Star formation is boosted (and quenched) from the inside-out: radial star formation profiles from MaNGA

NASA Astrophysics Data System (ADS)

Ellison, Sara L.; Sánchez, Sebastian F.; Ibarra-Medel, Hector; Antonio, Braulio; Mendel, J. Trevor; Barrera-Ballesteros, Jorge

2018-02-01

The tight correlation between total galaxy stellar mass and star formation rate (SFR) has become known as the star-forming main sequence. Using ˜487 000 spaxels from galaxies observed as part of the Sloan Digital Sky Survey Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, we confirm previous results that a correlation also exists between the surface densities of star formation (ΣSFR) and stellar mass (Σ⋆) on kpc scales, representing a `resolved' main sequence. Using a new metric (ΔΣSFR), which measures the relative enhancement or deficit of star formation on a spaxel-by-spaxel basis relative to the resolved main sequence, we investigate the SFR profiles of 864 galaxies as a function of their position relative to the global star-forming main sequence (ΔSFR). For galaxies above the global main sequence (positive ΔSFR) ΔΣSFR is elevated throughout the galaxy, but the greatest enhancement in star formation occurs at small radii (<3 kpc, or 0.5Re). Moreover, galaxies that are at least a factor of 3 above the main sequence show diluted gas phase metallicities out to 2Re, indicative of metal-poor gas inflows accompanying the starbursts. For quiescent/passive galaxies that lie at least a factor of 10 below the star-forming main sequence, there is an analogous deficit of star formation throughout the galaxy with the lowest values of ΔΣSFR in the central 3 kpc. Our results are in qualitative agreement with the `compaction' scenario in which a central starburst leads to mass growth in the bulge and may ultimately precede galactic quenching from the inside-out.

Comprehensive transcriptome analysis unravels the existence of crucial genes regulating primary metabolism during adventitious root formation in Petunia hybrida.

PubMed

Ahkami, Amirhossein; Scholz, Uwe; Steuernagel, Burkhard; Strickert, Marc; Haensch, Klaus-Thomas; Druege, Uwe; Reinhardt, Didier; Nouri, Eva; von Wirén, Nicolaus; Franken, Philipp; Hajirezaei, Mohammad-Reza

2014-01-01

To identify specific genes determining the initiation and formation of adventitious roots (AR), a microarray-based transcriptome analysis in the stem base of the cuttings of Petunia hybrida (line W115) was conducted. A microarray carrying 24,816 unique, non-redundant annotated sequences was hybridized to probes derived from different stages of AR formation. After exclusion of wound-responsive and root-regulated genes, 1,354 of them were identified which were significantly and specifically induced during various phases of AR formation. Based on a recent physiological model distinguishing three metabolic phases in AR formation, the present paper focuses on the response of genes related to particular metabolic pathways. Key genes involved in primary carbohydrate metabolism such as those mediating apoplastic sucrose unloading were induced at the early sink establishment phase of AR formation. Transcriptome changes also pointed to a possible role of trehalose metabolism and SnRK1 (sucrose non-fermenting 1- related protein kinase) in sugar sensing during this early step of AR formation. Symplastic sucrose unloading and nucleotide biosynthesis were the major processes induced during the later recovery and maintenance phases. Moreover, transcripts involved in peroxisomal beta-oxidation were up-regulated during different phases of AR formation. In addition to metabolic pathways, the analysis revealed the activation of cell division at the two later phases and in particular the induction of G1-specific genes in the maintenance phase. Furthermore, results point towards a specific demand for certain mineral nutrients starting in the recovery phase.

Comprehensive Transcriptome Analysis Unravels the Existence of Crucial Genes Regulating Primary Metabolism during Adventitious Root Formation in Petunia hybrida

PubMed Central

Ahkami, Amirhossein; Scholz, Uwe; Steuernagel, Burkhard; Strickert, Marc; Haensch, Klaus-Thomas; Druege, Uwe; Reinhardt, Didier; Nouri, Eva; von Wirén, Nicolaus; Franken, Philipp; Hajirezaei, Mohammad-Reza

2014-01-01

To identify specific genes determining the initiation and formation of adventitious roots (AR), a microarray-based transcriptome analysis in the stem base of the cuttings of Petunia hybrida (line W115) was conducted. A microarray carrying 24,816 unique, non-redundant annotated sequences was hybridized to probes derived from different stages of AR formation. After exclusion of wound-responsive and root-regulated genes, 1,354 of them were identified which were significantly and specifically induced during various phases of AR formation. Based on a recent physiological model distinguishing three metabolic phases in AR formation, the present paper focuses on the response of genes related to particular metabolic pathways. Key genes involved in primary carbohydrate metabolism such as those mediating apoplastic sucrose unloading were induced at the early sink establishment phase of AR formation. Transcriptome changes also pointed to a possible role of trehalose metabolism and SnRK1 (sucrose non-fermenting 1- related protein kinase) in sugar sensing during this early step of AR formation. Symplastic sucrose unloading and nucleotide biosynthesis were the major processes induced during the later recovery and maintenance phases. Moreover, transcripts involved in peroxisomal beta-oxidation were up-regulated during different phases of AR formation. In addition to metabolic pathways, the analysis revealed the activation of cell division at the two later phases and in particular the induction of G1-specific genes in the maintenance phase. Furthermore, results point towards a specific demand for certain mineral nutrients starting in the recovery phase. PMID:24978694

Electric-Field Control of Oxygen Vacancies and Magnetic Phase Transition in a Cobaltite/Manganite Bilayer

NASA Astrophysics Data System (ADS)

Cui, B.; Song, C.; Li, F.; Zhong, X. Y.; Wang, Z. C.; Werner, P.; Gu, Y. D.; Wu, H. Q.; Saleem, M. S.; Parkin, S. S. P.; Pan, F.

2017-10-01

Manipulation of oxygen vacancies (VO ) in single oxide layers by varying the electric field can result in significant modulation of the ground state. However, in many oxide multilayers with strong application potentials, e.g., ferroelectric tunnel junctions and solid-oxide fuel cells, understanding VO behavior in various layers under an applied electric field remains a challenge, owing to complex VO transport between different layers. By sweeping the external voltage, a reversible manipulation of VO and a corresponding fixed magnetic phase transition sequence in cobaltite/manganite (SrCoO3 -x/La0.45Sr0.55MnO3 -y ) heterostructures are reported. The magnetic phase transition sequence confirms that the priority of electric-field-induced VO formation or annihilation in the complex bilayer system is mainly determined by the VO formation energies and Gibbs free-energy differences, which is supported by theoretical analysis. We not only realize a reversible manipulation of the magnetic phase transition in an oxide bilayer but also provide insight into the electric-field control of VO engineering in heterostructures.

Sequence Directionality Dramatically Affects LCST Behavior of Elastin-Like Polypeptides.

PubMed

Li, Nan K; Roberts, Stefan; Quiroz, Felipe Garcia; Chilkoti, Ashutosh; Yingling, Yaroslava G

2018-04-30

Elastin-like polypeptides (ELP) exhibit an inverse temperature transition or lower critical solution temperature (LCST) transition phase behavior in aqueous solutions. In this paper, the thermal responsive properties of the canonical ELP, poly(VPGVG), and its reverse sequence poly(VGPVG) were investigated by turbidity measurements of the cloud point behavior, circular dichroism (CD) measurements, and all-atom molecular dynamics (MD) simulations to gain a molecular understanding of mechanism that controls hysteretic phase behavior. It was shown experimentally that both poly(VPGVG) and poly(VGPVG) undergo a transition from soluble to insoluble in aqueous solution upon heating above the transition temperature ( T t ). However, poly(VPGVG) resolubilizes upon cooling below its T t , whereas the reverse sequence, poly(VGPVG), remains aggregated despite significant undercooling below the T t . The results from MD simulations indicated that a change in sequence order results in significant differences in the dynamics of the specific residues, especially valines, which lead to extensive changes in the conformations of VPGVG and VGPVG pentamers and, consequently, dissimilar propensities for secondary structure formation and overall structure of polypeptides. These changes affected the relative hydrophilicities of polypeptides above T t , where poly(VGPVG) is more hydrophilic than poly(VPGVG) with more extended conformation and larger surface area, which led to formation of strong interchain hydrogen bonds responsible for stabilization of the aggregated phase and the observed thermal hysteresis for poly(VGPVG).

Hardware-In-The-Loop Testing of Continuous Control Algorithms for a Precision Formation Flying Demonstration Mission

NASA Technical Reports Server (NTRS)

Naasz, Bo J.; Burns, Richard D.; Gaylor, David; Higinbotham, John

2004-01-01

A sample mission sequence is defined for a low earth orbit demonstration of Precision Formation Flying (PFF). Various guidance navigation and control strategies are discussed for use in the PFF experiment phases. A sample PFF experiment is implemented and tested in a realistic Hardware-in-the-Loop (HWIL) simulation using the Formation Flying Test Bed (FFTB) at NASA's Goddard Space Flight Center.

Paleographic and sedimentologic significance of Mississippian sequence at Mt. Darby, Wyoming

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

Dejarnett, J.

1985-05-01

Mississippian strata at Mt. Darby comprise the Madison Group and the overlying Humbug Formation. This sequence, although initially transgressive, exhibits an overall regressive character produced by progradation of platform carbonates in response to sea level fluctuations related to Antler orogenic events. The Paine Member of the Lodgepole Limestone, the basal formation of the Madison Group, consists of relatively deep-water carbonates including a possible Waulsortian-type carbonate bank that accumulated on a Kinderhookian foreslope. At least five shoaling-upward grainstone cycles are recognizable in the Woodhurst Member of the Lodgepole Limestone. These cycles record Osagean deposition in shallow agitated environments that developed highmore » on a clinoform ramp. Shelf-margin and platform carbonates dominate the Mission Canyon Limestone, the upper formation of the Madison Group. this unit consists of two asymmetric deposition cycles, each with a thick regressive phase, capped by an evaporite solution breccia and an overlying thin transgressive phase. The Humbug Formation, a sequence of fine-grained carbonates and sandstones, represents part of a deltaic complex that developed offshore from the Meramecian karst plain. Humbug sediments were transported northward to the Mt. Darby area from the area of the present Uinta Mountains, or another deltaic system formed there. Deposition in the study area was apparently continuous upward from the Madison carbonates into the Humbug. The middle Meramecian shoreline trended northwest between the present locations of Mt. Darby and Haystack Peak.« less

Formation of sodium bismuth titanate-barium titanate during solid-state synthesis

DOE PAGES

Hou, Dong; Aksel, Elena; Fancher, Chris M.; ...

2017-01-12

Phase formation of sodium bismuth titanate (Na 0.5Bi 0.5TiO 3 or NBT) and its solid solution with barium titanate (BaTiO 3 or BT) during the calcination process is studied using in situ high-temperature diffraction. The reactant powders were mixed and heated to 1000°C, while X-ray diffraction patterns were recorded continuously. Phase evolutions from starting materials to final perovskite products are observed, and different transient phases are identified. The formation mechanism of NBT and NBT–xBT perovskite structures is discussed, and a reaction sequence is suggested based on the observations. The in situ study leads to a new processing approach, which ismore » the use of nano-TiO 2, and gives insights to the particle size effect for solid-state synthesis products. Lastly, it was found that the use of nano-TiO 2 as reactant powder accelerates the synthesis process, decreases the formation of transient phases, and helps to obtain phase-pure products using a lower thermal budget.« less

The Oligocene-Miocene stratigraphic evolution of the Majella carbonate platform (Central Apennines, Italy)

NASA Astrophysics Data System (ADS)

Brandano, Marco; Cornacchia, Irene; Raffi, Isabella; Tomassetti, Laura

2016-03-01

The stratigraphic architecture of the Bolognano Formation documents the evolution of the Majella carbonate platform in response to global and local changes that affected the Mediterranean area during the Oligocene-Miocene interval. The Bolognano Formation consists of a homoclinal ramp that developed in a warm, subtropical environment. Five different lithofacies associations have been identified: Lepidocyclina calcarenites, cherty marly limestones, bryozon calcarenites, hemipelagic marls and marly limestones, and Lithothamnion limestones. Each association corresponds to a single lithostratigraphic unit except for the Lepidocyclina calcarenites that form two distinct lithostratigraphic units (Lepidocyclina calcarenites 1 and 2). These six units reflect alternation of shallow-water carbonate production and drowning. Specifically, two of the three stages of shallow-water carbonate production regard the development of wide dune fields within the middle ramp, one stage dominated by red algae and a sea-grass carbonate factory, whereas the two drowning phases are represented by marly cherty limestones and calcareous marls. A new biostratigraphic framework for Bolognano Formation is presented, based on high-resolution analysis of calcareous nannofossil assemblages, which proved to be very useful for biostratigraphic constraints also in shallow-water settings. Using this approach, we have linked the first drowning phase, late Chattian-Aquitanian p.p. in age, to western Mediterranean volcanism and the Mi-1 event, and the second drowning phase, late Burdigalian-Serravallian in age, to the closure of the Indo-Pacific passage and the occurrence of the global Monterey event. These results permit a new deciphering, in terms of sequence stratigraphy, of the Bolognano Formation that is interpreted as a 2nd-order super-sequence that can be subdivided into 3 transgressive-regressive sequences.

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.

Metastable phase formation in undercooled Fe-Co melts under terrestrial and parabolic flight conditions

NASA Astrophysics Data System (ADS)

Hermann, R.; Löser, W.; Lindenkreuz, H. G.; Yang-Bitterlich, W.; Mickel, Ch.; Diefenbach, A.; Schneider, S.; Dreier, W.

2007-12-01

Soft magnetic Fe-Co alloys display primary fcc phase solidification for>19,5 at% Co in conventional near-equilibrium solidification processes. Undercooled Fe-Co melt drops within the composition range of 30 to 50 at% Co have been investigated with the electromagnetic levitation technique. The solidification kinetics was measured in situ using a high-resolution Siphotodiode. Melt drops were undercooled up to 263 K below the liquidus temperature and subsequently quenched onto a chill substrate in order to characterize the solidification sequence and microstructure. The transition from stable fcc phase to metastable bcc primary phase solidification has been observed after reaching a critical undercooling level. The critical undercooling increases with rising Co content. The growth velocity drops obviously after transition to metastable bcc phase formation. Parabolic flight experiments were performed in order to study the phase selection under reduced gravity conditions. Under microgravity conditions, a much smaller critical undercooling and an increased life time of the metastable bcc phase were obtained. This result was validated with TEM investigations. The appearance of Fe-O particles gives an indirect hint for an intermediate fcc phase formation from the metastable bcc phase at elevated temperature.

CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences

PubMed Central

Ruff, Kiersten M.; Harmon, Tyler S.; Pappu, Rohit V.

2015-01-01

We report the development and deployment of a coarse-graining method that is well suited for computer simulations of aggregation and phase separation of protein sequences with block-copolymeric architectures. Our algorithm, named CAMELOT for Coarse-grained simulations Aided by MachinE Learning Optimization and Training, leverages information from converged all atom simulations that is used to determine a suitable resolution and parameterize the coarse-grained model. To parameterize a system-specific coarse-grained model, we use a combination of Boltzmann inversion, non-linear regression, and a Gaussian process Bayesian optimization approach. The accuracy of the coarse-grained model is demonstrated through direct comparisons to results from all atom simulations. We demonstrate the utility of our coarse-graining approach using the block-copolymeric sequence from the exon 1 encoded sequence of the huntingtin protein. This sequence comprises of 17 residues from the N-terminal end of huntingtin (N17) followed by a polyglutamine (polyQ) tract. Simulations based on the CAMELOT approach are used to show that the adsorption and unfolding of the wild type N17 and its sequence variants on the surface of polyQ tracts engender a patchy colloid like architecture that promotes the formation of linear aggregates. These results provide a plausible explanation for experimental observations, which show that N17 accelerates the formation of linear aggregates in block-copolymeric N17-polyQ sequences. The CAMELOT approach is versatile and is generalizable for simulating the aggregation and phase behavior of a range of block-copolymeric protein sequences. PMID:26723608

La formation de l'inkisi (Supergroupe ouest-congolien) en Afrique centrale (Congo et Bas-Zaïre): un delta d'âge Paléozoïque comblant un bassin en extension

NASA Astrophysics Data System (ADS)

Alvarez, Philippe; Maurin, Jean-Christophe; Vicat, Jean-Paul

1995-02-01

The Inkisi Formation (West Congolian Supergroup) corresponds to a large deltaic body, which extends through Congo, Lower Zaire and Angola. In the Congo and Lower Zaire areas, the lower part of this formation is characterized by a fluvial conglomerate with elliptic pebbles. The red arkosic, channelized series from the Brazzaville-Kinshasa area involves delta plain distributary channels and delta front sequences. The transport direction of continental material is from north to south and the source area is the Chaillu basement. Glacial quartzitic pebbles are probably reworked from the fluvio-lacustrine Upper Diamictite Formation. The classical subdivisions of the Inkisi Formation - basal conglomerate (I 0), Lower part (I 1) and Upper part (I 2) - are not used. These subdivisions correspond to a fluvial conglomerate and to delta front and delta plain facies. The coastal onlap progressively covered the conglomerate and the distributary channels in the delta plain was prograding onto the delta front. The prodelta sequence could correspond to the Upper level of the Mpioka molassic Formation. The Inkisi delta was on the northern edge of an extensional basin controlled by NE-SW normal faults. The extension phase is dearly post Pan-African and occurred during the Palaeozoic, probably in relation to the Permian Karoo phase, and is also known in Angola.

Silicide phases formation in Co/c-Si and Co/a-Si systems during thermal annealing

NASA Astrophysics Data System (ADS)

Novaković, M.; Popović, M.; Zhang, K.; Lieb, K. P.; Bibić, N.

2014-03-01

The effect of the interface in cobalt-silicon bilayers on the silicide phase formation and microstructure has been investigated. Thin cobalt films were deposited by electron beam evaporation to a thickness of 50 nm on crystalline silicon (c-Si) or silicon with pre-amorphized surface (a-Si). After deposition one set of samples was annealed for 2 h at 200, 300, 400, 500, 600 and 700 °C. Another set of samples was irradiated with 400 keV Xe+ ions and then annealed at the same temperatures. Phase transitions were investigated with Rutherford backscattering spectroscopy, X-ray diffraction and cross-sectional transmission electron microscopy. No silicide formation was observed up to 400 °C, for both non-irradiated and ion-irradiated samples. When increasing the annealing temperature, the non-irradiated and irradiated Co/c-Si samples showed a similar behaviour: at 500 °C, CoSi appeared as the dominant silicide, followed by the formation of CoSi2 at 600 and 700 °C. In the case of non-irradiated Co/a-Si samples, no silicide formation occurred up to 700 °C, while irradiated samples with pre-amorphized substrate (Co/a-Si) showed a phase sequence similar to that in the Co/c-Si system. The observed phase transitions are found to be consistent with predictions of the effective heat of formation model.

Automatic Command Sequence Generation

NASA Technical Reports Server (NTRS)

Fisher, Forest; Gladded, Roy; Khanampompan, Teerapat

2007-01-01

Automatic Sequence Generator (Autogen) Version 3.0 software automatically generates command sequences for the Mars Reconnaissance Orbiter (MRO) and several other JPL spacecraft operated by the multi-mission support team. Autogen uses standard JPL sequencing tools like APGEN, ASP, SEQGEN, and the DOM database to automate the generation of uplink command products, Spacecraft Command Message Format (SCMF) files, and the corresponding ground command products, DSN Keywords Files (DKF). Autogen supports all the major multi-mission mission phases including the cruise, aerobraking, mapping/science, and relay mission phases. Autogen is a Perl script, which functions within the mission operations UNIX environment. It consists of two parts: a set of model files and the autogen Perl script. Autogen encodes the behaviors of the system into a model and encodes algorithms for context sensitive customizations of the modeled behaviors. The model includes knowledge of different mission phases and how the resultant command products must differ for these phases. The executable software portion of Autogen, automates the setup and use of APGEN for constructing a spacecraft activity sequence file (SASF). The setup includes file retrieval through the DOM (Distributed Object Manager), an object database used to store project files. This step retrieves all the needed input files for generating the command products. Depending on the mission phase, Autogen also uses the ASP (Automated Sequence Processor) and SEQGEN to generate the command product sent to the spacecraft. Autogen also provides the means for customizing sequences through the use of configuration files. By automating the majority of the sequencing generation process, Autogen eliminates many sequence generation errors commonly introduced by manually constructing spacecraft command sequences. Through the layering of commands into the sequence by a series of scheduling algorithms, users are able to rapidly and reliably construct the desired uplink command products. With the aid of Autogen, sequences may be produced in a matter of hours instead of weeks, with a significant reduction in the number of people on the sequence team. As a result, the uplink product generation process is significantly streamlined and mission risk is significantly reduced. Autogen is used for operations of MRO, Mars Global Surveyor (MGS), Mars Exploration Rover (MER), Mars Odyssey, and will be used for operations of Phoenix. Autogen Version 3.0 is the operational version of Autogen including the MRO adaptation for the cruise mission phase, and was also used for development of the aerobraking and mapping mission phases for MRO.

The influence of alloying on the phase formation sequence of ultra-thin nickel silicide films and on the inheritance of texture

NASA Astrophysics Data System (ADS)

Geenen, F. A.; Solano, E.; Jordan-Sweet, J.; Lavoie, C.; Mocuta, C.; Detavernier, C.

2018-05-01

The controlled formation of silicide materials is an ongoing challenge to facilitate the electrical contact of Si-based transistors. Due to the ongoing miniaturisation of the transistor, the silicide is trending to ever-thinner thickness's. The corresponding increase in surface-to-volume ratio emphasises the importance of low-energetic interfaces. Intriguingly, the thickness reduction of nickel silicides results in an abrupt change in phase sequence. This paper investigates the sequence of the silicides phases and their preferential orientation with respect to the Si(001) substrate, for both "thin" (i.e., 9 nm) and "ultra-thin" (i.e., 3 nm) Ni films. Furthermore, as the addition of ternary elements is often considered in order to tailor the silicides' properties, additives of Al, Co, and Pt are also included in this study. Our results show that the first silicide formed is epitaxial θ-Ni2Si, regardless of initial thickness or alloyed composition. The transformations towards subsequent silicides are changed through the additive elements, which can be understood through solubility arguments and classical nucleation theory. The crystalline alignment of the formed silicides with the substrate significantly differs through alloying. The observed textures of sequential silicides could be linked through texture inheritance. Our study illustrates the nucleation of a new phase drive to reduce the interfacial energy at the silicide-substrate interface as well as at the interface with the silicide which is being consumed for these sub-10 nm thin films.

Interfacial reactions between metal and gallium arsenide

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

Lin, J.C.; Schulz, K.J.; Hsieh, K.C.

1989-10-01

The phase formation sequence for GaAs/metal ternary diffusion couples is discussed. The diffusion path concept is introduced and is used with the phase diagram to understand interfacial reactions between GaAs and metal. The correlation between growth kinetics and interface morphology is discussed. Studies of bulk and thin film couples in two systems, GaAs/Pd and GaAs/Pt, are given to illustrate these concepts.

The three phases of galaxy formation

NASA Astrophysics Data System (ADS)

Clauwens, Bart; Schaye, Joop; Franx, Marijn; Bower, Richard G.

2018-05-01

We investigate the origin of the Hubble sequence by analysing the evolution of the kinematic morphologies of central galaxies in the EAGLE cosmological simulation. By separating each galaxy into disc and spheroidal stellar components and tracing their evolution along the merger tree, we find that the morphology of galaxies follows a common evolutionary trend. We distinguish three phases of galaxy formation. These phases are determined primarily by mass, rather than redshift. For M* ≲ 109.5M⊙ galaxies grow in a disorganised way, resulting in a morphology that is dominated by random stellar motions. This phase is dominated by in-situ star formation, partly triggered by mergers. In the mass range 109.5M⊙ ≲ M* ≲ 1010.5M⊙ galaxies evolve towards a disc-dominated morphology, driven by in-situ star formation. The central spheroid (i.e. the bulge) at z = 0 consists mostly of stars that formed in-situ, yet the formation of the bulge is to a large degree associated with mergers. Finally, at M* ≳ 1010.5M⊙ growth through in-situ star formation slows down considerably and galaxies transform towards a more spheroidal morphology. This transformation is driven more by the buildup of spheroids than by the destruction of discs. Spheroid formation in these galaxies happens mostly by accretion at large radii of stars formed ex-situ (i.e. the halo rather than the bulge).

Investigation of phase evolution of CaCu3Ti4O12 (CCTO) by in situ synchrotron high-temperature powder diffraction

NASA Astrophysics Data System (ADS)

Ouyang, Xin; Huang, Saifang; Zhang, Weijun; Cao, Peng; Huang, Zhaohui; Gao, Wei

2014-03-01

In situ synchrotron X-ray powder diffraction was used to study the high-temperature phase evolution of CaCu3Ti4O12 (CCTO) precursors prepared via solid-state and sol-gel methods. After the precursors are heated to 1225 °C, the CCTO phase is the main phase observed in the calcined powder, with the presence of some minor impurities. Comparing the two precursors, we found that the onset temperature for the CCTO phase formation is 800 °C in the sol-gel precursor, lower than that in the solid-state precursor (875 °C). Intermediate phases were only observed in the sol-gel precursor. Both precursors are able to be calcined to sub-micrometric sized powders. Based on the synchrotron data along with differential scanning calorimetry (DSC) and thermal gravimetric analysis (TGA), the phase formation sequence and mechanism during calcination are proposed in this study.

On the Precipitation in an Ag-Containing Mg-Gd-Zr Alloy

NASA Astrophysics Data System (ADS)

Zhang, Yu; Zhu, Yuman; Rong, Wei; Wu, Yujuan; Peng, Liming; Nie, Jian-Feng; Birbilis, Nick

2018-02-01

The evolution of precipitates in a high-strength Mg-2.4Gd-0.4Ag-0.1Zr (at. pct) alloy was investigated using high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM). The precipitation of Mg-2.4Gd-0.4Ag-0.1Zr includes β- and γ-type precipitates, the latter involving a hitherto unreported precipitation sequence that is the focus of the present study. The β-type precipitation sequence is described as follows: supersaturated solid solution (S.S.S.S.) → ordered solute clusters → zigzag GP zones → β' → βF' → β 1 → β. Compared with the precipitation sequence of the Mg-Gd system, the proposed β-type precipitation sequence includes ordered solute clusters, zigzag GP zones, and βF' , but excludes β″. The strain field around the coarsened β' phase is supposed to stimulate the formation of the β^'F phase. Furthermore, the βF' phase provides preferential nucleation site for the β 1 phase. The γ-type precipitation sequence is proposed as follows: S.S.S.S. → basal GP zones → γ''' → γ″ → γ. The crystal structures, morphologies, and orientations of the basal GP zone, γ''', γ″, γ phases were comprehensively examined and established herein. The results are described in the context of other, but similar, alloy systems. A holistic description of the precipitate evolution in Ag-containing Mg-Gd alloys is discussed and rationalized.

The Consolidation of Implicit Sequence Memory in Obstructive Sleep Apnea

PubMed Central

Malecek, Nick

2014-01-01

Obstructive Sleep Apnea (OSA) Syndrome is a relatively frequent sleep disorder characterized by disrupted sleep patterns. It is a well-established fact that sleep has beneficial effect on memory consolidation by enhancing neural plasticity. Implicit sequence learning is a prominent component of skill learning. However, the formation and consolidation of this fundamental learning mechanism remains poorly understood in OSA. In the present study we examined the consolidation of different aspects of implicit sequence learning in patients with OSA. We used the Alternating Serial Reaction Time task to measure general skill learning and sequence-specific learning. There were two sessions: a learning phase and a testing phase, separated by a 10-hour offline period with sleep. Our data showed differences in offline changes of general skill learning between the OSA and control group. The control group demonstrated offline improvement from evening to morning, while the OSA group did not. In contrast, we did not observe differences between the groups in offline changes in sequence-specific learning. Our findings suggest that disrupted sleep in OSA differently affects neural circuits involved in the consolidation of sequence learning. PMID:25329462

Secure multiple access for indoor optical wireless communications with time-slot coding and chaotic phase.

