hamagaki, H; Hamblen, J; Han, R; Hanks, J; Hartouni, E P; Haslum, E; Hayano, R; He, X; Heffner, M; Hemmick, T K; Hester, T; Hill, J C; Hohlmann, M; Holzmann, W; Homma, K; Hong, B; Horaguchi, T; Hornback, D; Huang, S; Ichihara, T; Ichimiya, R; Ide, J; Ikeda, Y; Imai, K; Inaba, M; Isenhower, D; Ishihara, M; Isobe, T; Issah, M; Isupov, A; Ivanischev, D; Jacak, B V; Jia, J; Jin, J; Johnson, B M; Joo, K S; Jouan, D; Jumper, D S; Kajihara, F; Kametani, S; Kamihara, N; Kamin, J; Kang, J H; Kapustinsky, J; Karatsu, K; Kawall, D; Kawashima, M; Kazantsev, A V; Kempel, T; Khanzadeev, A; Kijima, K M; Kim, B I; Kim, D H; Kim, D J; Kim, E; Kim, E-J; Kim, S H; Kim, Y-J; Kinney, E; Kiriluk, K; Kiss, A; Kistenev, E; Kochenda, L; Komkov, B; Konno, M; Koster, J; Kotchetkov, D; Kozlov, A; Král, A; Kravitz, A; Kunde, G J; Kurita, K; Kurosawa, M; Kwon, Y; Kyle, G S; Lacey, R; Lai, Y S; Lajoie, J G; Lebedev, A; Lee, D M; Lee, J; Lee, K; Lee, K B; Lee, K S; Leitch, M J; Leite, M A L; Leitner, E; Lenzi, B; Li, X; Liebing, P; Linden Levy, L A; Liška, T; Litvinenko, A; Liu, H; Liu, M X; Love, B; Luechtenborg, R; Lynch, D; Maguire, C F; Makdisi, Y I; Malakhov, A; Malik, M D; Manko, V I; Mannel, E; Mao, Y; Masui, H; Matathias, F; McCumber, M; McGaughey, P L; Means, N; Meredith, B; Miake, Y; Mignerey, A C; Mikeš, P; Miki, K; Milov, A; Mishra, M; Mitchell, J T; Mohanty, A K; Morino, Y; Morreale, A; Morrison, D P; Moukhanova, T V; Murata, J; Nagamiya, S; Nagle, J L; Naglis, M; Nagy, M I; Nakagawa, I; Nakamiya, Y; Nakamura, T; Nakano, K; Newby, J; Nguyen, M; Niida, T; Nouicer, R; Nyanin, A S; O'Brien, E; Oda, S X; Ogilvie, C A; Oka, M; Okada, K; Onuki, Y; Oskarsson, A; Ouchida, M; Ozawa, K; Pak, R; Pantuev, V; Papavassiliou, V; Park, I H; Park, J; Park, S K; Park, W J; Pate, S F; Pei, H; Peng, J-C; Pereira, H; Peresedov, V; Peressounko, D Yu; Pinkenburg, C; Pisani, R P; Proissl, M; Purschke, M L; Purwar, A K; Qu, H; Rak, J; Rakotozafindrabe, A; Ravinovich, I; Read, K F; Reygers, K; Riabov, V; Riabov, Y; Richardson, E; Roach, D; Roche, G; Rolnick, S D; Rosati, M; Rosen, C A; Rosendahl, S S E; Rosnet, P; Rukoyatkin, P; Ružička, P; Sahlmueller, B; Saito, N; Sakaguchi, T; Sakashita, K; Samsonov, V; Sano, S; Sato, T; Sawada, S; Sedgwick, K; Seele, J; Seidl, R; Semenov, A Yu; Seto, R; Sharma, D; Shein, I; Shibata, T-A; Shigaki, K; Shimomura, M; Shoji, K; Shukla, P; Sickles, A; Silva, C L; Silvermyr, D; Silvestre, C; Sim, K S; Singh, B K; Singh, C P; Singh, V; Slunečka, M; Soltz, R A; Sondheim, W E; Sorensen, S P; Sourikova, I V; Sparks, N A; Stankus, P W; Stenlund, E; Stoll, S P; Sugitate, T; Sukhanov, A; Sziklai, J; Takagui, E M; Taketani, A; Tanabe, R; Tanaka, Y; Tanida, K; Tannenbaum, M J; Tarafdar, S; Taranenko, A; Tarján, P; Themann, H; Thomas, T L; Todoroki, T; Togawa, M; Toia, A; Tomášek, L; Torii, H; Towell, R S; Tserruya, I; Tsuchimoto, Y; Vale, C; Valle, H; van Hecke, H W; Vazquez-Zambrano, E; Veicht, A; Velkovska, J; Vértesi, R; Vinogradov, A A; Virius, M; Vrba, V; Vznuzdaev, E; Wang, X R; Watanabe, D; Watanabe, K; Watanabe, Y; Wei, F; Wei, R; Wessels, J; White, S N; Winter, D; Wood, J P; Woody, C L; Wright, R M; Wysocki, M; Xie, W; Yamaguchi, Y L; Yamaura, K; Yang, R; Yanovich, A; Ying, J; Yokkaichi, S; You, Z; Young, G R; Younus, I; Yushmanov, I E; Zajc, W A; Zhang, C; Zhou, S; Zolin, L

2014-06-06

Charged-pion-interferometry measurements were made with respect to the second- and third-order event plane for Au+Au collisions at sqrt[s_{NN}]=200  GeV. A strong azimuthal-angle dependence of the extracted Gaussian-source radii was observed with respect to both the second- and third-order event planes. The results for the second-order dependence indicate that the initial eccentricity is reduced during the medium evolution, which is consistent with previous results. In contrast, the results for the third-order dependence indicate that the initial triangular shape is significantly reduced and potentially reversed by the end of the medium evolution, and that the third-order oscillations are largely dominated by the dynamical effects from triangular flow.

Mesoscale Particle-Based Model of Electrophoretic Deposition

DOE PAGES

Giera, Brian; Zepeda-Ruiz, Luis A.; Pascall, Andrew J.; ...

2016-12-20

In this paper, we present and evaluate a semiempirical particle-based model of electrophoretic deposition using extensive mesoscale simulations. We analyze particle configurations in order to observe how colloids accumulate at the electrode and arrange into deposits. In agreement with existing continuum models, the thickness of the deposit increases linearly in time during deposition. Resulting colloidal deposits exhibit a transition between highly ordered and bulk disordered regions that can give rise to an appreciable density gradient under certain simulated conditions. The overall volume fraction increases and falls within a narrow range as the driving force due to the electric field increasesmore » and repulsive intercolloidal interactions decrease. We postulate ordering and stacking within the initial layer(s) dramatically impacts the microstructure of the deposits. Finally, we find a combination of parameters, i.e., electric field and suspension properties, whose interplay enhances colloidal ordering beyond the commonly known approach of only reducing the driving force.« less

Development of high repetition rate nitric oxide planar laser induced fluorescence imaging

NASA Astrophysics Data System (ADS)

Jiang, Naibo

This thesis has documented the development of a MHz repitition rate pulse burst laser system. Second harmonic and third harmonic efficiencies are improved by adding a Phase Conjugate Mirror to the system. Some high energy fundamental, second harmonic, and third harmonic burst sequences consisting of 1--12 pulses separated in time by between 4 and 12 microseconds are now routinely obtained. The reported burst envelopes are quite uniform. We have also demonstrated the ability to generate ultra-high frequency sequences of broadly wavelength tunable, high intensity laser pulses using a home built injection seeded Optical Parametric Oscillator (OPO), pumped by the second and third harmonic output of the pulse burst laser. Typical OPO output burst sequences consist of 6--10 pulses, separated in time by between 6 and 10 microseconds. With third harmonic pumping of the OPO system, we studied four conditions, two-crystal Singly Resonant OPO (SRO) cavity, three-crystal OPO cavity, single pass two-crystal Doubly Resonant OPO (DRO) cavity and double pass two-crystal OPO cavity. The double pass two-crystal OPO cavity gives the best operation in burst mode. For single pass OPO, the average total OPO conversion efficiency is approximately 25%. For double pass OPO, the average total OPO conversion efficiency is approximately 35%. As a preliminary work, we studied 532nm pumping of a single crystal OPO cavity. With single pulse pumping, the conversion efficiency can reach 30%. For both 355nm and 532nm pumping OPO, we have demonstrated injection seeding. The OPO output light linewidth is significantly narrowed. Some preliminary etalon traces are also reported. By mixing the OPO signal output at 622nm with residual third harmonic at 355nm, we obtained 226nm burst sequences with average pulse energy of ˜0.2 mJ. Injection seeding of the OPO increases the energy achieved by a factor of ˜2. 226nm burst sequences with reasonably uniform burst envelopes are reported. Using the system we have obtained, for the first time by any known optical method, Planar Laser Induced Fluorescence (PLIF) image sequences at ultrahigh (≥100kHz) frame rates, in particular NO PLIF image sequences, have been obtained in a Mach 2 jet. We also studied the possibility of utilizing a 250 kHz pulsed Nd:YVO 4 laser as the master oscillator. 10-pulse-10-mus spacing burst sequences with reasonably uniform burst envelope have been obtained. The total energy of the burst sequence is ˜2.5J.

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.

Molecular analysis of carbon monoxide-oxidizing bacteria associated with recent Hawaiian volcanic deposits.

PubMed

Dunfield, Kari E; King, Gary M

2004-07-01

Genomic DNA extracts from four sites at Kilauea Volcano were used as templates for PCR amplification of the large subunit (coxL) of aerobic carbon monoxide dehydrogenase. The sites included a 42-year-old tephra deposit, a 108-year-old lava flow, a 212-year-old partially vegetated ash-and-tephra deposit, and an approximately 300-year-old forest. PCR primers amplified coxL sequences from the OMP clade of CO oxidizers, which includes isolates such as Oligotropha carboxidovorans, Mycobacterium tuberculosis, and Pseudomonas thermocarboxydovorans. PCR products were used to create clone libraries that provide the first insights into the diversity and phylogenetic affiliations of CO oxidizers in situ. On the basis of phylogenetic and statistical analyses, clone libraries for each site were distinct. Although some clone sequences were similar to coxL sequences from known organisms, many sequences appeared to represent phylogenetic lineages not previously known to harbor CO oxidizers. On the basis of average nucleotide diversity and average pairwise difference, a forested site supported the most diverse CO-oxidizing populations, while an 1894 lava flow supported the least diverse populations. Neither parameter correlated with previous estimates of atmospheric CO uptake rates, but both parameters correlated positively with estimates of microbial biomass and respiration. Collectively, the results indicate that the CO oxidizer functional group associated with recent volcanic deposits of the remote Hawaiian Islands contains substantial and previously unsuspected diversity.

Facies analysis and sequence stratigraphy of neoproterozoic Platform deposits in Adrar of Mauritania, Taoudeni basin, West Africa

NASA Astrophysics Data System (ADS)

Benan, C. A. A.; Deynoux, M.

The Neoproterozoic and Palaeozoic Taoudeni basin forms the flat-lying and unmetamorphosed sedimentary cover of the West African Craton. In the western part of this basin, the Char Group and the lower part of the Atar Group make up a 400-m-thick Neoproterozoic siliciclastic succession which rests on the Palaeoproterozoic metamorphic and granitic basement. Five erosional bounding surfaces of regional extent have been identified in this succession. These surfaces separate five stratigraphic units with lithofacies associations ranging from fluvial to coastal and fluvial-, tide-, or wave-dominated shallow marine deposits. Owing to their regional extent and their position within the succession, the erosive bounding surfaces correspond to relative sea-level falls, and accordingly the five stratigraphic units they bound represent allocyclic transgressive-regressive depositional sequences (S1-S5). Changes in the nature of the deposits forming the transgressive-regressive cycles reflect landward or seaward shifts of the stacked sequences. These successive relative sea-level changes are related to the reactivation of basement faults and tilting during rifting of the Pan-Afro-Brasiliano supercontinent 1000 m.y. ago. The stromatolite bearing carbonate-shale sequences which form the rest of the Atar Group mark the onset of a quiet period of homogeneous subsidence contemporaneous with the Pan-African I oceanization 800-700 m.y. ago.

Integrated diagenetic and sequence stratigraphy of a late Oligocene-early Miocene, mixed-sediment platform (Austral Basin, southern Patagonia): Resolving base-level and paleoceanographic changes, and paleoaquifer characteristics

NASA Astrophysics Data System (ADS)

Dix, George R.; Parras, Ana

2014-06-01

A condensed (~ 20-m-thick) marine transgressive-highstand succession comprises the upper San Julián Formation (upper Oligocene-lower Miocene) of the northern retroarc Austral Basin, southern Patagonia. Mixed-sediment facies identify a shelf-interior setting, part of an overall warm-temperate regional platform of moderate energy. Giant oyster-dominated skeletal-hiatal accumulations along the maximum flooding surface and forming high-energy event beds in the highstand succession preserve relict micrite in protected shelter porosity, and identify periods of reduced sediment accumulation. The stratigraphic distribution of marine-derived glaucony and diagenetic carbonates is spatially related to sequence development. Depositional siderite coincides with prominent marine transgression, defining transient mixing of marine and meteoric waters across coastal-plain deposits. Chemically evolved autochthonous glaucony coincides with periods of extended seafloor exposure and transgressions that bracket the marine succession, and within the oyster-dominated skeletal accumulations. Seafloor cement, likely once magnesian calcite, formed in association with an encrusting/boring biota along the maximum flooding surface in concert with incursion of cool (11-13 °C) water. The cement is present locally in skeletal event beds in the highstand succession suggesting a possible association with high-order base-level change and cooler water. As the highstand succession coincides with elevated global sea level in the late Oligocene-early Miocene, the locally marine-cemented glauconitic skeletal event beds in the highstand succession may identify higher order glacio-eustatic control. Local stratal condensation, however, is best explained by regional differences in basement subsidence. In the burial realm, carbonate diagenesis produced layers of phreatic calcrete coincident with skeletal-rich deposits. Zeolite (clinoptilolite-K) cement is restricted to the lowermost marine transgressive interval probably due to initial elevated metastability of reworked weathered silicates. Clay (illite)-cement is restricted to siliciclastic-rich intervals wherein skeletal carbonate did not buffer pore-water pH. Diagenetic carbonate geochemistry (Sr, Na, and δ18O and δ13C) shows that, with burial, the transgressive and highstand system tracts developed as distinct paleoaquifers resulting from different proximities to meteoric recharge zones.