PubMed

Liang, Tian; Wang, Ke; Lim, Christina; Wong, Elaine; Song, Tingting; Nirmalathas, Ampalavanapillai

2017-09-04

In this paper, we report a novel mechanism to simultaneously provide secure connections for multiple users in indoor optical wireless communication systems by employing the time-slot coding scheme together with chaotic phase sequence. The chaotic phase sequence is generated according to the logistic map and applied to each symbol to secure the transmission. Proof-of-concept experiments are carried out for multiple system capacities based on both 4-QAM and 16-QAM modulation formats, i.e. 1.25 Gb/s, 2 Gb/s and 2.5 Gb/s for 4-QAM, and 2.5 Gb/s, 3.33 Gb/s and 4 Gb/s for 16-QAM. Experimental results show that in all cases the added chaotic phase does not degrade the legitimate user's signal quality while the illegal user cannot detect the signal without the key.

In situ X-ray diffraction strain-controlled study of Ti–Nb–Zr and Ti–Nb–Ta shape memory alloys: crystal lattice and transformation features

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

Dubinskiy, S.; National University of Science and Technology “MISIS”, 4, Leninskiy prosp., Moscow 119049; Prokoshkin, S.

2014-02-15

Phase and structure transformations in biomedical Ti–21.8Nb–6.0Zr (TNZ) and Ti–19.7Nb–5.8Ta (TNT) shape memory alloys (at.%) under and without load in the − 150 to 100 °S temperature range are studied in situ using an original tensile module for a low-temperature chamber of an X-ray diffractometer. Alpha″- and beta-phase lattice parameters, the crystallographic resource of recovery strain, phase and structure transformation sequences, and microstress appearance and disappearance are examined, compared and discussed. For both alloys, the crystallographic resource of recovery strain decreases with temperature increase to become 4.5% for TNZ and 2.5% for TNT alloy (at RT). Loading at low temperaturesmore » leads to additional α″-phase formation and reorientation. Heating under load, as compared to strain-free heating, affects the reverse transformation sequence of both alloys in different ways. For TNZ alloy, strain-free heating results in simultaneous ω→β and α″→β transformations, whereas during heating under stress, they are sequential: β + ω→α″ precedes α″→β. For TNT alloy, strain-free heating results in reverse α″→β transformation, whereas during heating under stress, α″→β transformation is preceded by α″-phase reorientation. - Highlights: • Comparative in situ XRD analysis of Ti–Nb–Zr(Ta) shape memory alloys is realized. • Lattice parameters of β- and α″-phases are calculated in the − 150 to + 100 °C range. • The higher the temperature, the lower the α″→β transformation strain. • Loading at low temperatures results in α″-phase formation and reorientation. • Transformation sequences upon heating with and without loading are different.« less

The Spectral Energy Distribution of the Earliest Phases of Massive Star Formation from the Spizter and Herschel Archives

NASA Astrophysics Data System (ADS)

Klein, Randolf; Looney, Leslie; Henning, Thomas; Chakrabarti, Sukanya; Shenoy, Sachin

2015-08-01

Infrared Dark Clouds (IRDCs) are very good candidates for the earliest phases of massive star formation, but can only be found in regions with high infrared background. We have searched for early phases among cold and massive (M>100M⊙) cloud cores by selecting cores from millimeter continuum surveys (Faundez et al. 2004, Sridharan et al. 2005, Klein et al. 2005, Beltran et al. 2006) without associations at short wavelengths. We compared the millimeter continuum peak positions with IR and radio catalogs (2MASS, MSX, IRAS, and NVSS) and excluded cores that had sources associated with the cores' peaks. We compiled a list of 173 cores in over 117 regions that are candidates for very early phases of Massive Star Formation (MSF). Now with the Spitzer and Herschel archives, these cores can be characterized further. The GLIMPSE and MIPSGAL programs alone covered 86 of these regions. The Herschel Archive adds even longer wavelengths. We are compiling this data set to construct the complete spectral energy distribution (SED) in the mid- and far-infrared with good spatial resolution and broad spectral coverage. This allow us to disentangle the complex regions and model the SED of the deeply embedded protostars/clusters.We will be presenting the IR properties of all cores and their embedded source, attempt a characterization, and order the cores in an evolutionary sequence. The resulting properties can be compared to e.g. IRDCs, a class of objects suggested to be the earliest stages of MSF. With the relative large number of cores, we can try to answer questions like: How homogeneous or diverse are our regions in terms of their evolutionary stage? Where do our embedded sources fit in the evolutionary sequence of IRDCs, hot molecular cores, ultra-compact HII regions, etc? How is the MSF shaping the environment and vice versa? Can we extrapolate to the initial conditions of MSF using our evolutionary sequence?

Cathodoluminescence investigations on quartz cement in the sandstones of Khabour Formation from Iraqi Kurdistan Region, Northern Iraq

NASA Astrophysics Data System (ADS)

Omer, Muhamed F.; Friis, Henrik

2014-03-01

The Ordovician deltaic to shallow marine Khabour Formation in Northern Iraq consists mainly of sandstone with minor siltstone and interbedded shale. The sandstones are pervasively cemented by quartz that resulted in very little preserved primary porosity. Cathodoluminescence and petrographic studies showed that the silica cementation occurred in five successive phases which can be distinguished by their luminescence pattern. The precipitations of two phases have predated the major compaction process while the other phases are younger. The successive phases represent a sequence of changes in silica supply which were classified as very early and early, derived from dissolved biogenic silica that precipitated as opal/microquartz, possibly pre-compactional and of non-luminescent quartz overgrowth type. This was followed by phases whose silica supply derived from pressure solution of quartz, dissolution of feldspar, and hydrothermal fluids related to major thrust fault event. These successive quartz cement phases showed an increase in luminescence and the development of complicated zonation pattern in late-stage quartz cementation.

Driving forces of redistribution of elements during quasicrystalline phase formation under heating of mechanically alloyed Al65Cu23Fe12 powder

NASA Astrophysics Data System (ADS)

Tcherdyntsev, V. V.; Kaloshkin, S. D.; Shelekhov, E. V.; Principi, G.; Rodin, A. O.

2008-02-01

Al65Cu23Fe12 alloys were prepared by ball milling of the elemental powders mixture. Phase and structural transformations at heating of as-milled powders were investigated by X-ray diffraction analysis. Precision analysis of Mössbauer spectra was performed to check the adequacy of the fitting of X-ray diffraction patterns. The results were compared with the data of differential scanning and solution calorimetry, as well as with the thermodynamic literature data, in order to estimate the driving forces of redistribution of elements that preceded the formation of single-phase quasicrystalline structure. The heat of elements mixing, which is positive for Cu-Fe system and negative for Al-Fe and Al-Cu systems, was supposed to be a decisive factor for phase transformations during heating of the alloy. The correlation between sequence of phase transformations during heating and the thermodynamic data was discussed and the scheme describing phase transformations observed was proposed.

GUM 48d: AN EVOLVED H II REGION WITH ONGOING STAR FORMATION

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

Karr, J. L.; Ohashi, N.; Manoj, P.

2009-05-20

High-mass star formation and the evolution of H II regions have a substantial impact on the morphology and star formation history of molecular clouds. The H II region Gum 48d, located in the Centaurus Arm at a distance of 3.5 kpc, is an old, well evolved H II region whose ionizing stars have moved off the main sequence. As such, it represents a phase in the evolution of H II regions that is less well studied than the earlier, more energetic, main-sequence phase. In this paper, we use multiwavelength archive data from a variety of sources to perform a detailedmore » study of this interesting region. Morphologically, Gum 48d displays a ring-like faint H II region associated with diffuse emission from the associated photodissociation region, and is formed from part of a large, massive molecular cloud complex. There is extensive ongoing star formation in the region, at scales ranging from low to high mass, which is consistent with triggered star formation scenarios. We investigate the dynamical history and evolution of this region, and conclude that the original H II region was once larger and more energetic than the faint region currently seen. The proposed history of this molecular cloud complex is one of multiple, linked generations of star formation, over a period of 10 Myr. Gum 48d differs significantly in morphology and star formation from the other H II regions in the molecular cloud; these differences are likely the result of the advanced age of the region, and its different evolutionary status.« less

Tertiary fission-track ages from the Bagua syncline (northern Peru): Stratigraphic and tectonic implications

NASA Astrophysics Data System (ADS)

Naeser, C. W.; Crochet, J.-Y.; Jaillard, E.; Laubacher, G.; Mourier, T.; Sigé, B.

The results of five zircon fission-track ages of volcanic tuffs intercalated within the continental deposits of the Bagua syncline (northern Peru) are reported. These 2500-meter-thick deposits overlie mid-Campanian to lower Maastrichtian fine-grained red beds (Fundo El Triunfo Formation). The disconformable fluvial conglomerates of the Rentema Formation are associated with a 54 Ma tuff (upper Paleocene-lower Eocene?) and would reflect the Inca-1 tectonic phase. The Sambimera Formation (Eocene to mid-Miocene) is a coarsening-upward sequence (from lacustrine to fluvial) that contains three volcanic tuffs of 31, 29, and 12 Ma, respectively. A probable stratigraphic gap, upper Eocene-lower Oligocene, would be related to the late Eocene Inca-2 phase. Neither deformation nor sedimentary discontinuity has been recognized so far. However, the lacustrine to fluvial transition could relate to the late Oligocene Aymara tectonic phase. The unconformable fanglomerates and fluvial deposits of the San Antonio Formation contain in their upper part a 9 Ma tuff (mid-to upper Miocene), and thier base records a major tectonic event (Quechua-2 phase?). The unconformable fanglomerates of the Tambopara Formation date the folding of the Bagua syncline, which could be ascribed to the latest Miocene Quechua-3 tectonics. These formations are correlative with comparable deposits in the sub-Andean basins, suggesting that these eastern areas underwent strong tectonic subsidence of the foreland basin type since mid-Miocene times.

Tertiary fission-track ages from the Bagua syncline (northern Peru): Stratigraphic and tectonic implications

USGS Publications Warehouse

Naeser, C.W.; Crochet, J.-Y.; Jaillard, E.; Laubacher, G.; Mourier, T.; Sige, B.

1991-01-01

The results of five zircon fission-track ages of volcanic tuffs intercalated within the continental deposits of the Bagua syncline (northern Peru) are reported. These 2500-meter-thick deposits overlie mid-Campanian to lower Maastrichtian fine-grained red beds (Fundo El Triunfo Formation). The disconformable fluvial conglomerates of the Rentema Formation are associated with a 54 Ma tuff (upper Paleocene-lower Eocene?) and would reflect the Inca-1 tectonic phase. The Sambimera Formation (Eocene to mid-Miocene) is a coarsening-upward sequence (from lacustrine to fluvial) that contains three volcanic tuffs of 31, 29, and 12 Ma, respectively. A probable stratigraphic gap, upper Eocene-lower Oligocene, would be related to the late Eocene Inca-2 phase. Neither deformation nor sedimentary discontinuity has been recognized so far. However, the lacustrine to fluvial transition could relate to the late Oligocene Aymara tectonic phase. The unconformable fanglomerates and fluvial deposits of the San Antonio Formation contain in their upper part a 9 Ma tuff (mid-to upper Miocene), and thier base records a major tectonic event (Quechua-2 phase?). The unconformable fanglomerates of the Tambopara Formation date the folding of the Bagua syncline, which could be ascribed to the latest Miocene Quechua-3 tectonics. These formations are correlative with comparable deposits in the sub-Andean basins, suggesting that these eastern areas underwent strong tectonic subsidence of the foreland basin type since mid-Miocene times. ?? 1991.

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

Ghosh, S.K.; Zambrano, E.

The Trujillo Formation, overlying the Paleocene Cerro Verde and Valle Hondo formations, reveals a turbiditic origin in a lowstand shelf-edge and bathyal setting in two excellent road sections on the Valera-Carache road and many creek sections. The basal outcrop shows well developed fining upward (FU) sequences of proximal channel turbidite and overbank origin (abandonment phase) and minor coarsening upward (CU) sequences representing progradational pulse in overbank areas. The FU (and thinning-upward) sequence, overlying a shale, consists of: (a) basal stacked conglomeratic arenites (probably inner fan channels) with graded beds, imbricate casts and transported shells; (b) a sand/shale alternating unit (channelmore » margin/interchannel) with flame structure, lenticular bedding, infrequent Tb-d Sequence, rippled flats, and rare Planolites; and (c) a dark shale (overbank-interchannel lows) with scarce Chondrites and Scaladtuba traces. The CU sequence consists of thickening-upward heterolithic facies overlain by lenticular stacked pebbly arenites. The upper unit exposed near Puente Gomez is a typical progradational lobe starting with a basal shale, with intraformational diastems and slumped beds, and Tb-d and Tb-e sequences in thin intercalated sandstones; a heterolithic facies with flute/groove casts, Planolites, Thalassinoides and Neonereites occurs between the shale and a thick cross-stratified sandstone at the top. This CU lobe sequence is discordantly(?) overlain by a thin wedge of massive bedded pebbly sandstones of Middle Eocene(?) Misoa Formation. Unlike the southwesterly sourced subsurface turbidites, those in this area were probably sourced from both the south and north, though locally the southern source might have been more important.« less

Pathways through equilibrated states with coexisting phases for gas hydrate formation

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

Malolepsza, Edyta; Keyes, Tom

Under ambient conditions, water freezes to either hexagonal ice or a hexagonal/cubic composite ice. The presence of hydrophobic guest molecules introduces a competing pathway: gas hydrate formation, with the guests in clathrate cages. Here, the pathways of the phase transitions are sought as sequences of states with coexisting phases, using a generalized replica exchange algorithm designed to sample them in equilibrium, avoiding nonequilibrium processes. For a dilute solution of methane in water under 200 atm, initializing the simulation with the full set of replicas leads to methane trapped in hexagonal/cubic ice, while gradually adding replicas with decreasing enthalpy produces themore » initial steps of hydrate growth. Once a small amount of hydrate is formed, water rearranges to form empty cages, eventually transforming the remainder of the system to metastable β ice, a scaffolding for hydrates. It is suggested that configurations with empty cages are reaction intermediates in hydrate formation when more guest molecules are available. Furthermore, free energy profiles show that methane acts as a catalyst reducing the barrier for β ice versus hexagonal/cubic ice formation.« less

Pathways through equilibrated states with coexisting phases for gas hydrate formation

DOE PAGES

Malolepsza, Edyta; Keyes, Tom

2015-12-01

Under ambient conditions, water freezes to either hexagonal ice or a hexagonal/cubic composite ice. The presence of hydrophobic guest molecules introduces a competing pathway: gas hydrate formation, with the guests in clathrate cages. Here, the pathways of the phase transitions are sought as sequences of states with coexisting phases, using a generalized replica exchange algorithm designed to sample them in equilibrium, avoiding nonequilibrium processes. For a dilute solution of methane in water under 200 atm, initializing the simulation with the full set of replicas leads to methane trapped in hexagonal/cubic ice, while gradually adding replicas with decreasing enthalpy produces themore » initial steps of hydrate growth. Once a small amount of hydrate is formed, water rearranges to form empty cages, eventually transforming the remainder of the system to metastable β ice, a scaffolding for hydrates. It is suggested that configurations with empty cages are reaction intermediates in hydrate formation when more guest molecules are available. Furthermore, free energy profiles show that methane acts as a catalyst reducing the barrier for β ice versus hexagonal/cubic ice formation.« less

The Lesser Role of Starbursts in Star Formation at z = 2

NASA Astrophysics Data System (ADS)

Rodighiero, G.; Daddi, E.; Baronchelli, I.; Cimatti, A.; Renzini, A.; Aussel, H.; Popesso, P.; Lutz, D.; Andreani, P.; Berta, S.; Cava, A.; Elbaz, D.; Feltre, A.; Fontana, A.; Förster Schreiber, N. M.; Franceschini, A.; Genzel, R.; Grazian, A.; Gruppioni, C.; Ilbert, O.; Le Floch, E.; Magdis, G.; Magliocchetti, M.; Magnelli, B.; Maiolino, R.; McCracken, H.; Nordon, R.; Poglitsch, A.; Santini, P.; Pozzi, F.; Riguccini, L.; Tacconi, L. J.; Wuyts, S.; Zamorani, G.