Interface inequivalence of the InP/InAlAs/InP staggered double heterostructure grown by metalorganic chemical vapor deposition

NASA Astrophysics Data System (ADS)

Böhrer, J.; Krost, A.; Heitz, R.; Heinrichsdorff, F.; Eckey, L.; Bimberg, D.; Cerva, H.

1996-02-01

The optical and structural properties of the normal InAlAs on InP and the inverted InP on the InAlAs staggered band lineup interface grown by metalorganic chemical vapor deposition (MOCVD) are compared by use of transmission electron microscopy (TEM), time integrated, and time resolved photoluminescence. TEM images show that both interfaces are dissimilar. The normal interface is very abrupt. The inverted interface shows an additional graded layer of about 2.5 nm in width of In1-xAlxAsyP1-y with x (0.48-0) and y (1.0-0.0). A large optical anisotropy exists because of the inequivalence of the two interfaces. The larger spatial separation of the carriers at the inverted interface is responsible for a smaller overlap of the electron and hole wave functions and for that reason a one order of magnitude longer e-h luminescence decay time of 45 ns is observed. The normal interface transition shifts approximately to the third root of excitation while the inverted interface transition shifts logarithmically.

Eruptive history of the Ubehebe Crater cluster, Death Valley, California

NASA Astrophysics Data System (ADS)

Fierstein, Judy; Hildreth, Wes

2017-04-01

A sequence of late Holocene eruptions from the Ubehebe Crater cluster in Death Valley was short-lived, emplacing several phreatomagmatic and magmatic deposits. Seven craters form the main group, which erupted along a north-south alignment 1.5 km long. At least five more make a 500-m east-west alignment west of the main crater group. One more is an isolated shallow crater 400 m south of that alignment. All erupted through Miocene fanglomerate and sandstone, which are now distributed as comminuted matrix and lithic clasts in all Ubehebe deposits. Stratigraphic evidence showing that all Ubehebe strata were emplaced within a short time interval includes: (1) deposits from the many Ubehebe vents make a multi-package sequence that conformably drapes paleo-basement topography with no erosive gullying between emplacement units; (2) several crater rims that formed early in the eruptive sequence are draped smoothly by subsequent deposits; and (3) tack-welded to agglutinated spatter and bombs that erupted at various times through the sequence remained hot enough to oxidize the overlying youngest emplacement package. In addition, all deposits sufficiently consolidated to be drilled yield reliable paleomagnetic directions, with site mean directions showing no evidence of geomagnetic secular variation. Chemical analyses of juvenile components representing every eruptive package yield a narrow range in major elements [SiO2 (48.65-50.11); MgO (4.98-6.23); K2O (2.24-2.39)] and trace elements [Rb (28-33); Sr (1513-1588); Zr (373-404)]. Despite lithologic similarities, individual fall units can be traced outward from vent by recording layer thicknesses, maximum scoria and lithic sizes, and juvenile clast textural variations. This permits reconstruction of the eruptive sequence, which produced a variety of eruptive styles. The largest and northernmost of the craters, Ubehebe Crater, is the youngest of the group. Its largely phreatomagmatic deposits drape all of the others, thicken in paleogullies and thin over several newly created crater rims. Evidence in-hand virtually requires that the Ubehebe cluster of craters erupted over a brief time interval, not protracted over centuries.

Direct dry transfer of CVD graphene to an optical substrate by in situ photo-polymerization

NASA Astrophysics Data System (ADS)

Kessler, Felipe; Muñoz, Pablo A. R.; Phelan, Ciaran; Romani, Eric C.; Larrudé, Dunieskys R. G.; Freire, Fernando L.; Thoroh de Souza, Eunézio A.; de Matos, Christiano J. S.; Fechine, Guilhermino J. M.

2018-05-01

Here, we report on a method that allows graphene produced by chemical vapor deposition (CVD) to be directly transferred to an optically transparent photo resin, by in situ photo-polymerization of the latter, with high efficiency and low contamination. Two photocurable resins, A and B, with different viscosities but essentially the same chemical structure, were used. Raman spectroscopy and surface energy results show that large continuous areas of graphene were transferred with minimal defects to the lower viscosity resin (B), due to the better contact between the resin and graphene. As a proof-of-principle optical experiment, graphene on the polymeric substrate was subjected to high-intensity femtosecond infrared pulses and third-harmonic generation was observed with no noticeable degradation of the sample. A sheet third-order susceptibility χ (3) = 0.71 ×10-28m3V-2 was obtained, matching that of graphene on a glass substrate. These results indicate the suitability of the proposed transfer method, and of the photo resin, for the production of nonlinear photonic components and devices.

Palaeoclimate characteristics in interior Siberia of MIS 6-2: first insights from the Batagay permafrost mega-thaw slump in the Yana Highlands

NASA Astrophysics Data System (ADS)

Ashastina, Kseniia; Schirrmeister, Lutz; Fuchs, Margret; Kienast, Frank

2017-07-01

Syngenetic permafrost deposits formed extensively on and around the arising Beringian subcontinent during the Late Pleistocene sea level lowstands. Syngenetic deposition implies that all material, both mineral and organic, freezes parallel to sedimentation and remains frozen until degradation of the permafrost. Permafrost is therefore a unique archive of Late Pleistocene palaeoclimate. Most studied permafrost outcrops are situated in the coastal lowlands of northeastern Siberia; inland sections are, however, scarcely available. Here, we describe the stratigraphical, cryolithological, and geochronological characteristics of a permafrost sequence near Batagay in the Siberian Yana Highlands, the interior of the Sakha Republic (Yakutia), Russia, with focus on the Late Pleistocene Yedoma ice complex (YIC). The recently formed Batagay mega-thaw slump exposes permafrost deposits to a depth of up to 80 m and gives insight into a climate record close to Verkhoyansk, which has the most severe continental climate in the Northern Hemisphere. Geochronological dating (optically stimulated luminescence, OSL, and 14C ages) and stratigraphic implications delivered a temporal frame from the Middle Pleistocene to the Holocene for our sedimentological interpretations and also revealed interruptions in the deposition. The sequence of lithological units indicates a succession of several distinct climate phases: a Middle Pleistocene ice complex indicates cold stage climate. Then, ice wedge growth stopped due to highly increased sedimentation rates and eventually a rise in temperature. Full interglacial climate conditions existed during accumulation of an organic-rich layer - plant macrofossils reflected open forest vegetation existing under dry conditions during Marine Isotope Stage (MIS) 5e. The Late Pleistocene YIC (MIS 4-MIS 2) suggests severe cold-stage climate conditions. No alas deposits, potentially indicating thermokarst processes, were detected at the site. A detailed comparison of the permafrost deposits exposed in the Batagay thaw slump with well-studied permafrost sequences, both coastal and inland, is made to highlight common features and differences in their formation processes and palaeoclimatic histories. Fluvial and lacustrine influence is temporarily common in the majority of permafrost exposures, but has to be excluded for the Batagay sequence. We interpret the characteristics of permafrost deposits at this location as a result of various climatically induced processes that are partly seasonally controlled. Nival deposition might have been dominant during winter time, whereas proluvial and aeolian deposition could have prevailed during the snowmelt period and the dry summer season.

Stratigraphic, Granulometric and Geochemical Studies of a Major Plinian Eruption on Dominica, Lesser Antilles

NASA Astrophysics Data System (ADS)

Smith, A. L.; Daly, G.; Killingsworth, N.; Deuerling, K.; Schneider, S.; Fryxell, J. E.

2008-12-01

The island of Dominica, located in the center of the Lesser Antilles island arc has witnessed, probably within the last 100,000 years, three large volume Plinian eruptions. One of these, associated with the Morne Diablotins center, forms the Grande Savane pyroclastic flow fan, that extends off shore as a distinctive submarine feature for a distance of at least 14 km. Stratigraphical studies of road cuts and well-exposed sea cliffs indicate the fan is composed of an older unit composed of reworked deposits at the base followed by at least four sequences, based on the presence of paleosols, of block and ash flow deposits. The upper unit of block and ash flows is overlain, with no evidence of an intervening paleosol, by a sequence of ignimbrites and pumiceous surges (representing the Plinian eruption). There is no evidence of an initial Plinian fall deposit, so the lowest bed in the succession is an ignimbrite with a highly irregular base that cuts into the underlying block and ash flow deposits, the upper parts of which are colored red due to thermal effects. This lowest ignimbrite is welded (minimum porosity of 15%) throughout its thickness (maximum thickness of greater than 21 m), although a few outcrops near the margins show a thin (20-30 cm) non-welded but lithified zone beneath the welded zone. The remainder of the sequence is composed of lithified ignimbrite that can be subdivided into three units separated by pumiceous surge layers. The ignimbrite succession is overlain, with no obvious break, by a thin fall deposit containing accretionary lapilli and gas cavities, followed by three pumiceous surge deposits (lower and upper show planar stratification and the middle surge shows massive bedding); towards the north the upper two surge deposits are separated by thin pumiceous lapilli fall and ash fall deposits. This surge sequence extends laterally outside of the main area of ignimbrite deposition. The pumice clasts from the ignimbrites are andesitic in composition and show essentially no variation up stratigraphy. In contrast, the surges are more variable in composition, ranging from andesite to dacite. Modeling of these data will provide information on the dynamics of this major Plinian eruption including the effects of water/magma interaction.

A short introduction to cytogenetic studies in mammals with reference to the present volume.

PubMed

Graphodatsky, A; Ferguson-Smith, M A; Stanyon, R

2012-01-01

Genome diversity has long been studied from the comparative cytogenetic perspective. Early workers documented differences between species in diploid chromosome number and fundamental number. Banding methods allowed more detailed descriptions of between-species rearrangements and classes of differentially staining chromosome material. The infusion of molecular methods into cytogenetics provided a third revolution, which is still not exhausted. Chromosome painting has provided a global view of the translocation history of mammalian genome evolution, well summarized in the contributions to this special volume. More recently, FISH of cloned DNA has provided details on defining breakpoint and intrachromosomal marker order, which have helped to document inversions and centromere repositioning. The most recent trend in comparative molecular cytogenetics is to integrate sequencing information in order to formulate and test reconstructions of ancestral genomes and phylogenomic hypotheses derived from comparative cytogenetics. The integration of comparative cytogenetics and sequencing promises to provide an understanding of what drives chromosome rearrangements and genome evolution in general. We believe that the contributions in this volume, in no small way, point the way to the next phase in cytogenetic studies. Copyright © 2012 S. Karger AG, Basel.

A Deep Insight Into the Sialotranscriptome of the Chagas Disease Vector, Panstrongylus megistus (Hemiptera: Heteroptera)

PubMed Central

Ribeiro, José M. C.; Schwarz, Alexandra; Francischetti, Ivo M. B.

2015-01-01

Saliva of blood-sucking arthropods contains a complex cocktail of pharmacologically active compounds that assists feeding by counteracting their hosts’ hemostatic and inflammatory reactions. Panstrongylus megistus (Burmeister) is an important vector of Chagas disease in South America, but despite its importance there is only one salivary protein sequence publicly deposited in GenBank. In the present work, we used Illumina technology to disclose and publicly deposit 3,703 coding sequences obtained from the assembly of >70 million reads. These sequences should assist proteomic experiments aimed at identifying pharmacologically active proteins and immunological markers of vector exposure. A supplemental file of the transcriptome and deducted protein sequences can be obtained from http://exon.niaid.nih.gov/transcriptome/P_megistus/Pmeg-web.xlsx. PMID:26334808

Architectures and criteria for the design of high efficiency organic photovoltaic cells

DOEpatents

Rand, Barry; Forrest, Stephen R; Pendergrast Burk, Diane

2015-03-31

A method for fabricating an organic photovoltaic cell includes providing a first electrode; depositing a series of at least seven layers onto the first electrode, each layer consisting essentially of a different organic semiconductor material, the organic semiconductor material of at least an intermediate layer of the sequence being a photoconductive material; and depositing a second electrode onto the sequence of at least seven layers. One of the first electrode and the second electrode is an anode and the other is a cathode. The organic semiconductor materials of the series of at least seven layers are arranged to provide a sequence of decreasing lowest unoccupied molecular orbitals (LUMOs) and a sequence of decreasing highest occupied molecular orbitals (HOMOs) across the series from the anode to the cathode.

Distinguishing thrust sequences in gravity-driven fold and thrust belts

NASA Astrophysics Data System (ADS)

Alsop, G. I.; Weinberger, R.; Marco, S.