2011-10-01

Two main modes of star formation are know to control the growth of galaxies: a relatively steady one in disk-like galaxies, defining a tight star formation rate (SFR)-stellar mass sequence, and a starburst mode in outliers to such a sequence which is generally interpreted as driven by merging. Such starburst galaxies are rare but have much higher SFRs, and it is of interest to establish the relative importance of these two modes. PACS/Herschel observations over the whole COSMOS and GOODS-South fields, in conjunction with previous optical/near-IR data, have allowed us to accurately quantify for the first time the relative contribution of the two modes to the global SFR density in the redshift interval 1.5 < z < 2.5, i.e., at the cosmic peak of the star formation activity. The logarithmic distributions of galaxy SFRs at fixed stellar mass are well described by Gaussians, with starburst galaxies representing only a relatively minor deviation that becomes apparent for SFRs more than four times higher than on the main sequence. Such starburst galaxies represent only 2% of mass-selected star-forming galaxies and account for only 10% of the cosmic SFR density at z ~ 2. Only when limited to SFR > 1000 M sun yr-1, off-sequence sources significantly contribute to the SFR density (46% ± 20%). We conclude that merger-driven starbursts play a relatively minor role in the formation of stars in galaxies, whereas they may represent a critical phase toward the quenching of star formation and morphological transformation in galaxies.

Basin fill evolution and paleotectonic patterns along the Samfrau geosyncline: the Sauce Grande basin-Ventana foldbelt (Argentina) and Karoo basin-Cape foldbelt (South Africa) revisited

NASA Astrophysics Data System (ADS)

López-Gamundí, O. R.; Rossello, E. A.

As integral parts of du Toit's (1927) ``Samfrau Geosyncline'', the Sauce Grande basin-Ventana foldbelt (Argentina) and Karoo basin-Cape foldbelt (South Africa) share similar paleoclimatic, paleogeographic, and paleotectonic aspects related to the Late Paleozoic tectono-magmatic activity along the Panthalassan continental margin of Gondwanaland. Late Carboniferou-earliest Permian glacial deposits were deposited in the Sauce Grande (Sauce Grande Formation) and Karoo (Dwyka Formation) basins and Falkland-Malvinas Islands (Lafonia Formation) during an initial (sag) phase of extension. The pre-breakup position of the Falkland (Malvinas) Islands on the easternmost part of the Karoo basin (immediately east of the coast of South Africa) is supported by recent paleomagnetic data, lithofacies associations, paleoice flow directions and age similarities between the Dwyka and the Lafonia glacial sequences. The desintegration of the Gondwanan Ice Sheet (GIS) triggered widespread transgressions, reflected in the stratigraphic record by the presence of inter-basinally correlatable, open marine, fine-grained deposits (Piedra Azul Formation in the Sauce Grande basin, Prince Albert Formation in the Karoo basin and Port Sussex Formation in the Falkland Islands) capping glacial marine sediments. These early postglacial transgressive deposits, characterised by fossils of the Eurydesma fauna and Glossopteris flora, represent the maximum flooding of the basins. Cratonward foreland subsidence was triggered by the San Rafael orogeny (ca. 270 Ma) in Argentina and propogated along the Gondwanan margin. This subsidence phase generated sufficient space to accommodate thick synorogenic sequences derived from the orogenic flanks of the Sauce Grande and Karoo basins. Compositionally, the initial extensional phase of these basins was characterized by quartz-rich, craton-derived detritus and was followed by a compressional (foreland) phase characterized by a paleocurrent reversal and dominance of arc/foldbelt-derived material. In the Sauce Grande basin, tuffs are interbedded in the upper half of the synorogenic, foldbelt-derived Tunas Formation (Early-early Late? Permian). Likewise, the first widespread appearance of tuffs in the Karoo basin is in the Whitehill Formation, of late Early Permian (260 Ma) age. Silicic volcanism along the Andes and Patagonia (Choiyoi magmatic province) peaked between the late Early Permian and Late Permian. A link between these volcanics and the consanguineous airborne tuffs present in the Sauce Grande and Karoo basins is suggested on the basis of their similar compositions and ages.

In situ observation of shear-driven amorphization in silicon crystals

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

He, Yang; Zhong, Li; Fan, Feifei

Amorphous materials have attracted great interest in the scientific and technological fields. An amorphous solid usually forms under the externally driven conditions of melt-quenching, irradiation and severe mechanical deformation. However, its dynamic formation process remains elusive. Here we report the in situ atomic-scale observation of dynamic amorphization processes during mechanical straining of nanoscale silicon crystals by high resolution transmission electron microscopy (HRTEM). We observe the shear-driven amorphization (SDA) occurring in a dominant shear band. The SDA involves a sequence of processes starting with the shear-induced diamond-cubic to diamond-hexagonal phase transition that is followed by dislocation nucleation and accumulation in themore » newly formed phase, leading to the formation of amorphous silicon. The SDA formation through diamond-hexagonal phase is rationalized by its structural conformity with the order in the paracrystalline amorphous silicon, which maybe widely applied to diamond-cubic materials. Besides, the activation of SDA is orientation-dependent through the competition between full dislocation nucleation and partial gliding.« less

Dynamic covalent chemistry enables formation of antimicrobial peptide quaternary assemblies in a completely abiotic manner

NASA Astrophysics Data System (ADS)

Reuther, James F.; Dees, Justine L.; Kolesnichenko, Igor V.; Hernandez, Erik T.; Ukraintsev, Dmitri V.; Guduru, Rusheel; Whiteley, Marvin; Anslyn, Eric V.

2018-01-01

Naturally occurring peptides and proteins often use dynamic disulfide bonds to impart defined tertiary/quaternary structures for the formation of binding pockets with uniform size and function. Although peptide synthesis and modification are well established, controlling quaternary structure formation remains a significant challenge. Here, we report the facile incorporation of aryl aldehyde and acyl hydrazide functionalities into peptide oligomers via solid-phase copper-catalysed azide-alkyne cycloaddition (SP-CuAAC) click reactions. When mixed, these complementary functional groups rapidly react in aqueous media at neutral pH to form peptide-peptide intermolecular macrocycles with highly tunable ring sizes. Moreover, sequence-specific figure-of-eight, dumbbell-shaped, zipper-like and multi-loop quaternary structures were formed selectively. Controlling the proportions of reacting peptides with mismatched numbers of complementary reactive groups results in the formation of higher-molecular-weight sequence-defined ladder polymers. This also amplified antimicrobial effectiveness in select cases. This strategy represents a general approach to the creation of complex abiotic peptide quaternary structures.

Early Oligocene paleosols of the Dagshai Formation, India: A record of the oldest tropical weathering in the Himalayan foreland

NASA Astrophysics Data System (ADS)

Srivastava, Pankaj; Patel, Subhra; Singh, Nandita; Jamir, Toshienla; Kumar, Nandan; Aruche, Manini; Patel, Ramesh C.

2013-08-01

This study reports paleopedological features of the fossil soils that formed during the earliest phase of continental sedimentation in the Himalayan foreland. The fluvial sequence of the Dagshai Formation (31.6 ± 3.9 Ma to 30.3 ± 3.9 Ma) exposed along the Koshaliya River, NW Himalaya, contains four pedofacies (named Pedofacies A-D) of ferruginous paleosol sequences contained within overbank sediments. The Dagshai Formation unconformably overlies the marine Subathu Formation. Pedofacies A consists of 3-4 well-developed ferruginous paleosols overlain by gray sandstone beds. Pedofacies B-D are marked by a progressive decrease in pedogenesis. These paleosols occur as 0.5 m to 1.5 m thick Bw/Bt/Btk/Bk/Bss horizons that are marked by extensive development of rhizoliths, pedogenic carbonate, and iron-rich clay pedofeatures that correspond to modern Entisols, Inceptisols, Alfisols and Vertisols. Based on early Oligocene paleogeographic position of the northward-drifting Indian Plate, it is inferred that these paleosols were formed at ~ 18°N paleolatitude in the Dagshai sub-basin in the Himalayan foreland. Micromorphology, geochemical analyses, weathering indices, and stable isotope composition of paleosols indicate tropical climate (paleoprecipitation of 947-1256 mm and paleotemperature of ~ 25 °C) with an initial phase of monsoonal conditions during pedogenesis. These paleoclimatic conditions favored C3 paleovegetation immediately after the transition from greenhouse to icehouse conditions.

Geometry induced sequence of nanoscale Frank–Kasper and quasicrystal mesophases in giant surfactants

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

Yue, Kan; Huang, Mingjun; Marson, Ryan L.

Frank–Kasper (F-K) and quasicrystal phases were originally identified in metal alloys and only sporadically reported in soft materials. These unconventional sphere-packing schemes open up possibilities to design materials with different properties. The challenge in soft materials is how to correlate complex phases built from spheres with the tunable parameters of chemical composition and molecular architecture. Here, we report a complete sequence of various highly ordered mesophases by the self-assembly of specifically designed and synthesized giant surfactants, which are conjugates of hydrophilic polyhedral oligomeric silsesquioxane cages tethered with hydrophobic polystyrene tails. We show that the occurrence of these mesophases results frommore » nanophase separation between the heads and tails and thus is critically dependent on molecular geometry. Variations in molecular geometry achieved by changing the number of tails from one to four not only shift compositional phase boundaries but also stabilize F-K and quasicrystal phases in regions where simple phases of spheroidal micelles are typically observed. These complex self-assembled nanostructures have been identified by combining X-ray scattering techniques and real-space electron microscopy images. Brownian dynamics simulations based on a simplified molecular model confirm the architecture-induced sequence of phases. Our results demonstrate the critical role of molecular architecture in dictating the formation of supramolecular crystals with “soft” spheroidal motifs and provide guidelines to the design of unconventional self-assembled nanostructures.« less

Geometry induced sequence of nanoscale Frank–Kasper and quasicrystal mesophases in giant surfactants

PubMed Central

Yue, Kan; Huang, Mingjun; Marson, Ryan L.; He, Jinlin; Huang, Jiahao; Zhou, Zhe; Wang, Jing; Liu, Chang; Yan, Xuesheng; Wu, Kan; Guo, Zaihong; Liu, Hao; Ni, Peihong; Wesdemiotis, Chrys; Zhang, Wen-Bin; Glotzer, Sharon C.; Cheng, Stephen Z. D.

2016-01-01

Frank–Kasper (F-K) and quasicrystal phases were originally identified in metal alloys and only sporadically reported in soft materials. These unconventional sphere-packing schemes open up possibilities to design materials with different properties. The challenge in soft materials is how to correlate complex phases built from spheres with the tunable parameters of chemical composition and molecular architecture. Here, we report a complete sequence of various highly ordered mesophases by the self-assembly of specifically designed and synthesized giant surfactants, which are conjugates of hydrophilic polyhedral oligomeric silsesquioxane cages tethered with hydrophobic polystyrene tails. We show that the occurrence of these mesophases results from nanophase separation between the heads and tails and thus is critically dependent on molecular geometry. Variations in molecular geometry achieved by changing the number of tails from one to four not only shift compositional phase boundaries but also stabilize F-K and quasicrystal phases in regions where simple phases of spheroidal micelles are typically observed. These complex self-assembled nanostructures have been identified by combining X-ray scattering techniques and real-space electron microscopy images. Brownian dynamics simulations based on a simplified molecular model confirm the architecture-induced sequence of phases. Our results demonstrate the critical role of molecular architecture in dictating the formation of supramolecular crystals with “soft” spheroidal motifs and provide guidelines to the design of unconventional self-assembled nanostructures. PMID:27911786

Designing of deployment sequence for braking and drift systems in atmosphere of Mars and Venus

NASA Astrophysics Data System (ADS)

Vorontsov, Victor

2006-07-01

Analysis of project development and space research using contact method, namely, by means of automatic descent modules and balloons shows that designing formation of entry, descent and landing (EDL) sequence and operation in the atmosphere are of great importance. This process starts at the very beginning of designing, has undergone a lot of iterations and influences processing of normal operation results. Along with designing of descent module systems, including systems of braking in the atmosphere, designing of flight operation sequence and trajectories of motion in the atmosphere is performed. As the entire operation sequence and transfer from one phase to another was correctly chosen, the probability of experiment success on the whole and efficiency of application of various systems vary. By now the most extensive experience of Russian specialists in research of terrestrial planets has been gained with the help of automatic interplanetary stations “Mars”, “Venera”, “Vega” which had descent modules and drifting in the atmosphere balloons. Particular interest and complicity of formation of EDL and drift sequence in the atmosphere of these planets arise from radically different operation conditions, in particular, strongly rarefied atmosphere of the one planet and extremely dense atmosphere of another. Consequently, this determines the choice of braking systems and their parameters and method of EDL consequence formation. At the same time there are general fundamental methods and designed research techniques that allowed taking general technical approach to designing of EDL and drift sequence in the atmosphere.

General properties of magnetic CP stars

NASA Astrophysics Data System (ADS)

Glagolevskij, Yu. V.

2017-07-01

We present the review of our previous studies related to observational evidence of the fossil field hypothesis of formation and evolution of magnetic and non-magnetic chemically peculiar stars. Analysis of the observed data shows that these stars acquire their main properties in the process of gravitational collapse. In the non-stationary Hayashi phase, a magnetic field becomes weakened and its configuration complicated, but the fossil field global orientation remains. After a non-stationary phase, relaxation of young star's tangled field takes place and by the time of joining ZAMS (Zero Age Main Sequence) it is generally restored to a dipole structure. Stability of dipole structures allows them to remain unchanged up to the end of their life on the Main Sequence which is 109 years at most.

Origin of chemically distinct discs in the Auriga cosmological simulations

NASA Astrophysics Data System (ADS)

Grand, Robert J. J.; Bustamante, Sebastián; Gómez, Facundo A.; Kawata, Daisuke; Marinacci, Federico; Pakmor, Rüdiger; Rix, Hans-Walter; Simpson, Christine M.; Sparre, Martin; Springel, Volker

2018-03-01

The stellar disc of the Milky Way shows complex spatial and abundance structure that is central to understanding the key physical mechanisms responsible for shaping our Galaxy. In this study, we use six very high resolution cosmological zoom-in simulations of Milky Way-sized haloes to study the prevalence and formation of chemically distinct disc components. We find that our simulations develop a clearly bimodal distribution in the [α/Fe]-[Fe/H] plane. We find two main pathways to creating this dichotomy, which operate in different regions of the galaxies: (a) an early (z > 1) and intense high-[α/Fe] star formation phase in the inner region (R ≲ 5 kpc) induced by gas-rich mergers, followed by more quiescent low-[α/Fe] star formation; and (b) an early phase of high-[α/Fe] star formation in the outer disc followed by a shrinking of the gas disc owing to a temporarily lowered gas accretion rate, after which disc growth resumes. In process (b), a double-peaked star formation history around the time and radius of disc shrinking accentuates the dichotomy. If the early star formation phase is prolonged (rather than short and intense), chemical evolution proceeds as per process (a) in the inner region, but the dichotomy is less clear. In the outer region, the dichotomy is only evident if the first intense phase of star formation covers a large enough radial range before disc shrinking occurs; otherwise, the outer disc consists of only low-[α/Fe] sequence stars. We discuss the implication that both processes occurred in the Milky Way.

Hydrogen Bonded Squaramide-Based Foldable Module Induces Both β- and α-Turns in Hairpin Structures of α-Peptides in Water.

PubMed

Martínez, Luís; Martorell, Gabriel; Sampedro, Ángel; Ballester, Pablo; Costa, Antoni; Rotger, Carmen

2015-06-19

A novel tertiary squaramido-based reverse-turn module SQ is reported, and its conformational properties are evaluated. This module is easily incorporated into a α-peptide sequence by conventional solid-phase peptide synthesis. The structure characterization of the hybrid squaramido-peptide 4 is described, showing that the turn segment induces the formation of hairpin structures in water through the formation of both αSQ- and βSQ-turns.

Deformational history of part of the Acatlán Complex: Late Ordovician Early Silurian and Early Permian orogenesis in southern Mexico

NASA Astrophysics Data System (ADS)

Malone, J. R.; Nance, R. D.; Keppie, J. D.; Dostal, J.

2002-10-01

The Paleozoic Acatlán Complex of southern Mexico comprises polydeformed metasedimentary, granitoid, and mafic-ultramafic rocks variously interpreted as recording the closure of the Iapetus, Rheic, and Ouachitan Oceans. The complex is tectonically juxtaposed on its eastern margin against Grenville-age gneisses (Oaxacan Complex) that are unconformably overlain by Lower Paleozoic strata containing fossils of Gondwanan affinity. A thick siliciclastic unit (Chazumba and Cosoltepec Formations) at the base of the complex is considered part of a Lower Paleozoic accretionary prism with a provenance that isotopically resembles the Oaxacan Complex. This unit is tectonically overridden by a locally eclogitic mafic-ultramafic unit interpreted as a westward-obducted ophiolite, the emplacement of which was synchronous with mylonitic granitoid intrusion at ca. 440 Ma. Both units are unconformably overlain by a deformed volcano-sedimentary sequence (Tecomate Formation) attributed to a volcanic arc of presumed Devonian age. Deformed granitoids in contact with this sequence have been dated at ca. 371 (La Noria granite) and 287 Ma (Totoltepec pluton). Three phases of penetrative deformation (D 1-3) affect the Cosoltepec Formation; the last two correlate with two penetrative deformational phases that affect the Tecomate Formation. D 1 is of unknown kinematics but predates deposition of the Tecomate Formation and likely records obduction at ca. 440 Ma (Acatecan orogeny). A folded foliation in the Totoltepec pluton appears to record both deformational phases in the Tecomate Formation, bracketing D 2 and D 3 between 287 Ma and the deposition of the nonconformably overlying Leonardian Matzitzi Formation. D 2 records north-south dextral transpression and south-vergent thrusting and is attributed to the collision of Gondwana and southern Laurentia (Ouachitan orogeny) at ca. 290 Ma, the kinematics being consistent with the northward motion of Mexico that is required by most continental reconstructions for the final assembly of Pangea. D 3, which produced broadly north-south, upright folds, is also attributed to this collision and likely followed D 2 closely in the latest Paleozoic.

Virtual Cross-Linking of the Active Nemorubicin Metabolite PNU-159682 to Double-Stranded DNA.

PubMed

Scalabrin, Matteo; Quintieri, Luigi; Palumbo, Manlio; Riccardi Sirtori, Federico; Gatto, Barbara

2017-02-20

The DNA alkylating mechanism of PNU-159682 (PNU), a highly potent metabolite of the anthracycline nemorubicin, was investigated by gel-electrophoretic, HPLC-UV, and micro-HPLC/mass spectrometry (MS) measurements. PNU quickly reacted with double-stranded oligonucleotides, but not with single-stranded sequences, to form covalent adducts which were detectable by denaturing polyacrylamide gel electrophoresis (DPAGE). Ion-pair reverse-phase HPLC-UV analysis on CG rich duplex sequences having a 5'-CCCGGG-3' central core showed the formation of two types of adducts with PNU, which were stable and could be characterized by micro-HPLC/MS. The first type contained one alkylated species (and possibly one reversibly bound species), and the second contained two alkylated species per duplex DNA. The covalent adducts were found to produce effective bridging of DNA complementary strands through the formation of virtual cross-links reminiscent of those produced by classical anthracyclines in the presence of formaldehyde. Furthermore, the absence of reactivity of PNU with CG-rich sequence containing a TA core (CGTACG), and the minor reactivity between PNU and CGC sequences (TACGCG·CGCGTA) pointed out the importance of guanine sequence context in modulating DNA alkylation.

Analysis of ADP-glucose pyrophosphorylase expression during turion formation induced by abscisic acid in Spirodela polyrhiza (greater duckweed)

PubMed Central

2012-01-01

Background Aquatic plants differ in their development from terrestrial plants in their morphology and physiology, but little is known about the molecular basis of the major phases of their life cycle. Interestingly, in place of seeds of terrestrial plants their dormant phase is represented by turions, which circumvents sexual reproduction. However, like seeds turions provide energy storage for starting the next growing season. Results To begin a characterization of the transition from the growth to the dormant phase we used abscisic acid (ABA), a plant hormone, to induce controlled turion formation in Spirodela polyrhiza and investigated their differentiation from fronds, representing their growth phase, into turions with respect to morphological, ultra-structural characteristics, and starch content. Turions were rich in anthocyanin pigmentation and had a density that submerged them to the bottom of liquid medium. Transmission electron microscopy (TEM) of turions showed in comparison to fronds shrunken vacuoles, smaller intercellular space, and abundant starch granules surrounded by thylakoid membranes. Turions accumulated more than 60% starch in dry mass after two weeks of ABA treatment. To further understand the mechanism of the developmental switch from fronds to turions, we cloned and sequenced the genes of three large-subunit ADP-glucose pyrophosphorylases (APLs). All three putative protein and exon sequences were conserved, but the corresponding genomic sequences were extremely variable mainly due to the invasion of miniature inverted-repeat transposable elements (MITEs) into introns. A molecular three-dimensional model of the SpAPLs was consistent with their regulatory mechanism in the interaction with the substrate (ATP) and allosteric activator (3-PGA) to permit conformational changes of its structure. Gene expression analysis revealed that each gene was associated with distinct temporal expression during turion formation. APL2 and APL3 were highly expressed in earlier stages of turion development, while APL1 expression was reduced throughout turion development. Conclusions These results suggest that the differential expression of APLs could be used to enhance energy flow from photosynthesis to storage of carbon in aquatic plants, making duckweeds a useful alternative biofuel feedstock. PMID:22235974

Tuning the mesomorphic properties of phenoxy-terminated smectic liquid crystals: the effect of fluoro substitution.

PubMed

Thompson, Matthew; Carkner, Carolyn; Mosey, Nicholas J; Kapernaum, Nadia; Lemieux, Robert P

2015-05-21

The mesomorphic properties of phenoxy-terminated 5-alkoxy-2-(4-alkoxyphenyl)pyrimidine liquid crystals can be tuned in a predictable fashion with fluoro substituents on the phenoxy end-group. We show that an ortho-fluoro substituent promotes the formation of a tilted smectic C (SmC) phase whereas a para-fluoro substituent promotes the formation of an orthogonal smectic A (SmA) phase. The balance between SmA and SmC phases may be understood in terms of the energetic preference of the phenoxy end-groups to self-assemble via arene-arene interactions in a parallel or antiparallel geometry, and how these non-covalent interactions may cause either a suppression or enhancement of out-of-layer fluctuations at the interface of smectic layers. Calculations of changes in the potential energy of association ΔE for non-covalent dimers of fluoro-substituted n-butyloxybenzene molecules in parallel and antiparallel geometries support this hypothesis. We also show how mesomorphic properties can be further tuned by difluoro and perfluoro substitution, including difluoro substitution at the ortho positions, which uniquely promotes the formation of a SmC-nematic phase sequence.

Influences of the molecular fuel structure on combustion reactions towards soot precursors in selected alkane and alkene flames.

PubMed

Ruwe, Lena; Moshammer, Kai; Hansen, Nils; Kohse-Höinghaus, Katharina

2018-04-25

In this study, we experimentally investigate the high-temperature oxidation kinetics of n-pentane, 1-pentene and 2-methyl-2-butene (2M2B) in a combustion environment using flame-sampling molecular beam mass spectrometry. The selected C5 fuels are prototypes for linear and branched, saturated and unsaturated fuel components, featuring different C-C and C-H bond structures. It is shown that the formation tendency of species, such as polycyclic aromatic hydrocarbons (PAHs), yielded through mass growth reactions increases drastically in the sequence n-pentane < 1-pentene < 2M2B. This comparative study enables valuable insights into fuel-dependent reaction sequences of the gas-phase combustion mechanism that provide explanations for the observed difference in the PAH formation tendency. First, we investigate the fuel-structure-dependent formation of small hydrocarbon species that are yielded as intermediate species during the fuel decomposition, because these species are at the origin of the subsequent mass growth reaction pathways. Second, we review typical PAH formation reactions inspecting repetitive growth sequences in dependence of the molecular fuel structure. Third, we discuss how differences in the intermediate species pool influence the formation reactions of key aromatic ring species that are important for the PAH growth process underlying soot formation. As a main result it was found that for the fuels featuring a C[double bond, length as m-dash]C double bond, the chemistry of their allylic fuel radicals and their decomposition products strongly influences the combination reactions to the initially formed aromatic ring species and as a consequence, the PAH formation tendency.

Paleogeography and sedimentology of Upper Cretaceous turbidites, San Diego, California.

USGS Publications Warehouse

Nilsen, T.H.; Abbott, P.L.

1981-01-01

Upper Cretaceous (Campanian and Maestrichtian) marine strata of the Rosario Group in the San Diego area include the Point Loma Formation and overlying Cabrillo Formation. Thes units contain 6 facies associations which define a deep-sea fan deposited by westward-flowing sediment gravity flows that transported sediments derived chiefly from batholithic and pre-batholithic metamorphic rocks of the Peninsular Ranges. The sedimentary basin initially deepened abruptly. The fan then prograded westward into the basin, with a retrogradational phase recorded in the uppermost part of the sequence. The fan was deposited along the eastern edge of a forearc basin similar to that of the Great Valley sequence in northern California. The western part of the fan appears to have been truncated by late Cenozoic strike-slip faulting.-from Authors

Intrinsic folding of small peptide chains: spectroscopic evidence for the formation of beta-turns in the gas phase.

PubMed

Chin, Wutharath; Dognon, Jean-Pierre; Piuzzi, François; Tardivel, Benjamin; Dimicoli, Iliana; Mons, Michel

2005-01-19

Laser desorption of model peptides coupled to laser spectroscopic techniques enables the gas-phase observation of genuine secondary structures of biology. Spectroscopic evidence for the formation of beta-turns in gas-phase peptide chains containing glycine and phenylalanine residues establishes the intrinsic stability of these forms and their ability to compete with other stable structures. The precise characterization of local minima on the potential energy surface from IR spectroscopy constitutes an acute assessment for the state-of-the-art quantum mechanical calculations also presented. The observation of different types of beta-turns depending upon the residue order within the sequence is found to be consistent with the residue propensities in beta-turns of proteins, which suggests that the prevalence of glycine in type II and II' turns stems essentially from an energetic origin, already at play under isolated conditions.

The Formation of Galactic Bulges

NASA Astrophysics Data System (ADS)

Carollo, C. Marcella; Ferguson, Henry C.; Wyse, Rosemary F. G.