2018-04-01

Piggyback or foreland-propagating thrust sequences, where younger thrusts develop in the footwalls of existing thrusts, are generally assumed to be the typical order of thrust development in most orogenic settings. However, overstep or 'break-back' sequences, where later thrusts develop above and in the hangingwalls of earlier thrusts, may potentially form during cessation of movement in gravity-driven mass transport deposits (MTDs). In this study, we provide a detailed outcrop-based analysis of such an overstep thrust sequence developed in an MTD in the southern Dead Sea Basin. Evidence that may be used to discriminate overstep thrusting from piggyback thrust sequences within the gravity-driven fold and thrust belt includes upright folds and forethrusts that are cut by younger overlying thrusts. Backthrusts form ideal markers that are also clearly offset and cut by overlying younger forethrusts. Portions of the basal detachment to the thrust system are folded and locally imbricated in footwall synclines below forethrust ramps, and these geometries also support an overstep sequence. However, new 'short-cut' basal detachments develop below these synclines, indicating that movement continued on the basal detachment rather than it being abandoned as in classic overstep sequences. Further evidence for 'synchronous thrusting', where movement on more than one thrust occurs at the same time, is provided by displacement patterns on sequences of thrust ramp imbricates that systematically increases downslope towards the toe of the MTD. Older thrusts that initiate downslope in the broadly overstep sequence continue to move and therefore accrue greater displacements during synchronous thrusting. Our study provides a template to help distinguish different thrust sequences in both orogenic settings and gravity-driven surficial systems, with displacement patterns potentially being imaged in seismic sections across offshore MTDs.

Ordered mapping of 3 alphoid DNA subsets on human chromosome 22

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

Antonacci, R.; Baldini, A.; Archidiacono, N.

1994-09-01

Alpha satellite DNA consists of tandemly repeated monomers of 171 bp clustered in the centromeric region of primate chromosomes. Sequence divergence between subsets located in different human chromosomes is usually high enough to ensure chromosome-specific hybridization. Alphoid probes specific for almost every human chromosome have been reported. A single chromosome can carry different subsets of alphoid DNA and some alphoid subsets can be shared by different chromosomes. We report the physical order of three alphoid DNA subsets on human chromosome 22 determined by a combination of low and high resolution cytological mapping methods. Results visually demonstrate the presence of threemore » distinct alphoid DNA domains at the centromeric region of chromosome 22. We have measured the interphase distances between the three probes in three-color FISH experiments. Statistical analysis of the results indicated the order of the subsets. Two color experiments on prometaphase chromosomes established the order of the three domains relative to the arms of chromosome 22 and confirmed the results obtained using interphase mapping. This demonstrates the applicability of interphase mapping for alpha satellite DNA orderering. However, in our experiments, interphase mapping did not provide any information about the relationship between extremities of the repeat arrays. This information was gained from extended chromatin hybridization. The extremities of two of the repeat arrays were seen to be almost overlapping whereas the third repeat array was clearly separated from the other two. Our data show the value of extended chromatin hybridization as a complement of other cytological techniques for high resolution mapping of repetitive DNA sequences.« less

An exploratory drilling exhaustion sequence plot program

USGS Publications Warehouse

Schuenemeyer, J.H.; Drew, L.J.

1977-01-01

The exhaustion sequence plot program computes the conditional area of influence for wells in a specified rectangular region with respect to a fixed-size deposit. The deposit is represented by an ellipse whose size is chosen by the user. The area of influence may be displayed on computer printer plots consisting of a maximum of 10,000 grid points. At each point, a symbol is presented that indicates the probability of that point being exhausted by nearby wells with respect to a fixed-size ellipse. This output gives a pictorial view of the manner in which oil fields are exhausted. In addition, the exhaustion data may be used to estimate the number of deposits remaining in a basin. ?? 1977.

The influence of slope-angle ratio on the dynamics of granular flows: insights from laboratory experiments

NASA Astrophysics Data System (ADS)

Sulpizio, R.; Castioni, D.; Rodriguez-Sedano, L. A.; Sarocchi, D.; Lucchi, F.

2016-11-01

Laboratory experiments on granular flows using natural material were carried out in order to investigate the behaviour of granular flows passing over a break in slope. Sensors in the depositional area recorded the flow kinematics, while video footage permitted reconstruction of the deposit formation, which allowed investigation of the deposit shape as a function of the change in slope. We defined the slope-angle ratio as the proportion between slope angle in the depositional area and that of the channel. When the granular flow encounters the break in slope part of the flow front forms a bouncing clast zone due to elastic impact with the expansion box floor. During this process, part of the kinetic energy of the dense granular flow is transferred to elutriating fine ash, which subsequently forms turbulent ash cloud accompanying the granular flow until it comes to rest. Morphometric analysis of the deposits shows that they are all elliptical, with an almost constant minor axis and a variable major axis. The almost constant value of the minor axis relates to the spreading angle of flow at the end of the channel, which resembles the basal friction angle of the material. The variation of the major axis is interpreted to relate to the effect of competing inertial and frictional forces. This effect also reflects the partitioning of centripetal and tangential velocities, which changes as the flow passes over the break in slope. After normalization, morphometric data provided empirical relationships that highlight the dependence of runout from the product of slope-angle ratio and the difference in height between granular material release and deposit. The empirical relationships were tested against the runouts of hot avalanches formed during the 1944 ad eruption at Vesuvius, with differences among actual and calculated values are between 1.7 and 15 %. Velocity measurements of laboratory granular flows record deceleration paths at different breaks in slope. When normalized, the velocity data show third-order polynomial fit, highlighting a complex behaviour involving interplay between inertial and frictional forces. The theoretical velocity decays were tested against the data published for volcaniclastic debris flows of the 5-6 May 1998 event in the Sarno area. The comparison is very good for non-channelized debris flows, with significant differences between actual and calculated velocities for the channelized debris flows.

Comparison of Metabolic Pathways in Escherichia coli by Using Genetic Algorithms.

PubMed

Ortegon, Patricia; Poot-Hernández, Augusto C; Perez-Rueda, Ernesto; Rodriguez-Vazquez, Katya

2015-01-01

In order to understand how cellular metabolism has taken its modern form, the conservation and variations between metabolic pathways were evaluated by using a genetic algorithm (GA). The GA approach considered information on the complete metabolism of the bacterium Escherichia coli K-12, as deposited in the KEGG database, and the enzymes belonging to a particular pathway were transformed into enzymatic step sequences by using the breadth-first search algorithm. These sequences represent contiguous enzymes linked to each other, based on their catalytic activities as they are encoded in the Enzyme Commission numbers. In a posterior step, these sequences were compared using a GA in an all-against-all (pairwise comparisons) approach. Individual reactions were chosen based on their measure of fitness to act as parents of offspring, which constitute the new generation. The sequences compared were used to construct a similarity matrix (of fitness values) that was then considered to be clustered by using a k-medoids algorithm. A total of 34 clusters of conserved reactions were obtained, and their sequences were finally aligned with a multiple-sequence alignment GA optimized to align all the reaction sequences included in each group or cluster. From these comparisons, maps associated with the metabolism of similar compounds also contained similar enzymatic step sequences, reinforcing the Patchwork Model for the evolution of metabolism in E. coli K-12, an observation that can be expanded to other organisms, for which there is metabolism information. Finally, our mapping of these reactions is discussed, with illustrations from a particular case.

Comparison of Metabolic Pathways in Escherichia coli by Using Genetic Algorithms

PubMed Central

Ortegon, Patricia; Poot-Hernández, Augusto C.; Perez-Rueda, Ernesto; Rodriguez-Vazquez, Katya

2015-01-01

In order to understand how cellular metabolism has taken its modern form, the conservation and variations between metabolic pathways were evaluated by using a genetic algorithm (GA). The GA approach considered information on the complete metabolism of the bacterium Escherichia coli K-12, as deposited in the KEGG database, and the enzymes belonging to a particular pathway were transformed into enzymatic step sequences by using the breadth-first search algorithm. These sequences represent contiguous enzymes linked to each other, based on their catalytic activities as they are encoded in the Enzyme Commission numbers. In a posterior step, these sequences were compared using a GA in an all-against-all (pairwise comparisons) approach. Individual reactions were chosen based on their measure of fitness to act as parents of offspring, which constitute the new generation. The sequences compared were used to construct a similarity matrix (of fitness values) that was then considered to be clustered by using a k-medoids algorithm. A total of 34 clusters of conserved reactions were obtained, and their sequences were finally aligned with a multiple-sequence alignment GA optimized to align all the reaction sequences included in each group or cluster. From these comparisons, maps associated with the metabolism of similar compounds also contained similar enzymatic step sequences, reinforcing the Patchwork Model for the evolution of metabolism in E. coli K-12, an observation that can be expanded to other organisms, for which there is metabolism information. Finally, our mapping of these reactions is discussed, with illustrations from a particular case. PMID:25973143

A new methodology for inter- and intrafraction plan adaptation for the MR-linac

NASA Astrophysics Data System (ADS)

Kontaxis, C.; Bol, G. H.; Lagendijk, J. J. W.; Raaymakers, B. W.

2015-10-01

The new era of hybrid MRI and linear accelerator machines, including the MR-linac currently being installed in the University Medical Center Utrecht (Utrecht, The Netherlands), will be able to provide the actual anatomy and real-time anatomy changes of the patient’s target(s) and organ(s) at risk (OARs) during radiation delivery. In order to be able to take advantage of this input, a new generation of treatment planning systems is needed, that will allow plan adaptation to the latest anatomy state in an online regime. In this paper, we present a treatment planning algorithm for intensity-modulated radiotherapy (IMRT), which is able to compensate for patient anatomy changes. The system consists of an iterative sequencing loop open to anatomy updates and an inter- and intrafraction adaptation scheme that enables convergence to the ideal dose distribution without the need of a final segment weight optimization (SWO). The ability of the system to take into account organ motion and adapt the plan to the latest anatomy state is illustrated using artificial baseline shifts created for three different kidney cases. Firstly, for two kidney cases of different target volumes, we show that the system can account for intrafraction motion, delivering the intended dose to the target with minimal dose deposition to the surroundings compared to conventional plans. Secondly, for a third kidney case we show that our algorithm combined with the interfraction scheme can be used to deliver the prescribed dose while adapting to the changing anatomy during multi-fraction treatments without performing a final SWO.

Bulgarian Rila mountain forest ecosystems study site: site description and SO42-, NO3- deposition

Treesearch

Karl Zeller; Christo Bojinov; Evgeny Donev; Nedialko Nikolov

1998-01-01

Bulgaria's forest ecosystems (31 percent of the country's area) are considered vulnerable to dry and wet pollution deposition. Coniferous forests that cover one-third of the total forest land are particularly sensitive to pollution loads. The USDA Forest Service, Sofia University, and the Bulgarian Forest Research Institute (FRI) established a cooperative...

Complete Genome Sequences of Two Vesicular Stomatitis Virus Isolates Collected in Mexico.

PubMed

Velazquez-Salinas, Lauro; Isa, Pavel; Pauszek, Steven J; Rodriguez, Luis L

2017-09-14

We report two full-genome sequences of vesicular stomatitis New Jersey virus (VSNJV) obtained by Illumina next-generation sequencing of RNA isolated from epithelial suspensions of cattle naturally infected in Mexico. These genomes represent the first full-genome sequences of vesicular stomatitis New Jersey viruses circulating in Mexico deposited in the GenBank database.

TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data.

PubMed

Clark, Lindsay V; Sacks, Erik J

2016-01-01

In genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), read depth is important for assessing the quality of genotype calls and estimating allele dosage in polyploids. However, existing pipelines for GBS and RAD-seq do not provide read counts in formats that are both accurate and easy to access. Additionally, although existing pipelines allow previously-mined SNPs to be genotyped on new samples, they do not allow the user to manually specify a subset of loci to examine. Pipelines that do not use a reference genome assign arbitrary names to SNPs, making meta-analysis across projects difficult. We created the software TagDigger, which includes three programs for analyzing GBS and RAD-seq data. The first script, tagdigger_interactive.py, rapidly extracts read counts and genotypes from FASTQ files using user-supplied sets of barcodes and tags. Input and output is in CSV format so that it can be opened by spreadsheet software. Tag sequences can also be imported from the Stacks, TASSEL-GBSv2, TASSEL-UNEAK, or pyRAD pipelines, and a separate file can be imported listing the names of markers to retain. A second script, tag_manager.py, consolidates marker names and sequences across multiple projects. A third script, barcode_splitter.py, assists with preparing FASTQ data for deposit in a public archive by splitting FASTQ files by barcode and generating MD5 checksums for the resulting files. TagDigger is open-source and freely available software written in Python 3. It uses a scalable, rapid search algorithm that can process over 100 million FASTQ reads per hour. TagDigger will run on a laptop with any operating system, does not consume hard drive space with intermediate files, and does not require programming skill to use.

Fast, accurate and easy-to-pipeline methods for amplicon sequence processing

NASA Astrophysics Data System (ADS)

Antonielli, Livio; Sessitsch, Angela

2016-04-01

Next generation sequencing (NGS) technologies established since years as an essential resource in microbiology. While on the one hand metagenomic studies can benefit from the continuously increasing throughput of the Illumina (Solexa) technology, on the other hand the spreading of third generation sequencing technologies (PacBio, Oxford Nanopore) are getting whole genome sequencing beyond the assembly of fragmented draft genomes, making it now possible to finish bacterial genomes even without short read correction. Besides (meta)genomic analysis next-gen amplicon sequencing is still fundamental for microbial studies. Amplicon sequencing of the 16S rRNA gene and ITS (Internal Transcribed Spacer) remains a well-established widespread method for a multitude of different purposes concerning the identification and comparison of archaeal/bacterial (16S rRNA gene) and fungal (ITS) communities occurring in diverse environments. Numerous different pipelines have been developed in order to process NGS-derived amplicon sequences, among which Mothur, QIIME and USEARCH are the most well-known and cited ones. The entire process from initial raw sequence data through read error correction, paired-end read assembly, primer stripping, quality filtering, clustering, OTU taxonomic classification and BIOM table rarefaction as well as alternative "normalization" methods will be addressed. An effective and accurate strategy will be presented using the state-of-the-art bioinformatic tools and the example of a straightforward one-script pipeline for 16S rRNA gene or ITS MiSeq amplicon sequencing will be provided. Finally, instructions on how to automatically retrieve nucleotide sequences from NCBI and therefore apply the pipeline to targets other than 16S rRNA gene (Greengenes, SILVA) and ITS (UNITE) will be discussed.