2000-03-01

Part I. Introduction: What are galactic bulges?; Part II. The Epoch of Bulge Formation: Origin of bulges; Deep sub-mm surveys: High-z ULIRGs and the formation of spheroids; Ages and metallicities for stars in the galactic bulge; Integrated stellar populations of bulges: First results; HST-NICMOS observations of galactic bulges: Ages and dust; Inside-out bulge formation and the origin of the Hubble sequence; Part III. The Timescales of Bulge Formation: Constraints on the bulge formation timescale from stellar populations; Bulge building with mergers and winds; Role of winds, starbursts, and activity in bulge formation; Dynamical timescales of bulge formation; Part IV. Physical Processes in Bulge Formation: the role of bars for secular bulge formation; Bars and boxy/peanut-shaped bulges: an observational point of view; Boxy- and peanut-shaped bulges; A new class of bulges; The role of secondary bars in bulge formation; Radial transport of molecular gas to the nuclei of spiral galaxies; Dynamical evolution of bulge shapes; Two-component stellar systems: Phase-space constraints; Central NGC 2146 - a firehose-type bending instability?; Bulge formation: the role of the multi-phase ISM; Global evolution of a self-gravitating multi-phase ISM in the central kpc region of galaxies; Part V. Bulge Phenomenology: Bulge-disk decomposition of spiral galaxies in the near-infrared; The triaxial bulge of NGC 1371; The bulge-disk orthogonal decoupling in galaxies: NGC 4698 and NGC 4672; The kinematics and the origin of the ionized gas in NGC 4036; Optically thin thermal plasma in the galactic bulge; X-ray properties of bulges; The host galaxies of radio-loud AGN; The centers of radio-loud early-type galaxies with HST; Central UV spikes in two galactic spheroids; Conference summary: where do we stand?

Facies architecture and high resolution sequence stratigraphy of an aeolian, fluvial and shallow marine system in the Pennsylvanian Piauí Formation, Parnaíba Basin, Brazil

NASA Astrophysics Data System (ADS)

Vieira, Lucas Valadares; Scherer, Claiton Marlon dos Santos

2017-07-01

The Pennsylvanian Piauí Formation records the deposition of aeolian, fluvial and shallow marine systems accumulated in the cratonic sag Parnaíba basin. Characterization of the facies associations and sequence stratigraphic framework was done by detailed description and logging of outcrops. Six facies associations were recognized: aeolian dunes and interdunes, aeolian sandsheets, fluvial channels, tidally-influenced fluvial channels, shoreface and shoreface-shelf transition. Through correlation of stratigraphic surfaces, the facies associations were organized in system tracts, which formed eight high frequency depositional sequences, bounded by subaerial unconformities. These sequences are composed of a lowstand system tract (LST), that is aeolian-dominated or fluvial-dominated, a transgressive system tract (TST) that is formed by tidally-influenced fluvial channels and/or shoreface and shoreface-shelf transition deposits with retrogradational stacking, and a highstand system tract (HST), which is formed by shoreface-shelf transition and shoreface deposits with progradational stacking. Two low frequency cycles were determined by observing the stacking of the high frequency cycles. The Lower Sequence is characterized by aeolian deposits of the LST and an aggradational base followed by a progressive transgression, defining a general TST. The Upper Sequence is characterized by fluvial deposits and interfluve pedogenesis concurring with the aeolian deposits of the LST and records a subtle regression followed by transgression. The main control on sedimentation in the Piauí Formation was glacioeustasy, which was responsible for the changes in relative sea level. Even though, climate changes were associated with glacioeustatic phases and influenced the aeolian and fluvial deposition.

Development and testing of the data automation subsystem for the Mariner Mars 1971 spacecraft

NASA Technical Reports Server (NTRS)

1971-01-01

The data automation subsystem designed and built as part of the Mariner Mars 1971 program, sequences and controls the science instruments and formats all science data. A description of the subsystem with emphasis on major changes relative to Mariner Mars 1969 is presented. In addition, the complete test phase is described.

Specific DNA duplex formation at an artificial lipid bilayer: towards a new DNA biosensor technology.

PubMed

Werz, Emma; Korneev, Sergei; Montilla-Martinez, Malayko; Wagner, Richard; Hemmler, Roland; Walter, Claudius; Eisfeld, Jörg; Gall, Karsten; Rosemeyer, Helmut

2012-02-01

A novel technique is described which comprises a base-specific DNA duplex formation at a lipid bilayer-H(2) O-phase boundary layer. Two different probes of oligonucleotides both carrying a double-tailed lipid at the 5'-terminus were incorporated into stable artificial lipid bilayers separating two compartments (cis/trans-channel) of an optically transparent microfluidic sample carrier with perfusion capabilities. Both the cis- and trans-channels are filled with saline buffer. Injection of a cyanine-5-labeled target DNA sequence, which is complementary to only one of the oligonucleotide probes, into the cis-channel, followed by a thorough perfusion, leads to an immobilization of the labeled complementary oligonucleotide on the membrane as detected by single-molecule fluorescence spectroscopy and microscopy. In the case of fluorescent but non-complementary DNA sequences, no immobilized fluorescent oligonucleotide duplex could be detected on the membrane. This clearly verifies a specific duplex formation at the membrane interface. Copyright © 2012 Verlag Helvetica Chimica Acta AG, Zürich.

Formation of high-field magnetic white dwarfs from common envelopes

PubMed Central

Nordhaus, Jason; Wellons, Sarah; Spiegel, David S.; Metzger, Brian D.; Blackman, Eric G.

2011-01-01

The origin of highly magnetized white dwarfs has remained a mystery since their initial discovery. Recent observations indicate that the formation of high-field magnetic white dwarfs is intimately related to strong binary interactions during post-main-sequence phases of stellar evolution. If a low-mass companion, such as a planet, brown dwarf, or low-mass star, is engulfed by a post-main-sequence giant, gravitational torques in the envelope of the giant lead to a reduction of the companion’s orbit. Sufficiently low-mass companions in-spiral until they are shredded by the strong gravitational tides near the white dwarf core. Subsequent formation of a super-Eddington accretion disk from the disrupted companion inside a common envelope can dramatically amplify magnetic fields via a dynamo. Here, we show that these disk-generated fields are sufficiently strong to explain the observed range of magnetic field strengths for isolated, high-field magnetic white dwarfs. A higher-mass binary analogue may also contribute to the origin of magnetar fields. PMID:21300910

The stratigraphic sequence of Scafati (Italy) - An archive of 10,000 years of volcanism, soil formation and land use in the shade of Mount Vesuvius

NASA Astrophysics Data System (ADS)

Maerker, Michael; Vogel, Sebastian; Hoelzmann, Phillip; Rellini, Ivano

2014-05-01

In this study we carried out a detailed lithostratigraphic, pedological and micromorphological analysis at a stratigraphic sequence close to Scafati, about 3 km east of ancient Pompeii. It consists of a multilayered succession of repeated volcanic deposition and pedogenesis caused by several phases of volcanic activity of Somma-Vesuvius and volcanic quiescence. This comprises, at least, the last 10,000 years of sedimentation history, on one hand, reflecting the entire spectrum of eruption types of Somma-Vesuvius from Plinian, sub-Plinian, rather small eruptions to effusive volcanic events and, on the other hand, soil formations of different durations, intensities and soil-forming environments. Furthermore, the paleosols repeatedly reveal clear evidence of anthropogenic activity by means of agriculture. Hence, a landscape evolution model was developed trying to reconstruct the last 10,000 years of volcanic activity, soil formation and land use in the hinterland of Pompeii.

Causes of complexity in a fallout dominated plinian eruption sequence: 312 ka Fasnia Member, Diego Hernández Formation, Tenerife, Spain

NASA Astrophysics Data System (ADS)

Edgar, C. J.; Cas, R. A. F.; Olin, P. H.; Wolff, J. A.; Martí, J.; Simmons, J. M.

2017-10-01

The 312 ka Fasnia eruption from the Las Cañadas Caldera on Tenerife, Canary Islands, Spain, produced a complex sequence of twenty-two intercalated units, including 7 pumice fall, 7 ignimbrite and 8 ash surge and fall deposits that define two distinct eruption sequences (Lower and Upper Fasnia sequences). The fallout units themselves are internally complex, reflecting waxing and waning of the eruption column, while many of the ignimbrites reflect multiple intra-plinian partial column collapse events associated with the injection of lithic clasts into the eruption column. The Lower and Upper Fasnia eruption phases were each terminated by caldera collapse and complete column collapse events. Probable blockage of the conduit and vent system during Lower Fasnia caldera collapse event briefly terminated the eruption, resulting in a short-lived period of erosion and sedimentation prior to the onset of the Upper Fasnia phase. The transition to the Upper Fasnia eruption phase coincided with the eruption of more geochemically homogeneous pyroclasts. In total, 62 km3 of tephra were erupted, including 49 km3 of juvenile clasts and > 12 km3 of lithic clasts. The DRE volume of magma erupted was 13 km3 (Lower Fasnia > 5 km3, Upper Fasnia > 8 km3), two thirds of which ( 9-10 km3) was deposited purely by fallout. The Fasnia Member is one of the most complex plinian sequences known.

Depositional environments of the Rock Springs Formation, southwest flank of the Rock Springs Uplift, Wyoming.

USGS Publications Warehouse

Kirschbaum, M.A.

1986-01-01

This deltaic Upper Cretaceous Rock Springs Formation of the Mesaverde Group was deposited during early Campanian time near the end of the regressive phase of the Niobrara cyclothem. On the southwest end of the Uplift, part of the delta system is exposed near the seaward edge of a series of transgressive/regressive sequences, which consist of intertonguing prodelta, delta-front, and delta-plain deposits. Eight major delta-front sandstones are vertically stacked and laterally continuous throughout the main study area.-from Author

Proton-driven amide bond-cleavage pathways of gas-phase peptide ions lacking mobile protons.

PubMed

Bythell, Benjamin J; Suhai, Sándor; Somogyi, Arpád; Paizs, Béla

2009-10-07

The mobile proton model (Dongre, A. R., Jones, J. L., Somogyi, A. and Wysocki, V. H. J. Am. Chem. Soc. 1996, 118 , 8365-8374) of peptide fragmentation states that the ionizing protons play a critical role in the gas-phase fragmentation of protonated peptides upon collision-induced dissociation (CID). The model distinguishes two classes of peptide ions, those with or without easily mobilizable protons. For the former class mild excitation leads to proton transfer reactions which populate amide nitrogen protonation sites. This enables facile amide bond cleavage and thus the formation of b and y sequence ions. In contrast, the latter class of peptide ions contains strongly basic functionalities which sequester the ionizing protons, thereby often hindering formation of sequence ions. Here we describe the proton-driven amide bond cleavages necessary to produce b and y ions from peptide ions lacking easily mobilizable protons. We show that this important class of peptide ions fragments by different means from those with easily mobilizable protons. We present three new amide bond cleavage mechanisms which involve salt-bridge, anhydride, and imine enol intermediates, respectively. All three new mechanisms are less energetically demanding than the classical oxazolone b(n)-y(m) pathway. These mechanisms offer an explanation for the formation of b and y ions from peptide ions with sequestered ionizing protons which are routinely fragmented in large-scale proteomics experiments.

Novel in situ resistance measurement for the investigation of CIGS growth in a selenization process

NASA Astrophysics Data System (ADS)

Liu, Wei; Tian, Jian-Guo; Li, Zu-Bin; He, Qing; Li, Feng-Yan; Li, Chang-Jian; Sun, Yun

2009-03-01

During the selenization process of CIGS thin films, the relation between the element loss rate and the precursor depositions are analyzed. The growth of the CIGS thin films during the selenization process is investigated by the novel in situ resistance measurement, by which the formation of compound semiconductors can be observed directly and simultaneously. Their structures, phase evolutions and element losses are analyzed by XRD and XRF. Based on the experimental results, it can be concluded that the phase transforms have nothing to do with the deposition sequences of precursors, while the element loss rates are related to the deposition sequences in this process. In addition, element loss mechanisms of CIGS thin films prepared by the selenization process are analyzed by the phase evolutions and chemical combined path in the In, Ga-Se reaction processes. Moreover it is verified that the element losses are depressed by increasing the ramping-up rate finally. The results provide effective methods to fabricate high-quality CIGS thin films with low element losses.

VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences.

PubMed

Xu, Duo; Jaber, Yousef; Pavlidis, Pavlos; Gokcumen, Omer

2017-09-26

Constructing alignments and phylogenies for a given locus from large genome sequencing studies with relevant outgroups allow novel evolutionary and anthropological insights. However, no user-friendly tool has been developed to integrate thousands of recently available and anthropologically relevant genome sequences to construct complete sequence alignments and phylogenies. Here, we provide VCFtoTree, a user friendly tool with a graphical user interface that directly accesses online databases to download, parse and analyze genome variation data for regions of interest. Our pipeline combines popular sequence datasets and tree building algorithms with custom data parsing to generate accurate alignments and phylogenies using all the individuals from the 1000 Genomes Project, Neanderthal and Denisovan genomes, as well as reference genomes of Chimpanzee and Rhesus Macaque. It can also be applied to other phased human genomes, as well as genomes from other species. The output of our pipeline includes an alignment in FASTA format and a tree file in newick format. VCFtoTree fulfills the increasing demand for constructing alignments and phylogenies for a given loci from thousands of available genomes. Our software provides a user friendly interface for a wider audience without prerequisite knowledge in programming. VCFtoTree can be accessed from https://github.com/duoduoo/VCFtoTree_3.0.0 .

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.

Facile rhenium-peptide conjugate synthesis using a one-pot derived Re(CO)3 reagent.

PubMed

Chanawanno, Kullapa; Kondeti, Vinay; Caporoso, Joel; Paruchuri, Sailaja; Leeper, Thomas C; Herrick, Richard S; Ziegler, Christopher J

2016-03-21

We have synthesized two Re(CO)3-modified lysine complexes (1 and 2), where the metal is attached to the amino acid at the Nε position, via a one-pot Schiff base formation reaction. These compounds can be used in the solid phase synthesis of peptides, and to date we have produced four conjugate systems incorporating neurotensin, bombesin, leutenizing hormone releasing hormone, and a nuclear localization sequence. We observed uptake into human umbilical vascular endothelial cells as well as differential uptake depending on peptide sequence identity, as characterized by fluorescence and rhenium elemental analysis.

Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases.