Microbial diversity in nonsulfur, sulfur and iron geothermal steam vents.

PubMed

Benson, Courtney A; Bizzoco, Richard W; Lipson, David A; Kelley, Scott T

2011-04-01

Fumaroles, commonly called steam vents, are ubiquitous features of geothermal habitats. Recent studies have discovered microorganisms in condensed fumarole steam, but fumarole deposits have proven refractory to DNA isolation. In this study, we report the development of novel DNA isolation approaches for fumarole deposit microbial community analysis. Deposit samples were collected from steam vents and caves in Hawaii Volcanoes National Park, Yellowstone National Park and Lassen Volcanic National Park. Samples were analyzed by X-ray microanalysis and classified as nonsulfur, sulfur or iron-dominated steam deposits. We experienced considerable difficulty in obtaining high-yield, high-quality DNA for cloning: only half of all the samples ultimately yielded sequences. Analysis of archaeal 16S rRNA gene sequences showed that sulfur steam deposits were dominated by Sulfolobus and Acidianus, while nonsulfur deposits contained mainly unknown Crenarchaeota. Several of these novel Crenarchaeota lineages were related to chemoautotrophic ammonia oxidizers, indicating that fumaroles represent a putative habitat for ammonia-oxidizing Archaea. We also generated archaeal and bacterial enrichment cultures from the majority of the deposits and isolated members of the Sulfolobales. Our results provide the first evidence of Archaea in geothermal steam deposits and show that fumaroles harbor diverse and novel microbial lineages. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Reworked calcretes: their significance in the reconstruction of alluvial sequences (Permian and Triassic, Minorca, Balearic Islands, Spain)

NASA Astrophysics Data System (ADS)

Gómez-Gras, D.; Alonso-Zarza, A. M.

2003-05-01

The Permian and Triassic of Minorca (Balearic Islands) consists of a 670-m-thick, red, alluvial succession that includes in situ calcrete profiles and reworked calcrete material. In the Permian succession, the calcretes vary from laminar forms developed on the Carboniferous basement to weakly developed nodular calcretes in fluvial sediments. The palaeosols in the Triassic are mostly dolomitic, and the profiles reach up to Stage III of soil development (Spec. Pap.-Geol. Surv. Am. 203, (1995) 1). The clasts, formed through reworking of the palaeosol profiles, are about 0.5-10 cm across and include mosaics of calcite/dolomite crystals, brecciated clasts, rhizolith fragments, and aggregates of clay and/or silt. These clasts appear in three different types of deposits. Type 1 corresponds to lenticular bodies that fill small scour surfaces, and consists only of intraformational conglomerates. These deposits are interpreted as ephemeral channels and sheet-floods that represent the interfluvial drainage systems that captured only the precipitation falling on the alluvial plain. Type 2 includes sand dune 3-D bodies with flat bottoms and convex tops. These bodies are about 20 cm high and 2 m wide, and were formed by floodwaters that flowed down the levees of the major streams. Type 3 channel deposits contain reworked calcretes and extrabasinal clasts, which overlie erosive surfaces and are found in layers within cross-bedded sandstones and conglomerates. These are interpreted as channel-floor lag deposits of major channels that entered from distant uplands and drained the alluvial plain. Variations in the aggradation rates of the floodplain resulted in five different infill stages. In the lowstand to early transgressive interval, as in stages I (P1) and IV (B1), the fluvial deposits filled palaeovalleys; calcretes and reworked calcrete deposits were of difficult formation (apart from terraces) and preservation. Accommodation space was at its greatest in the transgressive, stages II (P2) and V (B2). This caused the greatest aggradation of the floodplains, which are formed of thick sequences of fine-grained sediments, isolated meandering channels, weakly developed calcretes (compound) and reworked calcrete deposits, mostly of types 1 and 2. The density of channels notably increased in stage III (P3), highstand interval, because of the reduction of accommodation space, this could favour the formation of composite or even cumulative palaeosols, but of difficult preservation. Reworked calcrete deposits are mostly of type 3, but types 1 and 2 are also recognised. The reworked calcrete deposits are an important part of the Permian and Triassic fluvial sediments and their occurrence and characteristics are important in order to interpret the infill of terrestrial basins and the construction of floodplains.

Significance of third-order elasticity for determination of the pressure coefficient of the light emission in strained quantum wells

NASA Astrophysics Data System (ADS)

Łepkowski, S. P.

2008-10-01

We investigate the contribution arising from third-order elasticity to the pressure coefficient of the light emission (dEE/dP) in strained zinc-blende InGaAs/GaAs and InGaN/GaN quantum wells (QWs) grown in a (001) direction. In the framework of the third-order elasticity theory, we develop a model of pressure tuning of strains in these structures, which is then used to determine the coefficient dEE/dP . In the calculations of dEE/dP , we use a consistent set of the second- and third-order elastic constants which has been obtained from ab initio calculations. Our results indicate that the usage of third-order elasticity leads to significant reduction in dEE/dP in strained (001)-oriented InGaAs/GaAs and InGaN/GaN QWs, in comparison to the values of dEE/dP obtained by using the linear theory of elasticity. In the case of InGaAs/GaAs QWs, the values of dEE/dP calculated using third-order elasticity are in reasonable agreement with experimental data. For InGaN/GaN QWs, better agreement between theoretical and experimental values of dEE/dP is obtained when instead of third-order elasticity, pressure dependence of the second-order elastic constants is taken into account.

Sequence stratigraphy and high-frequency cycles: New aspects for a quantitative evaluation of the Gulf of Suez basin, Egypt

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

Nio, S.D.; Yang, C.S.; Tewfik, N.

1993-09-01

A new development in the application of sequence stratigraphic concepts in marine as well as continental basins is the recognition of high-frequency cyclic patterns in rock successions in the subsurface. Studies of six wells from the northern, central, and southern parts of the Gulf of Suez show the presence of well-preserved, high-frequency cycles with periodicities similar to the orbitally forced Malankovitch parameters. Subsurface rock successions, third-order sequences, and high-frequency cycles were compared with outcrops. After establishing the biostratigraphic framework for the above-mentioned wells, a sequence analysis was performed. Sequence boundaries and maximum flooding positions in each well were calibrated withmore » the occurrences and evaluation of the high-frequency cycles. It became obvious that there is an intimate relationship between these high-frequency Milankovitch cycles and sequence organization. In addition, a close relationship can be observed in the subsurface as well as in outcrops between high-frequency climatic changes (connected to the Milankovitch cycles) and (litho)facies variability. Quantitative evaluations of each sequence and/or systems tract can be computed with the International Geoservices' cyclicity analysis tool (MILABAR). The results are summarized in a well composite chart, rate (NAR), and ratio of preserved time. In correlations between the wells, an accuracy of 500-100 Ka can be obtained. The quantitative evaluation of the sequence and high-frequency cycle analysis gave some new aspects concerning the (litho)facies and geodynamic development during the pre- as well as the synrift stages of the Gulf of Suez Basin.« less

Breakdown of the single-exchange approximation in third-order symmetry-adapted perturbation theory.

PubMed

Lao, Ka Un; Herbert, John M

2012-03-22

We report third-order symmetry-adapted perturbation theory (SAPT) calculations for several dimers whose intermolecular interactions are dominated by induction. We demonstrate that the single-exchange approximation (SEA) employed to derive the third-order exchange-induction correction (E(exch-ind)((30))) fails to quench the attractive nature of the third-order induction (E(ind)((30))), leading to one-dimensional potential curves that become attractive rather than repulsive at short intermolecular separations. A scaling equation for (E(exch-ind)((30))), based on an exact formula for the first-order exchange correction, is introduced to approximate exchange effects beyond the SEA, and qualitatively correct potential energy curves that include third-order induction are thereby obtained. For induction-dominated systems, our results indicate that a "hybrid" SAPT approach, in which a dimer Hartree-Fock calculation is performed in order to obtain a correction for higher-order induction, is necessary not only to obtain quantitative binding energies but also to obtain qualitatively correct potential energy surfaces. These results underscore the need to develop higher-order exchange-induction formulas that go beyond the SEA. © 2012 American Chemical Society

Genetic and grade and tonnage models for sandstone-hosted roll-type uranium deposits, Texas Coastal Plain, USA

USGS Publications Warehouse

Hall, Susan M.; Mihalasky, Mark J.; Tureck, Kathleen; Hammarstrom, Jane M.; Hannon, Mark

2017-01-01

The coincidence of a number of geologic and climatic factors combined to create conditions favorable for the development of mineable concentrations of uranium hosted by Eocene through Pliocene sandstones in the Texas Coastal Plain. Here 254 uranium occurrences, including 169 deposits, 73 prospects, 6 showings and 4 anomalies, have been identified. About 80 million pounds of U3O8 have been produced and about 60 million pounds of identified producible U3O8 remain in place. The development of economic roll-type uranium deposits requires a source, large-scale transport of uranium in groundwater, and deposition in reducing zones within a sedimentary sequence. The weight of the evidence supports a source from thick sequences of volcanic ash and volcaniclastic sediment derived mostly from the Trans-Pecos volcanic field and Sierra Madre Occidental that lie west of the region. The thickest accumulations of source material were deposited and preserved south and west of the San Marcos arch in the Catahoula Formation. By the early Oligocene, a formerly uniformly subtropical climate along the Gulf Coast transitioned to a zoned climate in which the southwestern portion of Texas Coastal Plain was dry, and the eastern portion humid. The more arid climate in the southwestern area supported weathering of volcanic ash source rocks during pedogenesis and early diagenesis, concentration of uranium in groundwater and movement through host sediments. During the middle Tertiary Era, abundant clastic sediments were deposited in thick sequences by bed-load dominated fluvial systems in long-lived channel complexes that provided transmissive conduits favoring transport of uranium-rich groundwater. Groundwater transported uranium through permeable sandstones that were hydrologically connected with source rocks, commonly across formation boundaries driven by isostatic loading and eustatic sea level changes. Uranium roll fronts formed as a result of the interaction of uranium-rich groundwater with either (1) organic-rich debris adjacent to large long-lived fluvial channels and barrier–bar sequences or (2) extrinsic reductants entrained in formation water or discrete gas that migrated into host units via faults and along the flanks of salt domes and shale diapirs. The southwestern portion of the region, the Rio Grande embayment, contains all the necessary factors required for roll-type uranium deposits. However, the eastern portion of the region, the Houston embayment, is challenged by a humid environment and a lack of source rock and transmissive units, which may combine to preclude the deposition of economic deposits. A grade and tonnage model for the Texas Coastal Plain shows that the Texas deposits represent a lower tonnage subset of roll-type deposits that occur around the world, and required aggregation of production centers into deposits based on geologic interpretation for the purpose of conducting a quantitative mineral resource assessment.

Communicating the Benefits of a Full Sequence of High School Science Courses

ERIC Educational Resources Information Center

Nicholas, Catherine Marie

2014-01-01

High school students are generally uninformed about the benefits of enrolling in a full sequence of science courses, therefore only about a third of our nation's high school graduates have completed the science sequence of Biology, Chemistry and Physics. The lack of students completing a full sequence of science courses contributes to the deficit…

Late-kinematic timing of orogenic gold deposits and significance for computer-based exploration techniques with emphasis on the Yilgarn Block, Western Australia

USGS Publications Warehouse

Groves, D.I.; Goldfarb, R.J.; Knox-Robinson, C. M.; Ojala, J.; Gardoll, S.; Yun, G.Y.; Holyland, P.

2000-01-01

Orogenic gold deposits are a widespread coherent group of epigenetic ore deposits that are sited in accretionary or collisional orogens. They formed over a large crustal-depth range from deep-seated low-salinity H2O-CO2 + CH4 + N2 ore fluids and with Au transported as thio-complexes. Regional structures provide the main control on deposit distribution. In many terranes, first-order faults or shear zones appear to have controlled regional fluid flow, with greatest ore-fluid fluxes in, and adjacent to, lower-order faults, shear zones and/or large folds. Highly competent and/or chemically reactive rocks are the most common hosts to the larger deposits. Focusing of supralithostatic ore fluids into dilatant zones appears to occur late during the evolutionary history of the host terranes, normally within D3 or D4 in a D1-D4 deformation sequence. Reactivation of suitably oriented pre-existing structures during a change in far-field stress orientation is a factor common to many deposits, and repeated reactivation may account for multiple mineralization episodes in some larger deposits. Absolute robust ages of mineralization support their late-kinematic timing, and, in general, suggest that deposits formed diachronously towards the end of the 100 to 200 m.y. long evolutionary history of hosting orogens. For example, in the Yilgarn Block, a region specifically emphasised in this study, orogenic gold deposits formed in the time interval between 40 and 90 m.y., with most about 60 to 70 m.y., after the youngest widespread basic-ultrabasic volcanism and towards the end of felsic magmatism. The late timing of orogenic gold deposits is pivotal to geologically-based exploration methodologies. This is because the present structural geometries of: (i) the deposits, (ii) the hosting goldfields, and (iii) the enclosing terranes are all essentially similar to those during gold mineralization, at least in their relative position to each other. Thus, interpretation of geological maps and cross-sections and three-dimensional models can be used to accurately simulate the physical conditions that existed at the time of ore deposition. It is particularly significant that the deposits are commonly related to repetitive and predictable geometries, such as structural heterogeneities within or adjacent to first-order structures, around rigid granitoid bodies, or in specific "locked-up" fold-thrust structures. Importantly, the two giant greenstone-hosted goldfields, Kalgoorlie and Timmins, show a remarkably similar geometry at the regional scale. Computer-based stress mapping and GIS-based prospectivity mapping are two computer-based quantitative methodologies that can utilize and take advantage of the late timing aspect of this deposit type to provide important geological aids in exploration, both in broad regions and more localized goldfields. Both require an accurate and consistent solid geology map, stress mapping requires knowledge of the far-field stresses during mineralization, and the empirical prospectivity mapping requires data from a significant number of known deposits in the terrane. The Kalgoorlie Terrane, in the Yilgarn Block, meets these criteria, and illustrates the potential of these methodologies in the exploration for orogenic gold deposits. Low minimum stress anomalies, interpreted to represent dilational zones during gold-related deformation, coincide well with the positions of known goldfields rather than individual gold deposits in the terrane, and there are additional as-yet unexplained anomalies. The prospectivity analysis confirms that predictable and repetitive factors controlling the siting of deposits are: (i) proximity to, and orientation and curvature of, granitoid-greenstone contacts, (ii) proximity to segments of crustal faults which strike in a preferred direction, (iii) proximity to specific lithological contacts which have similar preferred strike, (iv) proximity to anticlinal structures, and (v) the presence of preferred

Conservation laws and rogue waves for a higher-order nonlinear Schrödinger equation with variable coefficients in the inhomogeneous fiber

NASA Astrophysics Data System (ADS)

Du, Zhong; Tian, Bo; Wu, Xiao-Yu; Liu, Lei; Sun, Yan

2017-07-01

Subpicosecond or femtosecond optical pulse propagation in the inhomogeneous fiber can be described by a higher-order nonlinear Schrödinger equation with variable coefficients, which is investigated in the paper. Via the Ablowitz-Kaup-Newell-Segur system and symbolic computation, the Lax pair and infinitely-many conservation laws are deduced. Based on the Lax pair and a modified Darboux transformation technique, the first- and second-order rogue wave solutions are constructed. Effects of the groupvelocity dispersion and third-order dispersion on the properties of the first- and second-order rouge waves are graphically presented and analyzed: The groupvelocity dispersion and third-order dispersion both affect the ranges and shapes of the first- and second-order rogue waves: The third-order dispersion can produce a skew angle of the first-order rogue wave and the skew angle rotates counterclockwise with the increase of the groupvelocity dispersion, when the groupvelocity dispersion and third-order dispersion are chosen as the constants; When the groupvelocity dispersion and third-order dispersion are taken as the functions of the propagation distance, the linear, X-shaped and parabolic trajectories of the rogue waves are obtained.

Steady-state sulfur critical loads and exceedances for protection of aquatic ecosystems in the U.S. Southern Appalachian Mountains.

PubMed

McDonnell, Todd C; Sullivan, Timothy J; Hessburg, Paul F; Reynolds, Keith M; Povak, Nicholas A; Cosby, Bernard J; Jackson, William; Salter, R Brion

2014-12-15

Atmospherically deposited sulfur (S) causes stream water acidification throughout the eastern U.S. Southern Appalachian Mountain (SAM) region. Acidification has been linked with reduced fitness and richness of aquatic species and changes to benthic communities. Maintaining acid-base chemistry that supports native biota depends largely on balancing acidic deposition with the natural resupply of base cations. Stream water acid neutralizing capacity (ANC) is maintained by base cations that mostly originate from weathering of surrounding lithologies. When ambient atmospheric S deposition exceeds the critical load (CL) an ecosystem can tolerate, stream water chemistry may become lethal to biota. This work links statistical predictions of ANC and base cation weathering for streams and watersheds of the SAM region with a steady-state model to estimate CLs and exceedances. Results showed that 20.1% of the total length of study region streams displayed ANC <100 μeq∙L(-1), a level at which effects to biota may be anticipated; most were 4th or lower order streams. Nearly one-third of the stream length within the study region exhibited CLs of S deposition <50 meq∙m(-2)∙yr(-1), which is less than the regional average S deposition of 60 meq∙m(-2)∙yr(-1). Owing to their geologic substrates, relatively high elevation, and cool and moist forested conditions, the percentage of stream length in exceedance was highest for mountain wilderness areas and in national parks, and lowest for privately owned valley bottom land. Exceedance results were summarized by 12-digit hydrologic unit code (subwatershed) for use in developing management goals and policy objectives, and for long-term monitoring. Copyright © 2014 Elsevier Ltd. All rights reserved.

Controls on facies and sequence stratigraphy of an upper Miocene carbonate ramp and platform, Melilla basin, NE Morocco

USGS Publications Warehouse

Cunningham, K.J.; Collins, Luke S.

2002-01-01

Upwelling of cool seawater, paleoceanographic circulation, paleoclimate, local tectonics and relative sea-level change controlled the lithofacies and sequence stratigraphy of a carbonate ramp and overlying platform that are part of a temporally well constrained carbonate complex in the Melilla basin, northeastern Morocco. At Melilla, from oldest to youngest, a third-order depositional sequence within the carbonate complex contains (1) a retrogradational, transgressive, warm temperate-type rhodalgal ramp; (2) an early highstand, progradational, bioclastic platform composed mainly of a temperate-type, bivalve-rich molechfor facies; and (3) late highstand, progradational to downstepping, subtropical/tropical-type chlorozoan fringing Porites reefs. The change from rhodalgal ramp to molechfor platform occurred at 7.0??0.14 Ma near the Tortonian/Messinian boundary. During a late stage in the development of the bioclastic platform a transition from temperate-type molechfor facies to subtropical/tropical-type chlorozoan facies occurred and is bracketed by chron 3An.2n (??? 6.3-6.6 Ma). Comparison to a well-dated carbonate complex in southeastern Spain at Cabo de Gata suggests that upwelling of cool seawater influenced production of temperate-type limestone within the ramp and platform at Melilla during postulated late Tortonian-early Messinian subtropical/tropical paleoclimatic conditions in the western Paleo-Mediterranean region. The upwelling of cool seawater across the bioclastic platform at Melilla could be related to the beginning of 'siphoning' of deep, cold Atlantic waters into the Paleo-Mediterranean Sea at 7.17 Ma. The facies change within the bioclastic platform from molechfor to chlorozoan facies may be coincident with a reduction of the siphoning of Atlantic waters and the end of upwelling at Melilla during chron 3An.2n. The ramp contains one retrogradational parasequence and the bioclastic platform three progradational parasequences. Minor erosional surfaces that bound the upper surface of the ramp and upper surface of the oldest platform parasequence are related to relative falls in sea level induced by local volcanism and associated tectonic uplift. These local relative falls had little influence on a broader-scale rise to stillstand in relative sea level that controlled development of the transgressive and early highstand systems tracts represented in the ramp and platform, respectively. ?? 2002 Elsevier Science B.V. All rights reserved.

Late Devonian shale deposition based on known and predicted occurrence of Foerstia in Michigan basin

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

Matthews, R.D.

The fossil Foerstia (Protosalvinia) marks a time zone within Late Devonian shale sequences in the eastern US. Its recent discovery in Michigan has led to more accurate correlations among the three large eastern basins. Subdivisions of the Devonian-Mississippi shale sequence in Michigan based on gamma-ray correlations reveal an idealized black shale geometry common to other eastern black shales, such as the Sunbury of Michigan and Ohio, the Clegg Creek of Indiana, the Dunkirk of Pennsylvania and New York, and the lower Huron of Ohio and West Virginia. In Michigan, Foerstia occurs at a stratigraphic position postulated to mark a majormore » change in depositional conditions and source areas. This position strengthens the physical and paleontologic evidence for a formal division of the Antrim. Isopach maps of the shale sequence above and below Foerstia show a relatively uniform and continuous black shale deposit (units 1A, 1B, and 1C) below Foerstia. This deposit is unlike the wedge of sediment found above Foerstia, which is composed of a western facies (Ellsworth) and an eastern facies (upper Antrim) that should be combined in a single stratigraphic unit conforming to Forgotson's concept of a format.« less

Paleosoils in the loess deposits of eastern Uzbekistan

NASA Astrophysics Data System (ADS)

Abdunazarov, U. K.; Stelmakh, A. G.

2010-12-01

Loess deposits of the eastern Uzbekistan are difficult to study the stratigraphy of the object. Clarification of the relationship of age and genetic features of the considered entities by traditional methods is difficult due to scarcity of remnants of the fauna and flora, the active Quaternary tectonics, the homogeneity of the rocks, especially the formation of loess sequences, specific conditions of geological and tectonic development, etc. In this regard, particularly relevant is the study of loess deposits by paleosoils subdivision and correlation. Paleosoils, which are present in the sections of loess sequences, distinct from loess-like loams, dividing them among themselves. Color these paleosoils noticeable brownish or brown, while the loess is a powdery mildew gray rock. Typically, the general scheme of occurrence of loess cover is linked with levels of relief mountainous areas. Recent studies show that the loess in the piedmont plains overlie a complex manner and include uneven paleosoils. Therefore, loess sequences of different geomorphological levels from the lower parts of slopes to the watershed have been studied in research paleosoils. The scheme was drawn up as a result of the studies. This scheme shows the main horizons paleosoils in loess deposits. Even-aged paleosoils and share their loess were identified in this scheme.

Metal organic chemical vapor deposition of environmental barrier coatings for the inhibition of solid deposit formation from heated jet fuel

NASA Astrophysics Data System (ADS)

Mohan, Arun Ram

Solid deposit formation from jet fuel compromises the fuel handling system of an aviation turbine engine and increases the maintenance downtime of an aircraft. The deposit formation process depends upon the composition of the fuel, the nature of metal surfaces that come in contact with the heated fuel and the operating conditions of the engine. The objective of the study is to investigate the effect of substrate surfaces on the amount and nature of solid deposits in the intermediate regime where both autoxidation and pyrolysis play an important role in deposit formation. A particular focus has been directed to examining the effectiveness of barrier coatings produced by metal organic chemical vapor deposition (MOCVD) on metal surfaces for inhibiting the solid deposit formation from jet fuel degradation. In the first part of the experimental study, a commercial Jet-A sample was stressed in a flow reactor on seven different metal surfaces: AISI316, AISI 321, AISI 304, AISI 347, Inconel 600, Inconel 718, Inconel 750X and FecrAlloy. Examination of deposits by thermal and microscopic analysis shows that the solid deposit formation is influenced by the interaction of organosulfur compounds and autoxidation products with the metal surfaces. The nature of metal sulfides was predicted by Fe-Ni-S ternary phase diagram. Thermal stressing on uncoated surfaces produced coke deposits with varying degree of structural order. They are hydrogen-rich and structurally disordered deposits, spherulitic deposits, small carbon particles with relatively ordered structures and large platelets of ordered carbon structures formed by metal catalysis. In the second part of the study, environmental barrier coatings were deposited on tube surfaces to inhibit solid deposit formation from the heated fuel. A new CVD system was configured by the proper choice of components for mass flow, pressure and temperature control in the reactor. A bubbler was designed to deliver the precursor into the reactor for the deposition of metal and metal oxide functional coatings by MOCVD. Alumina was chosen as a candidate for metal oxide coating because of its thermal and phase stability. Platinum was chosen as a candidate to utilize the oxygen spillover process to maintain a self-cleaning surface by oxidizing the deposits formed during thermal stressing. Two metal organic precursors, aluminum trisecondary butoxide and aluminum acetylacetonate, were used as precursors to coat tubes of varying diameters. The morphology and uniformity of the coatings were characterized by electron microscopy and energy-dispersive x-ray spectroscopy. The coating was characterized by x-ray photoelectron spectroscopy to obtain the surface chemical composition. This is the first study conducted to examine the application of MOCVD to coat internal surfaces of tubes with varying diameters. In the third part of the study, the metal oxide coatings, alumina from aluminum acetylacetonate, alumina from aluminum trisecondary butoxide, zirconia from zirconium acetylacetonate, tantalum oxide from tantalum pentaethoxide and the metal coating, platinum from platinum acetylacetonate were deposited by MOCVD on AISI304. The chemical composition and the surface acidity of the coatings were characterized by x-ray photoelectron spectroscopy. The morphology of the coatings was characterized by electron microscopy. The coated substrates were tested in the presence of heated Jet-A in a flow reactor to evaluate their effectiveness in inhibiting the solid deposit formation. All coatings inhibited the formation of metal sulfides and the carbonaceous solid deposits formed by metal catalysis. The coatings also delayed the accumulation of solid carbonaceous deposits. In particular, it has been confirmed that the surface acidity of the metal oxide coatings affects the formation of carbonaceous deposits. Bimolecular addition reactions promoted by the Bronsted acid sites appear to lead to the formation of carbonaceous solid deposits depending on the surface acidity of the coatings. In the last part of the study, the residual carbon was incorporated in the zirconia coating by deposition with and without oxygen. As carbon surface is less active towards coke deposition, presence of residual carbon in the coating was expected to reduce its activity towards carbon deposition. The residual carbon in the coating was characterized by Raman spectroscopy and thermal analysis. However, it has been observed that residual carbon in the coating beyond a certain concentration compromises the integrity of the coating during the process of cooling the substrate from deposition temperature to room temperature. It has been found that residual carbon in the zirconia coating does not appear to affect the activity of the surface towards carbon deposition.