PubMed

Meinhardt, Lyndel W; Costa, Gustavo Gilson Lacerda; Thomazella, Daniela P T; Teixeira, Paulo José P L; Carazzolle, Marcelo Falsarella; Schuster, Stephan C; Carlson, John E; Guiltinan, Mark J; Mieczkowski, Piotr; Farmer, Andrew; Ramaraj, Thiruvarangan; Crozier, Jayne; Davis, Robert E; Shao, Jonathan; Melnick, Rachel L; Pereira, Gonçalo A G; Bailey, Bryan A

2014-02-27

The basidiomycete Moniliophthora roreri is the causal agent of Frosty pod rot (FPR) disease of cacao (Theobroma cacao), the source of chocolate, and FPR is one of the most destructive diseases of this important perennial crop in the Americas. This hemibiotroph infects only cacao pods and has an extended biotrophic phase lasting up to sixty days, culminating in plant necrosis and sporulation of the fungus without the formation of a basidiocarp. We sequenced and assembled 52.3 Mb into 3,298 contigs that represent the M. roreri genome. Of the 17,920 predicted open reading frames (OFRs), 13,760 were validated by RNA-Seq. Using read count data from RNA sequencing of cacao pods at 30 and 60 days post infection, differential gene expression was estimated for the biotrophic and necrotrophic phases of this plant-pathogen interaction. The sequencing data were used to develop a genome based secretome for the infected pods. Of the 1,535 genes encoding putative secreted proteins, 1,355 were expressed in the biotrophic and necrotrophic phases. Analysis of the data revealed secretome gene expression that correlated with infection and intercellular growth in the biotrophic phase and invasive growth and plant cellular death in the necrotrophic phase. Genome sequencing and RNA-Seq was used to determine and validate the Moniliophthora roreri genome and secretome. High sequence identity between Moniliophthora roreri genes and Moniliophthora perniciosa genes supports the taxonomic relationship with Moniliophthora perniciosa and the relatedness of this fungus to other basidiomycetes. Analysis of RNA-Seq data from infected plant tissues revealed differentially expressed genes in the biotrophic and necrotrophic phases. The secreted protein genes that were upregulated in the biotrophic phase are primarily associated with breakdown of the intercellular matrix and modification of the fungal mycelia, possibly to mask the fungus from plant defenses. Based on the transcriptome data, the upregulated secreted proteins in the necrotrophic phase are hypothesized to be actively attacking the plant cell walls and plant cellular components resulting in necrosis. These genes are being used to develop a new understanding of how this disease interaction progresses and to identify potential targets to reduce the impact of this devastating disease.

Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases

PubMed Central

2014-01-01

Background The basidiomycete Moniliophthora roreri is the causal agent of Frosty pod rot (FPR) disease of cacao (Theobroma cacao), the source of chocolate, and FPR is one of the most destructive diseases of this important perennial crop in the Americas. This hemibiotroph infects only cacao pods and has an extended biotrophic phase lasting up to sixty days, culminating in plant necrosis and sporulation of the fungus without the formation of a basidiocarp. Results We sequenced and assembled 52.3 Mb into 3,298 contigs that represent the M. roreri genome. Of the 17,920 predicted open reading frames (OFRs), 13,760 were validated by RNA-Seq. Using read count data from RNA sequencing of cacao pods at 30 and 60 days post infection, differential gene expression was estimated for the biotrophic and necrotrophic phases of this plant-pathogen interaction. The sequencing data were used to develop a genome based secretome for the infected pods. Of the 1,535 genes encoding putative secreted proteins, 1,355 were expressed in the biotrophic and necrotrophic phases. Analysis of the data revealed secretome gene expression that correlated with infection and intercellular growth in the biotrophic phase and invasive growth and plant cellular death in the necrotrophic phase. Conclusions Genome sequencing and RNA-Seq was used to determine and validate the Moniliophthora roreri genome and secretome. High sequence identity between Moniliophthora roreri genes and Moniliophthora perniciosa genes supports the taxonomic relationship with Moniliophthora perniciosa and the relatedness of this fungus to other basidiomycetes. Analysis of RNA-Seq data from infected plant tissues revealed differentially expressed genes in the biotrophic and necrotrophic phases. The secreted protein genes that were upregulated in the biotrophic phase are primarily associated with breakdown of the intercellular matrix and modification of the fungal mycelia, possibly to mask the fungus from plant defenses. Based on the transcriptome data, the upregulated secreted proteins in the necrotrophic phase are hypothesized to be actively attacking the plant cell walls and plant cellular components resulting in necrosis. These genes are being used to develop a new understanding of how this disease interaction progresses and to identify potential targets to reduce the impact of this devastating disease. PMID:24571091

Efficient Covalent Bond Formation in Gas-Phase Peptide-Peptide Ion Complexes with the Photoleucine Stapler

NASA Astrophysics Data System (ADS)

Shaffer, Christopher J.; Andrikopoulos, Prokopis C.; Řezáč, Jan; Rulíšek, Lubomír; Tureček, František

2016-04-01

Noncovalent complexes of hydrophobic peptides GLLLG and GLLLK with photoleucine (L*) tagged peptides G(L* n L m )K (n = 1,3, m = 2,0) were generated as singly charged ions in the gas phase and probed by photodissociation at 355 nm. Carbene intermediates produced by photodissociative loss of N2 from the L* diazirine rings underwent insertion into X-H bonds of the target peptide moiety, forming covalent adducts with yields reaching 30%. Gas-phase sequencing of the covalent adducts revealed preferred bond formation at the C-terminal residue of the target peptide. Site-selective carbene insertion was achieved by placing the L* residue in different positions along the photopeptide chain, and the residues in the target peptide undergoing carbene insertion were identified by gas-phase ion sequencing that was aided by specific 13C labeling. Density functional theory calculations indicated that noncovalent binding to GL*L*L*K resulted in substantial changes of the (GLLLK + H)+ ground state conformation. The peptide moieties in [GL*L*LK + GLLLK + H]+ ion complexes were held together by hydrogen bonds, whereas dispersion interactions of the nonpolar groups were only secondary in ground-state 0 K structures. Born-Oppenheimer molecular dynamics for 100 ps trajectories of several different conformers at the 310 K laboratory temperature showed that noncovalent complexes developed multiple, residue-specific contacts between the diazirine carbons and GLLLK residues. The calculations pointed to the substantial fluidity of the nonpolar side chains in the complexes. Diazirine photochemistry in combination with Born-Oppenheimer molecular dynamics is a promising tool for investigations of peptide-peptide ion interactions in the gas phase.

A hybrid aluminium alloy and its zoo of interacting nano-precipitates

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

Wenner, Sigurd, E-mail: sigurd.wenner@ntnu.no; Marioara, Calin Daniel; Andersen, Sigmund Jarle

An alloy with aluminium as its base element is heat treated to form a multitude of precipitate phases known from different classes of industrial alloys: Al–Cu(–Mg), Al–Mg–Si–Cu, and Al–Zn–Mg. Nanometer-sized needle-shaped particles define the starting point of the phase nucleation, after which there is a split in the precipitation sequence into six phases of highly diverse compositions and morphologies. There are several unique effects of phases from different alloy systems being present in the same host lattice, of which we concentrate on two: the replacement of Ag by Zn on the Ω interface and the formation of combined plates ofmore » the θ′ and C phases. Using atomically resolved scanning transmission electron microscopy and energy-dispersive X-ray spectroscopy, we investigate the formation mechanisms, crystal structures and compositions of the precipitates. - Graphical abstract: Display Omitted - Highlights: • An aluminium alloy composition in-between the 2/6/7xxx systems was investigated. • Six different phases from the three systems coexist in an over-aged state. • All phases with 〈001〉{sub Al} coherencies can nucleate on 6xxx needle precipitates. • Modified theta′ and omega interfaces are observed.« less

Omega flight-test data reduction sequence. [computer programs for reduction of navigation data

NASA Technical Reports Server (NTRS)

Lilley, R. W.

1974-01-01

Computer programs for Omega data conversion, summary, and preparation for distribution are presented. Program logic and sample data formats are included, along with operational instructions for each program. Flight data (or data collected in flight format in the laboratory) is provided by the Ohio University Omega receiver base in the form of 6-bit binary words representing the phase of an Omega station with respect to the receiver's local clock. All eight Omega stations are measured in each 10-second Omega time frame. In addition, an event-marker bit and a time-slot D synchronizing bit are recorded. Program FDCON is used to remove data from the flight recorder tape and place it on data-processing cards for later use. Program FDSUM provides for computer plotting of selected LOP's, for single-station phase plots, and for printout of basic signal statistics for each Omega channel. Mean phase and standard deviation are printed, along with data from which a phase distribution can be plotted for each Omega station. Program DACOP simply copies the Omega data deck a controlled number of times, for distribution to users.

Growth and characterization of Pt-Si droplets for silicon nanowires synthesis

NASA Astrophysics Data System (ADS)

Khumalo, Z. M.; Topić, M.; Mtshali, C. B.; Blumenthal, M.

2018-02-01

The formation of platinum silicide phases as a function of the annealing temperature was investigated using in-situ real-time Rutherford backscattering spectrometry. The in-situ real-time RBS revealed the reaction of platinum and silicon to start at about 220 °C to form platinum silicide phases, Pt2Si and PtSi in sequence. Scanning electron microscope revealed the morphological change in the platinum layer (formation of droplets) at 800 °C. The particle induced X-ray emission analysis showed the variation of platinum intensity, in the droplets areas, between 1600 and 2000 counts. The surrounding areas are left almost uncovered due to platinum film dewetting. In-plane as well as out-of-plane silicon nanowires were observed to form at 800 °C and 1000 °C using pulsed laser ablation and thermal annealing techniques, respectively.

Germination and Outgrowth of Single Spores of Saccharomyces cerevisiae Viewed by Scanning Electron and Phase-Contrast Microscopy

PubMed Central

Rousseau, Paul; Halvorson, Harlyn O.; Bulla, Lee A.; Julian, Grant St.

1972-01-01

Single spores of Saccharomyces cerevisiae were examined during germination and outgrowth by scanning electron and phase-contrast microscopy. Also determined were changes in cell weight and light absorbance, trehalose utilization, and synthesis of protein and KOH-soluble carbohydrates. These studies reveal that development of the vegetative cell from a spore follows a definite sequence of events involving dramatic physical and chemical modifications. These changes are: initial rapid loss in cellular absorbance followed later by an abrupt gain in absorbance; reduction in cell weight and a subsequent progressive increase; modification of the spore surface with concomitant diminution in refractility; elongation of the cell and augmentation of surface irregularities; rapid decline in trehalose content of the cell accompanied by extensive formation of KOH-soluble carbohydrates; and bud formation. Images PMID:4551750

Aspects of the palynology of the Chinle Formation (Upper Triassic), Colorado Plateau, Arizona, Utah, and New Mexico

USGS Publications Warehouse

Scott, Richard A.

1982-01-01

This study deals with 16 palynological samples from Arizona, New Mexico, and Utah, that represent six members of the Chinle Formation of Late Triassic age. The samples, in ascending sequence, show a gradual change in the spore-bisaccate ratio from a preponderance of spores to numerical dominance of bisaccate pollen grains. This change is interpreted to indicate a climatic trend toward increasing aridity. The trend is thought to represent the decreasing energy phase of the oldest of three depositional cycles posited by Lupe (1977, 1979). The late Karnian age indicated for the Chinle Formation by pollen and spores is based on material from the lower part of the formation, leaving open the possibility that the upper part of the Chinle may be younger.

Formation and tectonic evolution of the Pattani Basin, Gulf of Thailand

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

Bustin, R.M.; Chonchawalit, A.

The stratigraphic and structural evolution of the Pattani Basin, the most prolific petroleum basin in Thailand, reflects the extensional tectonic regime of continental Southeast Asia. E-W extension resulting from the northward collision of India with Eurasia since the Early Tertiary resulted in the formation of a series of N-S-trending sedimentary basins, which include the Pattani Basin. The sedimentary succession in the Pattani Basin is divisible into synrift and postrift sequences. Deposition of the synrift sequence accompanied rifting and extension, with episodic block faulting and rapid subsidence. The synrift sequence comprises three stratigraphic units: (1) Upper Eocene to Lower Olikgocene alluvial-fan,more » braided-river, and floodplain deposits; (2) Upper oligocene to Lowe Miocene floodplain and channel deposits; and (3) a Lower Miocene regressive package consisting of marine to nonmarine sediments. Post-rift succession comprises: (1) a Lower to Middle Miocene regressive package of shallow marine sediments through floodplain and channel deposits; (2) an upper Lower Miocene transgressive sequence; and (3) and Upper Miocene to Pleistocene transgressive succession. The post-rift phase is characterized by slower subsidence and decreased sediment influx. The present-day shallow-marine condition in the Gulf of Thailand is the continuation of this latest transgressive phase. The subsidence and thermal history of the Pattani Basin is consistent with a nonuniform lithospheric-stretching model. The amount of extension as well as surface heat flow generally increases from the margin to the basin center. The crustal stretching factor ({beta}) varies form 1.3 at the basin margin to 2.8 in the center. The subcrustal stretching factor ({delta}) ranges from 1.3 at the basin margin to more than 3.0 in the basin center. 31 refs., 13 figs., 4 tabs.« less

Blends of cysteine-containing proteins

NASA Astrophysics Data System (ADS)

Barone, Justin

2005-03-01

Many agricultural wastes are made of proteins such as keratin, lactalbumin, gluten, and albumin. These proteins contain the amino acid cysteine. Cysteine allows for the formation of inter-and intra-molecular sulfur-sulfur bonds. Correlations are made between the properties of films made from the proteins and the amino acid sequence. Blends of cysteine-containing proteins show possible synergies in physical properties at intermediate concentrations. FT-IR spectroscopy shows increased hydrogen bonding at intermediate concentrations suggesting that this contributes to increased physical properties. DSC shows limited miscibility and the formation of new crystalline phases in the blends suggesting that this too contributes.

Incommensurateness in nanotwinning models of modulated martensites

NASA Astrophysics Data System (ADS)

Benešová, Barbora; Frost, Miroslav; Kampschulte, Malte; Melcher, Christof; Sedlák, Petr; Seiner, Hanuš

2015-11-01

We study the formation of modulated martensites in ferromagnetic shape memory alloys by a mathematical model originating from the nanotwinning concept. The results show that the incommensurateness, systematically observed in experiments for the modulated phases, may be understood as a precursor effect of the intermartensitic transitions, and its appearance does not contradict the nanotwinning concept itself. The model sufficiently explains the different levels of incommensurateness reported from different experimental observations for the 14-layered and 10-layered martensites of the Ni-Mn-Ga alloy and outlines the mechanism of formation of faults in the stacking sequences of these materials.