Glacial morphology and depositional sequences of the Antarctic Continental Shelf

USGS Publications Warehouse

ten Brink, Uri S.; Schneider, Christopher

1995-01-01

Proposes a simple model for the unusual depositional sequences and morphology of the Antarctic continental shelf. It considers the regional stratal geometry and the reversed morphology to be principally the results of time-integrated effects of glacial erosion and sedimentation related to the location of the ice grounding line. The model offers several guidelines for stratigraphic interpretation of the Antarctic shelf and a Northern Hemisphere shelf, both of which were subject to many glacial advances and retreats. -Authors

Banded iron-formations of late Proterozoic age in the central eastern desert, Egypt: geology and tectonic setting.

USGS Publications Warehouse

Sims, P.K.; James, H.L.

1984-01-01

Iron-formation occurs as stratigraphic units within a layered andesite-basalt sequence. The sequence is metamorphosed to greenschist facies, intruded by syntectonic granodiorite and post-tectonic granite, and complexly deformed and grossly fragmented; the rocks are allochthonous along thrust faults. The iron deposits are chemical precipitates, accumulated during lulls in volcanism, apparently in an intraoceanic island-arc environment. The deposits are of the Algoma type of iron-formation.-G.J.N.

A physical map of a BAC clone contig covering the entire autosome insertion between ovine MHC Class IIa and IIb

PubMed Central

2012-01-01

Background The ovine Major Histocompatibility Complex (MHC) harbors genes involved in overall resistance/susceptibility of the host to infectious diseases. Compared to human and mouse, the ovine MHC is interrupted by a large piece of autosome insertion via a hypothetical chromosome inversion that constitutes ~25% of ovine chromosome 20. The evolutionary consequence of such an inversion and an insertion (inversion/insertion) in relation to MHC function remains unknown. We previously constructed a BAC clone physical map for the ovine MHC exclusive of the insertion region. Here we report the construction of a high-density physical map covering the autosome insertion in order to address the question of what the inversion/insertion had to do with ruminants during the MHC evolution. Results A total of 119 pairs of comparative bovine oligo primers were utilized to screen an ovine BAC library for positive clones and the orders and overlapping relationships of the identified clones were determined by DNA fingerprinting, BAC-end sequencing, and sequence-specific PCR. A total of 368 positive BAC clones were identified and 108 of the effective clones were ordered into an overlapping BAC contig to cover the consensus region between ovine MHC class IIa and IIb. Therefore, a continuous physical map covering the entire ovine autosome inversion/insertion region was successfully constructed. The map confirmed the bovine sequence assembly for the same homologous region. The DNA sequences of 185 BAC-ends have been deposited into NCBI database with the access numbers HR309252 through HR309068, corresponding to dbGSS ID 30164010 through 30163826. Conclusions We have constructed a high-density BAC clone physical map for the ovine autosome inversion/insertion between the MHC class IIa and IIb. The entire ovine MHC region is now fully covered by a continuous BAC clone contig. The physical map we generated will facilitate MHC functional studies in the ovine, as well as the comparative MHC evolution in ruminants. PMID:22897909

Sedimentary manganese metallogenesis in response to the evolution of the Earth system

NASA Astrophysics Data System (ADS)

Roy, Supriya

2006-08-01

The concentration of manganese in solution and its precipitation in inorganic systems are primarily redox-controlled, guided by several Earth processes most of which were tectonically induced. The Early Archean atmosphere-hydrosphere system was extremely O 2-deficient. Thus, the very high mantle heat flux producing superplumes, severe outgassing and high-temperature hydrothermal activity introduced substantial Mn 2+ in anoxic oceans but prevented its precipitation. During the Late Archean, centered at ca. 2.75 Ga, the introduction of Photosystem II and decrease of the oxygen sinks led to a limited buildup of surface O 2-content locally, initiating modest deposition of manganese in shallow basin-margin oxygenated niches (e.g., deposits in India and Brazil). Rapid burial of organic matter, decline of reduced gases from a progressively oxygenated mantle and a net increase in photosynthetic oxygen marked the Archean-Proterozoic transition. Concurrently, a massive drawdown of atmospheric CO 2 owing to increased weathering rates on the tectonically expanded freeboard of the assembled supercontinents caused Paleoproterozoic glaciations (2.45-2.22 Ga). The spectacular sedimentary manganese deposits (at ca. 2.4 Ga) of Transvaal Supergroup, South Africa, were formed by oxidation of hydrothermally derived Mn 2+ transferred from a stratified ocean to the continental shelf by transgression. Episodes of increased burial rate of organic matter during ca. 2.4 and 2.06 Ga are correlatable to ocean stratification and further rise of oxygen in the atmosphere. Black shale-hosted Mn carbonate deposits in the Birimian sequence (ca. 2.3-2.0 Ga), West Africa, its equivalents in South America and those in the Francevillian sequence (ca. 2.2-2.1 Ga), Gabon are correlatable to this period. Tectonically forced doming-up, attenuation and substantial increase in freeboard areas prompted increased silicate weathering and atmospheric CO 2 drawdown causing glaciation on the Neoproterozoic Rodinia supercontinent. Tectonic rifting and mantle outgassing led to deglaciation. Dissolved Mn 2+ and Fe 2+ concentrated earlier in highly saline stagnant seawater below the ice cover were exported to shallow shelves by transgression during deglaciation. During the Sturtian glacial-interglacial event (ca. 750-700 Ma), interstratified Mn oxide and BIF deposits of Damara sequence, Namibia, was formed. The Varangian (≡ Marinoan; ca. 600 Ma) cryogenic event produced Mn oxide and BIF deposits at Urucum, Jacadigo Group, Brazil. The Datangpo interglacial sequence, South China (Liantuo-Nantuo ≡ Varangian event) contains black shale-hosted Mn carbonate deposits. The Early Paleozoic witnessed several glacioeustatic sea level changes producing small Mn carbonate deposits of Tiantaishan (Early Cambrian) and Taojiang (Mid-Ordovician) in black shale sequences, China, and the major Mn oxide-carbonate deposits of Karadzhal-type, Central Kazakhstan (Late Devonian). The Mesozoic period of intense plate movements and volcanism produced greenhouse climate and stratified oceans. During the Early Jurassic OAE, organic-rich sediments host many Mn carbonate deposits in Europe (e.g., Úrkút, Hungary) in black shale sequences. The Late Jurassic giant Mn Carbonate deposit at Molango, Mexico, was also genetically related to sea level change. Mn carbonates were always derived from Mn oxyhydroxides during early diagenesis. Large Mn oxide deposits of Cretaceous age at Groote Eylandt, Australia and Imini-Tasdremt, Morocco, were also formed during transgression-regression in greenhouse climate. The Early Oligocene giant Mn oxide-carbonate deposit of Chiatura (Georgia) and Nikopol (Ukraine) were developed in a similar situation. Thereafter, manganese sedimentation was entirely shifted to the deep seafloor and since ca. 15 Ma B.P. was climatically controlled (glaciation-deglaciation) assisted by oxygenated polar bottom currents (AABW, NADW). The changes in climate and the sea level were mainly tectonically forced.

Phylogenetic analysis of eIF4E-family members

PubMed Central

Joshi, Bhavesh; Lee, Kibwe; Maeder, Dennis L; Jagus, Rosemary

2005-01-01

Background Translation initiation in eukaryotes involves the recruitment of mRNA to the ribosome which is controlled by the translation factor eIF4E. eIF4E binds to the 5'-m7Gppp cap-structure of mRNA. Three dimensional structures of eIF4Es bound to cap-analogues resemble 'cupped-hands' in which the cap-structure is sandwiched between two conserved Trp residues (Trp-56 and Trp-102 of H. sapiens eIF4E). A third conserved Trp residue (Trp-166 of H. sapiens eIF4E) recognizes the 7-methyl moiety of the cap-structure. Assessment of GenBank NR and dbEST databases reveals that many organisms encode a number of proteins with homology to eIF4E. Little is understood about the relationships of these structurally related proteins to each other. Results By combining sequence data deposited in the Genbank databases, we have identified sequences encoding 411 eIF4E-family members from 230 species. These sequences have been deposited into an internet-accessible database designed for sequence comparisons of eIF4E-family members. Most members can be grouped into one of three classes. Class I members carry Trp residues equivalent to Trp-43 and Trp-56 of H. sapiens eIF4E and appear to be present in all eukaryotes. Class II members, possess Trp→Tyr/Phe/Leu and Trp→Tyr/Phe substitutions relative to Trp-43 and Trp-56 of H. sapiens eIF4E, and can be identified in Metazoa, Viridiplantae, and Fungi. Class III members possess a Trp residue equivalent to Trp-43 of H. sapiens eIF4E but carry a Trp→Cys/Tyr substitution relative to Trp-56 of H. sapiens eIF4E, and can be identified in Coelomata and Cnidaria. Some eIF4E-family members from Protista show extension or compaction relative to prototypical eIF4E-family members. Conclusion The expansion of sequenced cDNAs and genomic DNAs from all eukaryotic kingdoms has revealed a variety of proteins related in structure to eIF4E. Evolutionarily it seems that a single early eIF4E gene has undergone multiple gene duplications generating multiple structural classes, such that it is no longer possible to predict function from the primary amino acid sequence of an eIF4E-family member. The variety of eIF4E-family members provides a source of alternatives on the eIF4E structural theme that will benefit structure/function analyses and therapeutic drug design. PMID:16191198

Synovial deposition of wild-type transthyretin-derived amyloid in knee joint osteoarthritis patients.

PubMed

Takanashi, Tetsuo; Matsuda, Masayuki; Yazaki, Masahide; Yamazaki, Hideshi; Nawata, Masashi; Katagiri, Yoshiki; Ikeda, Shu-Ichi

2013-09-01

To investigate histological features of deposited amyloid in the synovial tissue and its clinical significance in knee joint osteoarthritis (OA) patients. We prospectively enrolled 232 consecutive patients who underwent arthroplasty or total replacement of the knee joint for treatment of OA. Congo red staining and immunohistochemistry were performed in the synovial tissue obtained at surgery. When transthyretin (TTR)-derived amyloid was positive, we analyzed all 4 exons of the TTR gene using the direct DNA sequencing method in order to detect mutations. We analyzed 322 specimens in this study. Twenty-six specimens (8.1%) obtained from 21 patients (5 men and 16 women; mean, 79.0 ± 4.6 years) showed deposition of amyloid, which was positively stained with the anti-TTR antibody. Eighteen patients showed inhomogeneous accumulations of amyloid in the loose connective tissue under the synovial epithelia sometimes with nodule formation, while in the remaining three, small vessels in the adipose tissue were involved. Medical records of these patients revealed nothing remarkable in the clinical course, laboratory data or macroscopic intraarticular findings at surgery. No mutations were detectable in the TTR gene analysis. Wild-type TTR-derived amyloid may affect the synovial tissue as a result of long-term mechanical stress or as a part of senile systemic amyloidosis in approximately 8% of knee joint OA patients. No obvious clinical significance was found in synovial deposition of amyloid.

Attribute of trace fossils of Laisong flysch sediments, Manipur, India

NASA Astrophysics Data System (ADS)

Khaidem, Kumar S.; Rajkumar, Hemanta S.; Soibam, Ibotombi

2015-07-01

The depositional basin in which the Late Eocene-Early Oligocene Laisong flysch sediments Barail Group, Manipur region (Indo-Myanmar ranges) have been deposited is generally considered to be of deep marine environment. However, field observation indicates the presence of many shallow environment signature characteristics of marginal to sublittoral marine settings, in addition to the general occurrence of deep marine turbidites. To address this aspect, ichnological analyses of the Laisong Formation has been attempted for elucidating palaeoenvironmental setting prevalent during the deposition of these sediments. Presence of 36 ichnospecies belonging to 33 ichnogenera has so far been identified. The ichnospecies may be grouped into different ichnofacies such as Skolithos-Cruziana mixed ichnofacies, Cruziana ichnofacies, Skolithos ichnofacies, Zoophycos ichnofacies, Nereites ichnofacies and Teredolites ichnofacies which decrease in abundance in this order of sequence with Skolithos-Cruziana mixed ichnofacies being the most dominant. The above-mentioned ichnofacies are found associated with sedimentary structures such as large sole marks, parallel laminations, massive and structureless beds, rip-up clasts, etc., which are characteristics of submarine fan deposits below the storm wave base and current ripples, herringbone structures, hummocky cross stratifications, pot casts, rain prints, etc., that marked shallow marginal marine setting such as tidal flats, deltas and shoreface. With such observations it is very likely that the Laisong sediments were formed in a tectonically active basin with varied bathymetric ranges indicating alternate transgressive and regressive nature.

Petrogenesis and depositional history of felsic pyroclastic rocks from the Melka Wakena archaeological site-complex in South central Ethiopia

NASA Astrophysics Data System (ADS)

Resom, Angesom; Asrat, Asfawossen; Gossa, Tegenu; Hovers, Erella

2018-06-01

The Melka Wakena archaeological site-complex is located at the eastern rift margin of the central sector of the Main Ethiopian Rift (MER), in south central Ethiopia. This wide, gently sloping rift shoulder, locally called the "Gadeb plain" is underlain by a succession of primary pyroclastic deposits and intercalated fluvial sediments as well as reworked volcaniclastic rocks, the top part of which is exposed by the Wabe River in the Melka Wakena area. Recent archaeological survey and excavations at this site revealed important paleoanthropological records. An integrated stratigraphic, petrological, and major and trace element geochemical study has been conducted to constrain the petrogenesis of the primary pyroclastic deposits and the depositional history of the sequence. The results revealed that the Melka Wakena pyroclastic deposits are a suite of mildly alkaline, rhyolitic pantellerites (ash falls, pumiceous ash falls and ignimbrites) and slightly dacitic ash flows. These rocks were deposited by episodic volcanic eruptions during early to middle Pleistocene from large calderas along the Wonji Fault Belt (WFB) in the central sector of the MER and from large silicic volcanic centers at the eastern rift shoulder. The rhyolitic ash falls, pumiceous ash falls and ignimbrites have been generated by fractional crystallization of a differentiating basaltic magma while the petrogenesis of the slightly dacitic ash flows involved some crustal contamination and assimilation during fractionation. Contemporaneous fluvial activities in the geomorphologically active Gadeb plain deposited overbank sedimentary sequences (archaeology bearing conglomerates and sands) along meandering river courses while a dense network of channels and streams have subsequently down-cut through the older volcanic and sedimentary sequences, redepositing the reworked volcaniclastic sediments further downstream.

Hidden Ice Worlds - Pleistocene glacigenic deposits in Essex, England. Application of the novel systematic approach to thin-section description.

NASA Astrophysics Data System (ADS)

Leszczynska, Karolina; Boreham, Julie; Boreham, Steve

2013-04-01

In the 'Hidden Ice Worlds' research project a novel systematic approach for thin-section description (Leszczynska et al., 2011) is applied to analyse the internal structure of 8 m thick periglacially disturbed sequence from the Royal Oak Pit - a small disused quarry in East Anglia, Essex, east of Chelmsford, near Danbury. Danbury Hill is situated on the south-eastern margin of the Elsterian (Anglian) till sheet. This area was glaciated only once, during the Pleistocene, Elsterian (Anglian) glaciation (480-420 ka BP), however two local ice-sheet margin fluctuations are envisaged (inter alia Turner, 1970 and others). The stratigraphical sequence of the Royal Oak Pit comprises: massive gravel, arranged in sheets, overlain by fine silty-clay and silty-sand with ripple marks and planar cross beds, overlain by a 50 cm thick unit of massive gravel gradually changing into periglacially disturbed silty-clayey-gravel with the bottom 50 cm of fine laminated silty clay. This sequence is situated on the lee side of Danbury Hill, at over 50 m OD. This is an atypical location for the periglacially disturbed deposits of such a substantial thickness (up to 8 m), which usually occur in the lower areas. The deposits at this site were investigated at a macro-scale using field-section logging, ground penetrating radar survey, clast lithology, clay mineralogy analysis and loss-on-ignition and at a micro-scale using thin-section analysis. There are two main aims of the project presented: • To describe the genesis and to discern the main processes associated with the formation of the unusually thick periglacially disturbed unit at the Danbury Hill slope and • To test the novel, tree-based, systematic approach as a guiding tool for thin for thin-section description of Quaternary deposits (Leszczynska et al., 2011). The results of the micromorphological analyses of the deposits from the Royal Oak Pit allow a new hypothesis for the origin of the sequence to be put forward. The main process responsible for the evolution of the deposits consist of multiple phases of freezing and thawing of the deposit and associated physical reworking, subsequent to Elsterian (Anglian). Inversion of the topography is proposed as a necessary condition for the formation and preservation of the periglacially disturbed sequence on hill slope at such elevated location. The novel systematic approach proved to be a useful tool in guiding the thin-section description, regardless of the type of the deposit and the aim of the research. Reference: Leszczynska, K., Boreham, J. and Boreham, S., 2011. A novel methodological approach for thin-section description and its application to periglacially disturbed Pleistocene deposits from Danbury, Essex, UK. Netherlands Journal of Geosciences 90: 271-291. Turner, C., 1970. Middle Pleistocene deposits at Marks Tey, Essex. Philosophical Transactions of the Royal Society of London, series B 257: 373-440.

Evidence of cyclic climatic changes recorded in clay mineral assemblages from a continental Paleocene-Eocene sequence, northwestern Argentina

NASA Astrophysics Data System (ADS)

Do Campo, Margarita; Bauluz, Blanca; del Papa, Cecilia; White, Timothy; Yuste, Alfonso; Mayayo, Maria Jose

2018-06-01

The continental Paleocene-Eocene sequence investigated in this study belongs to the Salta Group, deposited in an intracontinental rift, the Salta Basin (NW Argentina), that evolved from the lower Cretaceous to the middle Paleogene, and is subdivided into the Pirgua, the Balbuena and the Santa Barbara Subgroups. The Maíz Gordo Formation (200 m thick) is the middle unit of the Santa Bárbara Subgroup, deposited during late post-rift sedimentation. We studied the mineralogy of fine-grained horizons of this formation by X-ray diffraction and Scanning Electron Microscopy (SEM) in order to examine the connection between vertical changes in clay mineralogy in alluvial sediments and paleosols, and global paleoclimatic changes registered during the Paleogene. Paleosols vary from calcic vertisols in the lowermost levels, to inseptisols and gleysols in intermediate positions, to gleyed oxisols in the upper section, indicating increased chemical weathering through time. Clay mineral relative abundances vary with a general increase in kaolinite content from bottom to top. However, at one site there are significant variations in kaolinite/muscovite (Kln/Ms) that define five cycles of kaolinite abundance and Kln/Ms. that indicate cyclic patterns of paleoprecipitation and paleotemperature. These are interpreted as several short-lived hyperthermals during the Paleocene-early Eocene in the Southern Hemisphere, which correlate with well-established episodes of warmth documented from the Northern Hemisphere.

Sedimentology of the Argo and Gascoyne abyssal plains, NW Australia: Report on Ocean Drilling Program Leg 123 (Sept. 1–Nov. 1, 1988)

USGS Publications Warehouse

Thurow, Jürgen

1988-01-01

Ocean Drilling Program Leg 123 drilled two sites in the Indian Ocean in order to study the rifting and early spreading of one of the world’s oldest ocean basins.Site 765 was drilled in 5714 meters of water on the Argo Abyssal Plain northwest of Australia. The sedimentary succession records the opening of an ocean basin, from the first sediments deposited atop young oceanic crust, to the present day. The oldest sediments are microlaminated brown silty claystones, locally rich in calcareous bioclasts. Most of the sequence is dominated by turbidites (primarily calcareous) which probably originated within canyons cut into the margin of the drowned platform of the North West Shelf of Australia.Site 766 is located in 3998 meters of water, at the base of the steep western margin of the Exmouth Plateau. The oldest sediments penetrated are glauconitic, volcaniclastic, and bioclastic sandstones and siltstones, which are interbedded with inclined basaltic sills. These sediments were deposited by a prograding submarine fan system which shed shallow marine sediments westward or northwestward off of the western rim of the Exmouth Plateau. Sandstones are succeeded by silty claystones, recording gradual abandonment or redirection of the fan system. An overlying sequence of pelagic and hemipelagic clayey and zeolitic calcareous oozes and chalks is succeeded by featureless and homogeneous pelagic nannofossil oozes.

Dynamics of the formation of laser-induced periodic surface structures (LIPSS) upon femtosecond two-color double-pulse irradiation of metals, semiconductors, and dielectrics

NASA Astrophysics Data System (ADS)

Höhm, S.; Herzlieb, M.; Rosenfeld, A.; Krüger, J.; Bonse, J.

2016-06-01

In order to address the dynamics and physical mechanisms of LIPSS formation for three different classes of materials (metals, semiconductors, and dielectrics), two-color double-fs-pulse experiments were performed on Titanium, Silicon and Fused Silica. For that purpose a Mach-Zehnder interferometer generated polarization controlled (parallel or cross-polarized) double-pulse sequences at 400 nm and 800 nm wavelength, with inter-pulse delays up to a few picoseconds. Multiple of these two-color double-pulse sequences were collinearly focused by a spherical mirror to the sample surfaces. The fluence of each individual pulse (400 nm and 800 nm) was always kept below its respective ablation threshold and only the joint action of both pulses lead to the formation of LIPSS. Their resulting characteristics (periods, areas) were analyzed by scanning electron microscopy. The periods along with the LIPSS orientation allow a clear identification of the pulse which dominates the energy coupling to the material. For strong absorbing materials (Silicon, Titanium), a wavelength-dependent plasmonic mechanism can explain the delay-dependence of the LIPSS. In contrast, for dielectrics (Fused Silica) the first pulse always dominates the energy deposition and LIPSS orientation, supporting a non-plasmonic formation scenario. For all materials, these two-color experiments confirm the importance of the ultrafast energy deposition stage for LIPSS formation.

Stratigraphy and paleogeographic significance of a Late Pennsylvanian to Early Permian channeled slope sequence in the Darwin Basin, southern Darwin Hills, east-central California

USGS Publications Warehouse

Stevens, Calvin H.; Stone, Paul; Magginetti, Robert T.; Ritter, Scott M.

2015-01-01

The complex stratigraphy of late Paleozoic rocks in the southern Darwin Hills consists of regionally extensive Mississippian and Early to Middle Pennsylvanian rocks overlain by latest Pennsylvanian to Early Permian rocks, herein called the Darwin Hills sequence. Deposition of this latter sequence marked the beginning of the Darwin Basin. In Mississippian time, a carbonate platform prograded westward over slightly older slope deposits. In the Late Mississippian this platform was exposed to erosion and siliciclastic sediments were deposited. In Early to Middle Pennsylvanian time the area subsided, forming a west-facing ramp that was subjected to deformation and erosion in Middle or early Late Pennsylvanian time. Later this area was tilted westward and deep-water sediments were deposited on this slope. In latest Pennsylvanian to earliest Permian time, a major channel was cut through the older Pennsylvanian rocks and into the Upper Mississippian strata. This channel was gradually filled with increasingly finer grained, deep-water sediment as the area evolved into a basin floor by Early Permian (Sakmarian) time. Expansion of the Darwin Basin in Artinskian time led to a second phase of deposition represented by strata of the regionally extensive Darwin Canyon Formation. The geology in this small area thus documents tectonic events occurring during the early development of the Darwin Basin.

The determination of third order linear models from a seventh order nonlinear jet engine model

NASA Technical Reports Server (NTRS)

Lalonde, Rick J.; Hartley, Tom T.; De Abreu-Garcia, J. Alex

1989-01-01

Results are presented that demonstrate how good reduced-order models can be obtained directly by recursive parameter identification using input/output (I/O) data of high-order nonlinear systems. Three different methods of obtaining a third-order linear model from a seventh-order nonlinear turbojet engine model are compared. The first method is to obtain a linear model from the original model and then reduce the linear model by standard reduction techniques such as residualization and balancing. The second method is to identify directly a third-order linear model by recursive least-squares parameter estimation using I/O data of the original model. The third method is to obtain a reduced-order model from the original model and then linearize the reduced model. Frequency responses are used as the performance measure to evaluate the reduced models. The reduced-order models along with their Bode plots are presented for comparison purposes.

Temperature Oscillations in Loop Heat Pipes - A Revisit

NASA Technical Reports Server (NTRS)

Ku, Jentung

2018-01-01

Three types of temperature oscillation have been observed in the loop heat pipes. The first type is an ultra-high frequency temperature oscillation with a period on the order of seconds or less. This type of temperature oscillation is of little significance in spacecraft thermal control because the amplitude is in the noise level. The second type is a high frequency, low amplitude temperature oscillation with a period on the order of seconds to minutes and an amplitude on the order of one Kelvin. It is caused by the back-and-forth movement of the vapor front near the inlet or outlet of the condenser. The third type is a low frequency, high amplitude oscillation with a period on the order of hours and an amplitude on the order of tens of Kelvin. It is caused by the modulation of the net heat load into the evaporator by the attached large thermal mass which absorbs and releases energy alternately. Several papers on LHP temperature oscillation have been published. This paper presents a further study on the underlying physical processes during the LHP temperature oscillation, with an emphasis on the third type of temperature oscillation. Specifically, equations governing the thermal and hydraulic behaviors of LHP operation will be used to describe interactions among LHP components, heat source, and heat sink. The following sequence of events and their interrelationship will also be explored: 1) maxima and minima of reservoir and thermal mass temperatures; 2) the range of the vapor front movement inside the condenser; 3) rates of change of the reservoir and thermal mass temperatures; 4) the rate of heat absorption and heat release by the thermal mass and the rate of vapor front movement; and 5) inflection points of the reservoir and thermal mass temperatures.

Intranasal Deposition of Accuspray™ Aerosol in Anatomically Correct Models of 2-, 5-, and 12-Year-Old Children.

PubMed

Laube, Beth L; Sharpless, Gail; Vikani, Ami R; Harrand, Vincent; Zinreich, Simeon J; Sedberry, Keith; Knaus, Darin; Barry, James; Papania, Mark

2015-10-01

To our knowledge, quantification of intranasal deposition of aerosol generated by Accuspray(™) (AS) in children has never been published. We hypothesized that deposition would vary significantly with age and with placement of the device within, or outside, of the nostril. We tested these hypotheses in anatomically-correct physical models based on CT scans of 2-, 5-, and 12-year-old children with normal, intranasal airways. Models included a removable anterior nose (AN) with exterior facial features and interior nasal vestibule and nasal valve area and a main nasal airway (MNA), subdivided into upper (superior turbinates and olfactory area), middle (middle turbinates), and lower (inferior turbinates and nasopharynx) thirds. Aerosol was generated from distilled water admixed with (99m)technetium pertechnetate and administered during static airflow by AS inserted inside the right nostril (eight runs/model), or outside the right nostril (six runs/model). Mean aerosol Dv(50) ± standard deviation was 67.8 ± 24.7 μm. Deposition was quantified by 2D gamma scintigraphy and expressed as percentage of the emitted dose. When placed inside the nostril, mean (± standard deviation) deposition within the MNA was significantly less in the 2-year-old, compared to the 5- and 12-year-old, averaging 46.8 ± 33.8% (AN:55.4 ± 29.9%), 75.4 ± 26.7% (AN:23.3 ± 13.6%), and 72.1 ± 18.5% (AN:25.8 ± 18.5%), respectively (p<0.05). When placed outside the nostril, MNA was significantly less in the 2- and 5-year-old compared to the 12-year-old, with 1.4 ± 2.5% (AN:69.7 ± 40.7%), 7.4 ± 9.0% (AN:77.8 ± 32.8%), and 21.1 ± 29.1% (AN:29.2 ± 19.3%), respectively (p<0.05). Deposition in the MNA of all age models was highest when AS was placed inside the nostril (p<0.05). Deposition in the lower third was significantly increased for the 5- and 12-year-old and in the middle third of the 5-year-old when AS was placed inside the nostril. These results indicate that age and device placement play important roles in terms of intranasal deposition, when administering aerosol with Accuspray(™) to children.

Peri-equatorial paleolatitudes for Jurassic radiolarian cherts of Greece

USGS Publications Warehouse

Aiello, I.W.; Hagstrum, J.T.; Principi, G.

2008-01-01

Radiolarian-rich sediments dominated pelagic deposition over large portions of the Tethys Ocean during middle to late Jurassic time as shown by extensive bedded chert sequences found in both continental margin and ophiolite units of the Mediterranean region. Which paleoceanographic mechanisms and paleotectonic setting favored radiolarian deposition during the Jurassic, and the nature of a Tethys-wide change from biosiliceous to biocalcareous (mainly nannofossil) deposition at the beginning of Cretaceous time, have remained open questions. Previous paleomagnetic analyses of Jurassic red radiolarian cherts in the Italian Apennines indicate that radiolarian deposition occurred at low peri-equatorial latitudes, similar to modern day deposition of radiolarian-rich sediments within equatorial zones of high biologic productivity. To test this result for other sectors of the Mediterranean region, we undertook paleomagnetic study of Mesozoic (mostly middle to upper Jurassic) red radiolarian cherts within the Aegean region on the Peloponnesus and in continental Greece. Sampled units are from the Sub-Pelagonian Zone on the Argolis Peninsula, the Pindos-Olonos Zone on the Koroni Peninsula, near Karpenissi in central Greece, and the Ionian Zone in the Varathi area of northwestern Greece. Thermal demagnetization of samples from all sections removed low-temperature viscous and moderate-temperature overprint magnetizations that fail the available fold tests. At Argolis and Koroni, however, the cherts carry a third high-temperature magnetization that generally exhibits a polarity stratigraphy and passes the available fold tests. We interpret the high-temperature component to be the primary magnetization acquired during chert deposition and early diagenesis. At Kandhia and Koliaky (Argolis), the primary declinations and previous results indicate clockwise vertical-axis rotations of ??? 40?? relative to "stable" Europe. Due to ambiguities in hemispheric origin (N or S) and thus paleomagnetic polarity, the observed declinations could indicate either clockwise (CW) or counterclockwise (CCW) vertical-axis rotations. Thus at Adriani (Koroni), the primary declinations indicate either CW or CCW rotations of ??? 95?? or ??? 84??, depending on paleomagnetic polarity and age. The primary inclinations for all Peloponnesus sites indicate peri-equatorial paleolatitudes similar to those found for coeval radiolarian cherts exposed in other Mediterranean orogenic belts. Our new paleomagnetic data support the interpretation that Mesozoic radiolarites within the Tethys Ocean were originally deposited along peri-equatorial belts of divergence and high biologic productivity. ?? 2007 Elsevier B.V. All rights reserved.

Design, Test, and Evaluation of a Transonic Axial Compressor Rotor with Splitter Blades

DTIC Science & Technology

2013-09-01

parameters .......................................................17 Figure 13. Third-order spline fit for blade camber line distribution...18 Figure 14. Third-order spline fit for blade thickness distribution .....................................19 Figure 15. Blade...leading edge: third-order spline fit for thickness distribution ...............20 Figure 16. Blade leading edge and trailing edge slope blending

Using palynology to re-assess the Dead Sea laminated sediments - Indeed varves?

NASA Astrophysics Data System (ADS)

Bookman, Revital; Lopez-Merino, Lourdes; Belmaker, Reuven; Eshel, Amram; Epshtein Epshtein, Valentina; Leroy, Suzanne

2017-04-01

Lacustrine laminated sediments are often varves representing annual rhythmic deposition. The Dead Sea high-stand laminated sections consist of mm-scale alternating detrital and authigenic aragonite laminae. Previous studies assumed these laminae were varves; detritus deposition during the winter and aragonite in the summer. These sequences were used for varve counting and chronology, however this assumption has never been robustly validated. Here, we report an examination of the seasonal deposition of detrital and aragonite couplets from two well-known Late Holocene laminated sections at the Ze'elim fan-delta using palynology and grain-size distribution analyses. These analyses are complemented by the study of contemporary flash-flood samples and multivariate statistical analysis. Because transport affects the pollen preservation state, well-preserved (mostly) air-borne transported pollen was analysed separately from badly-preserved pollen and fungal spores, which are more indicative of water transport and reworking from soils. Our results indicate that (i) both detrital and aragonite laminae were deposited during the rainy season; (ii) aragonite laminae have significantly lower reworked pollen and fungal spore concentrations than detrital and flash-flood samples; and (iii) detrital laminae are composed of recycling of local and distal sources, with coarser particles that were initially deposited in the Dead Sea watershed and later transported via run-off to the lake. The conclusions suggest that detrital and aragonite couplets in the Dead Sea laminated sediments are most likely not varves and that the laminae deposition is related to the occurrence of flash-flood events. Consequently, at least for the Holocene sequences, laminated sediments cannot be considered as varves and Quaternary laminated sequences should be re-evaluated. The Dead Sea Basin laminated sequences (as the ICDP Dead Sea Deep Drilling Project record) should be used for the reconstruction of palaeo-flash flood records that will have a significant impact on understanding the palaeo-hydrology of the DSB and its implication to high-resolution climatic interpretation.

Magnetic and electrical characterization of nickel-rich NiFe thin films synthesized by atomic layer deposition and subsequent thermal reduction.

PubMed

Espejo, A P; Zierold, R; Gooth, J; Dendooven, J; Detavernier, C; Escrig, J; Nielsch, K

2016-08-26

Nickel-rich NiFe thin films (Ni92Fe8, Ni89Fe11 and Ni83Fe17) were prepared by combining atomic layer deposition (ALD) with a subsequent thermal reduction process. In order to obtain Ni x Fe1-x O y films, one ALD supercycle was performed according to the following sequence: m NiCp2/O3, with m = 1, 2 or 3, followed by one FeCp2/O3 cycle. The supercycle was repeated n times. The thermal reduction process in hydrogen atmosphere was investigated by in situ x-ray diffraction studies as a function of temperature. The metallic nickel iron alloy thin films were investigated and characterized with respect to crystallinity, morphology, resistivity, and magnetism. As proof-of-concept magnetic properties of an array of Ni83Fe17, close to the perfect Permalloy stoichiometry, nanotubes and an isolated tube were investigated.

Magnetic and electrical characterization of nickel-rich NiFe thin films synthesized by atomic layer deposition and subsequent thermal reduction

NASA Astrophysics Data System (ADS)

Espejo, A. P.; Zierold, R.; Gooth, J.; Dendooven, J.; Detavernier, C.; Escrig, J.; Nielsch, K.

2016-08-01

Nickel-rich NiFe thin films (Ni92Fe8, Ni89Fe11 and Ni83Fe17) were prepared by combining atomic layer deposition (ALD) with a subsequent thermal reduction process. In order to obtain Ni x Fe1-x O y films, one ALD supercycle was performed according to the following sequence: m NiCp2/O3, with m = 1, 2 or 3, followed by one FeCp2/O3 cycle. The supercycle was repeated n times. The thermal reduction process in hydrogen atmosphere was investigated by in situ x-ray diffraction studies as a function of temperature. The metallic nickel iron alloy thin films were investigated and characterized with respect to crystallinity, morphology, resistivity, and magnetism. As proof-of-concept magnetic properties of an array of Ni83Fe17, close to the perfect Permalloy stoichiometry, nanotubes and an isolated tube were investigated.

Quantitative Susceptibility Mapping as a Possible Tool to Radiographically Diagnose Sentinel Headache Associated with Intracranial Aneurysm: Case Report.

PubMed

Nakagawa, Daichi; Cushing, Cameron; Nagahama, Yasunori; Allan, Lauren; Hasan, David

2017-07-01

Sentinel headache (SH) occurs before aneurysm rupture in an estimated 15%-60% of cases of aneurysmal subarachnoid hemorrhage (aSAH). By definition, noncontrast computed tomography (CT) scan of the brain and lumbar puncture are both negative in patients presenting with SH. One of the theories explaining this phenomenon is that microhemorrhage (MH) from the aneurysm wall contribute to iron deposition in the interface between the aneurysm wall and brain parenchyma. Quantitative susceptibility mapping (QSM) is a recently introduced magnetic resonance imaging (MRI) technique that has proven capable of localizing the deposition of paramagnetic metals, particularly ferric iron. Thus, the QSM sequence may be able to detect iron deposition secondary to MH. A 76-year-old male presented with the "worst headache of my life." Noncontrast head CT scan and lumbar puncture were negative. Magnetic resonance angiography (MRA) of the brain revealed an anterior communicating artery (A-com) aneurysm measuring 7 mm with a large bleb. T1-weighted imaging (WI), T2-WI, MRA, T2 star-weighted angiography (SWAN), and QSM sequences were obtained. T2-WI, SWAN, and QSM revealed isointense, hypointense, and hyperintense signals, respectively, at the interface of the aneurysm wall and brain tissue. These findings were consistent with deposition of ferric iron at this interface. The A-com aneurysm was treated with coil embolization, and the patient exhibited no postoperative deficits. The MRI QSM sequence can localize iron deposition resulting from MH within an aneurysmal wall. This sequence may be a promising imaging tool for screening patients presenting with SH. Copyright © 2017 Elsevier Inc. All rights reserved.

Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access.

PubMed

Taboada, Eduardo N; Graham, Morag R; Carriço, João A; Van Domselaar, Gary

2017-01-01

Public health labs and food regulatory agencies globally are embracing whole genome sequencing (WGS) as a revolutionary new method that is positioned to replace numerous existing diagnostic and microbial typing technologies with a single new target: the microbial draft genome. The ability to cheaply generate large amounts of microbial genome sequence data, combined with emerging policies of food regulatory and public health institutions making their microbial sequences increasingly available and public, has served to open up the field to the general scientific community. This open data access policy shift has resulted in a proliferation of data being deposited into sequence repositories and of novel bioinformatics software designed to analyze these vast datasets. There also has been a more recent drive for improved data sharing to achieve more effective global surveillance, public health and food safety. Such developments have heightened the need for enhanced analytical systems in order to process and interpret this new type of data in a timely fashion. In this review we outline the emergence of genomics, bioinformatics and open data in the context of food safety. We also survey major efforts to translate genomics and bioinformatics technologies out of the research lab and into routine use in modern food safety labs. We conclude by discussing the challenges and opportunities that remain, including those expected to play a major role in the future of food safety science.

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.

The stratigraphy of the southern Pab Range, Pakistan

NASA Astrophysics Data System (ADS)

White, H. J.

The Cretaceous strata exposed in the southern Pab Range, southeast Baluchistan, Pakistan is investigated. It records the precollision deposition history of the Indo-Pakistani continental shelf. The strata comprise two depositional successions, namely, The Early to Late Cretaceous Sembar-Goru-Parh sequence and the Maestrichtian Mughal Kot-Pab sequence. The former began with deposition of black shales on the continental slope (Sembar Formation), succeeded by calcareous shale, marl and micstone of outer shelf origin (Goru Formation), and ended with inner shelf platform carbonates (Parh Limestone). These deep to shallow water lithofacies prograted westward over the continental shelf of the north-advancing Subcontinent. The Mughal Kot-Pab propagation contains the first significant influx of terrigenous sand reaching the western portion of the continental shelf. Deposition environments in the Mughal Kot Formation include inner shelf, prodelta, delta front and distributary channel. A thick succession of shoreface cycles comprises the Pab sandstone.

Patterns of maternal yolk hormones in eastern screech owl eggs (Megascops asio)

USGS Publications Warehouse

Hahn, D. Caldwell

2011-01-01

Owl clutches typically hatch asynchronously, and brood size hierarchies develop. In this study, we describe intra-clutch variation of testosterone, androstenedione, estradiol, and corticosterone in Eastern screech owl egg yolks. In order to assess whether these hormones may have originated in the follicle, we also characterize variation of testosterone, androstenedione, and corticosterone within the exterior, intermediate, and interior regions of the yolk. Concentrations of testosterone and androstenedione were distributed relatively evenly across egg lay order with the exception of first-laid eggs that had significantly lower concentrations of both androgens than eggs later in the laying sequence. Corticosterone and estradiol did not vary with laying order. Our results suggest that when food is abundant, yolk hormones are deposited in patterns that minimize sibling differences except to reduce dominance by the first-hatching chick. Testosterone and androstenedione concentrations varied throughout the yolk, while corticosterone was evenly distributed throughout the yolk. This supports a follicular origin for both yolk androgens, and an adrenal origin for yolk corticosterone.