Formation of Al15Mn3Si2 Phase During Solidification of a Novel Al-12%Si-4%Cu-1.2%Mn Heat-Resistant Alloy and Its Thermal Stability

NASA Astrophysics Data System (ADS)

Suo, Xiaojing; Liao, Hengcheng; Hu, Yiyun; Dixit, Uday S.; Petrov, Pavel

2018-02-01

The formation of Al15Mn3Si2 phase in Al-12Si-4Cu-1.2Mn (wt.%) alloy during solidification was investigated by adopting CALPHAD method and microstructural observation by optical microscopy, SEM-EDS, TEM-EDS/SAD and XRD analysis; SEM fixed-point observation method was applied to evaluate its thermal stability. As-cast microstructural observation consistently demonstrates the solidification sequence of the studied alloy predicted by phase diagram calculation. Based on the phase diagram calculation, SEM-EDS, TEM-EDS/SAD and XRD analysis, as well as evidences on Al-Si-Mn-Fe compounds from the literature, the primary and eutectic Mn-rich phases with different morphologies in the studied alloy are identified to be Al15Mn3Si2 that has a body-centered cubic (BCC) structure with a lattice constant of a = 1.352 nm. SEM fixed-point observation and XRD analysis indicate that Al15Mn3Si2 phase has more excellent thermal stability at high temperature than that of CuAl2 phase and can serve as the major strengthening phase in heat-resistant aluminum alloy that has to face a high-temperature working environment. Results of tension test show that addition of Mn can improve the strength of Al-Si-Cu alloy, especially at elevated temperature.

Dynamics of a two-phase flow through a minichannel: Transition from churn to slug flow

NASA Astrophysics Data System (ADS)

Górski, Grzegorz; Litak, Grzegorz; Mosdorf, Romuald; Rysak, Andrzej

2016-04-01

The churn-to-slug flow bifurcations of two-phase (air-water) flow patterns in a 2mm diameter minichannel were investigated. With increasing a water flow rate, we observed the transition of slugs to bubbles of different sizes. The process was recorded by a digital camera. The sequences of light transmission time series were recorded by a laser-phototransistor sensor, and then analyzed using the recurrence plots and recurrence quantification analysis (RQA). Due to volume dependence of bubbles velocities, we observed the formation of periodic modulations in the laser signal.

WE-DE-206-03: MRI Image Formation - Slice Selection, Phase Encoding, Frequency Encoding, K-Space, SNR

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

Lin, C.

Magnetic resonance imaging (MRI) has become an essential part of clinical imaging due to its ability to render high soft tissue contrast. Instead of ionizing radiation, MRI use strong magnetic field, radio frequency waves and field gradients to create diagnostic useful images. It can be used to image the anatomy and also functional and physiological activities within the human body. Knowledge of the basic physical principles underlying MRI acquisition is vitally important to successful image production and proper image interpretation. This lecture will give an overview of the spin physics, imaging principle of MRI, the hardware of the MRI scanner,more » and various pulse sequences and their applications. It aims to provide a conceptual foundation to understand the image formation process of a clinical MRI scanner. Learning Objectives: Understand the origin of the MR signal and contrast from the spin physics level. Understand the main hardware components of a MRI scanner and their purposes Understand steps for MR image formation including spatial encoding and image reconstruction Understand the main kinds of MR pulse sequences and their characteristics.« less

Aqueous Biphasic Systems for the Synthesis of Formates by Catalytic CO2 Hydrogenation: Integrated Reaction and Catalyst Separation for CO2 -Scrubbing Solutions.

PubMed

Scott, Martin; Blas Molinos, Beatriz; Westhues, Christian; Franciò, Giancarlo; Leitner, Walter

2017-03-22

Aqueous biphasic systems were investigated for the production of formate-amine adducts by metal-catalyzed CO 2 hydrogenation, including typical scrubbing solutions as feedstocks. Different hydrophobic organic solvents and ionic liquids could be employed as the stationary phase for cis-[Ru(dppm) 2 Cl 2 ] (dppm=bis-diphenylphosphinomethane) as prototypical catalyst without any modification or tagging of the complex. The amines were found to partition between the two phases depending on their structure, whereas the formate-amine adducts were nearly quantitatively extracted into the aqueous phase, providing a favorable phase behavior for the envisaged integrated reaction/separation sequence. The solvent pair of methyl isobutyl carbinol (MIBC) and water led to the most practical and productive system and repeated use of the catalyst phase was demonstrated. The highest single batch activity with a TOF av of approximately 35 000 h -1 and an initial TOF of approximately 180 000 h -1 was achieved in the presence of NEt 3 . Owing to higher stability, the highest productivities were obtained with methyl diethanolamine (Aminosol CST 115) and monoethanolamine (MEA), which are used in commercial scale CO 2 -scrubbing processes. Saturated aqueous solutions (CO 2 overpressure 5-10 bar) of MEA could be converted into the corresponding formate adducts with average turnover frequencies up to 14×10 3  h -1 with an overall yield of 70 % based on the amine, corresponding to a total turnover number of 150 000 over eleven recycling experiments. This opens the possibility for integrated approaches to carbon capture and utilization. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Phase 2 of the array automated assembly task for the low cost solar array project

NASA Technical Reports Server (NTRS)

Campbell, R. B.; Davis, J. R.; Ostroski, J. W.; Rai-Choudhury, P.; Rohatgi, A.; Seman, E. J.; Stapleton, R. E.

1979-01-01

The process sequence for the fabrication of dendritic web silicon into solar panels was modified to include aluminum back surface field formation. Plasma etching was found to be a feasible technique for pre-diffusion cleaning of the web. Several contacting systems were studied. The total plated Pd-Ni system was not compatible with the process sequence; however, the evaporated TiPd-electroplated Cu system was shown stable under life testing. Ultrasonic bonding parameters were determined for various interconnect and contact metals but the yield of the process was not sufficiently high to use for module fabrication at this time. Over 400 solar cells were fabricated according to the modified sequence. No sub-process incompatibility was seen. These cells were used to fabricate four demonstration modules. A cost analysis of the modified process sequence resulted in a selling price of $0.75/peak watt.

The Fate of Exoplanetary Systems and the Implications for White Dwarf Pollution

NASA Astrophysics Data System (ADS)

Veras, D.; Mustill, A. J.; Bonsor, A.; Wyatt, M. C.

2013-09-01

Mounting discoveries of extrasolar planets orbiting post-main-sequence stars motivate studies to understand the fate of these planets. Also, polluted white dwarfs (WDs) likely represent dynamically active systems at late times. Here, we perform full-lifetime simulations of one-, two- and three-planet systems from the endpoint of formation to several Gyr into the WD phase of the host star. We outline the physical and computational processes which must be considered for post-main-sequence planetary studies, and characterize the challenges in explaining the robust observational signatures of infrared excess in white dwarfs by appealing to late-stage planetary systems.

Free energy determinants of secondary structure formation: III. beta-turns and their role in protein folding.

PubMed

Yang, A S; Hitz, B; Honig, B

1996-06-21

The stability of beta-turns is calculated as a function of sequence and turn type with a Monte Carlo sampling technique. The conformational energy of four internal hydrogen-bonded turn types, I, I', II and II', is obtained by evaluating their gas phase energy with the CHARMM force field and accounting for solvation effects with the Finite Difference Poisson-Boltzmann (FDPB) method. All four turn types are found to be less stable than the coil state, independent of the sequence in the turn. The free-energy penalties associated with turn formation vary between 1.6 kcal/mol and 7.7 kcal/mol, depending on the sequence and turn type. Differences in turn stability arise mainly from intraresidue interactions within the two central residues of the turn. For each combination of the two central residues, except for -Gly-Gly-, the most stable beta-turn type is always found to occur most commonly in native proteins. The fact that a model based on local interactions accounts for the observed preference of specific sequences suggests that long-range tertiary interactions tend to play a secondary role in determining turn conformation. In contrast, for beta-hairpins, long-range interactions appear to dominate. Specifically, due to the right-handed twist of beta-strands, type I' turns for -Gly-Gly- are found to occur with high frequency, even when local energetics would dictate otherwise. The fact that any combination of two residues is found able to adopt a relatively low-energy turn structure explains why the amino acid sequence in turns is highly variable. The calculated free-energy cost of turn formation, when combined with related numbers obtained for alpha-helices and beta-sheets, suggests a model for the initiation of protein folding based on metastable fragments of secondary structure.

Aromatic residues engineered into the beta-turn nucleation site of ubiquitin lead to a complex folding landscape, non-native side-chain interactions, and kinetic traps.

PubMed

Rea, Anita M; Simpson, Emma R; Meldrum, Jill K; Williams, Huw E L; Searle, Mark S

2008-12-02

The fast folding of small proteins is likely to be the product of evolutionary pressures that balance the search for native-like contacts in the transition state with the minimum number of stable non-native interactions that could lead to partially folded states prone to aggregation and amyloid formation. We have investigated the effects of non-native interactions on the folding landscape of yeast ubiquitin by introducing aromatic substitutions into the beta-turn region of the N-terminal beta-hairpin, using both the native G-bulged type I turn sequence (TXTGK) as well as an engineered 2:2 XNGK type I' turn sequence. The N-terminal beta-hairpin is a recognized folding nucleation site in ubiquitin. The folding kinetics for wt-Ub (TLTGK) and the type I' turn mutant (TNGK) reveal only a weakly populated intermediate, however, substitution with X = Phe or Trp in either context results in a high propensity to form a stable compact intermediate where the initial U-->I collapse is visible as a distinct kinetic phase. The introduction of Trp into either of the two host turn sequences results in either complex multiphase kinetics with the possibility of parallel folding pathways, or formation of a highly compact I-state stabilized by non-native interactions that must unfold before refolding. Sequence substitutions with aromatic residues within a localized beta-turn capable of forming non-native hydrophobic contacts in both the native state and partially folded states has the undesirable consequence that folding is frustrated by the formation of stable compact intermediates that evolutionary pressures at the sequence level may have largely eliminated.

Massive star formation by accretion. II. Rotation: how to circumvent the angular momentum barrier?

NASA Astrophysics Data System (ADS)

Haemmerlé, L.; Eggenberger, P.; Meynet, G.; Maeder, A.; Charbonnel, C.; Klessen, R. S.

2017-06-01

Context. Rotation plays a key role in the star-formation process, from pre-stellar cores to pre-main-sequence (PMS) objects. Understanding the formation of massive stars requires taking into account the accretion of angular momentum during their PMS phase. Aims: We study the PMS evolution of objects destined to become massive stars by accretion, focusing on the links between the physical conditions of the environment and the rotational properties of young stars. In particular, we look at the physical conditions that allow the production of massive stars by accretion. Methods: We present PMS models computed with a new version of the Geneva Stellar Evolution code self-consistently including accretion and rotation according to various accretion scenarios for mass and angular momentum. We describe the internal distribution of angular momentum in PMS stars accreting at high rates and we show how the various physical conditions impact their internal structures, evolutionary tracks, and rotation velocities during the PMS and the early main sequence. Results: We find that the smooth angular momentum accretion considered in previous studies leads to an angular momentum barrier and does not allow the formation of massive stars by accretion. A braking mechanism is needed in order to circumvent this angular momentum barrier. This mechanism has to be efficient enough to remove more than two thirds of the angular momentum from the inner accretion disc. Due to the weak efficiency of angular momentum transport by shear instability and meridional circulation during the accretion phase, the internal rotation profiles of accreting stars reflect essentially the angular momentum accretion history. As a consequence, careful choice of the angular momentum accretion history allows circumvention of any limitation in mass and velocity, and production of stars of any mass and velocity compatible with structure equations.

Characterization of bacteria isolated from palaeoproterozoic metasediments for sequestration of carbon dioxide and formation of calcium carbonate.

PubMed

Srivastava, Shaili; Bharti, Randhir K; Thakur, Indu Shekhar

2015-01-01

Bacterial community of palaeoproterozoic metasediments was enriched in the chemostat in the presence of different concentrations of NaHCO3. Six bacterial isolates were isolated from the chemostat on nutrient agar plates on the basis of distinct morphology. Denaturing gradient gel electrophoresis (DGGE) proved the presence of six operational taxonomic units (OTUs) at 50 and 100 mM NaHCO3. The OTU was reduced to three and one at enrichment concentration of 150 and 200 mM NaHCO3 respectively. These six isolates were tested for sequestration of carbon dioxide by (14)C metabolic labeling of NaH(14)CO3. Among the six isolates, one of the bacterium showed better potency to fix radiolabeled NaH(14)CO3. The isolate (ISTD04) was identified as Serratia sp. by 16S ribosomal RNA (16S rRNA) sequence analysis and was found to be same as the DGGE OTU sequence at 200-mM NaHCO3 concentration. The bacterium was tested for product formation in form of calcite crystals in presence of 5 % CO2. Scanning electron microscopy (SEM) of product formed by the bacterium revealed defined faceted rhombohedral structure which resembled calcite and vaterite phases of the crystal. Formation of calcium carbonate crystals was further confirmed by Fourier transform infrared (FTIR) spectroscopy as carbonate group showing strong vibration at 1,456 cm(-1). Major calcite phase diffraction peaks were determined by X-ray diffraction (XRD) analysis, and energy-dispersive X-ray (EDX) analysis showed the presence of CaO (72 %) and carbon (18 %). Bacterium use bicarbonate as carbon source for their growth as well as by-product formation in form of calcite shows carbon circulation and storage.

DNA - peptide polyelectrolyte complexes: Phase control by hybridization

NASA Astrophysics Data System (ADS)

Vieregg, Jeffrey; Lueckheide, Michael; Marciel, Amanda; Leon, Lorraine; Tirrell, Matthew

DNA is one of the most highly-charged molecules known, and interacts strongly with charged molecules in the cell. Condensation of long double-stranded DNA is one of the classic problems of biophysics, but the polyelectrolyte behavior of short and/or single-stranded nucleic acids has attracted far less study despite its importance for both biological and engineered systems. We report here studies of DNA oligonucleotides complexed with cationic peptides and polyamines. As seen previously for longer sequences, double-stranded oligonucleotides form solid precipitates, but single-stranded oligonucleotides instead undergo liquid-liquid phase separation to form coacervate droplets. Complexed oligonucleotides remain competent for hybridization, and display sequence-dependent environmental response. We observe similar behavior for RNA oligonucleotides, and methylphosphonate substitution of the DNA backbone indicates that nucleic acid charge density controls whether liquid or solid complexes are formed. Liquid-liquid phase separations of this type have been implicated in formation of membraneless organelles in vivo, and have been suggested as protocells in early life scenarios; oligonucleotides offer an excellent method to probe the physics controlling these phenomena.

Course 6: Star Formation

NASA Astrophysics Data System (ADS)

Natta, A.

Contents 1 Introduction 2 Collapse of molecular cores 2.1 Giant molecular clouds and cores 2.2 Conditions for collapse 2.3 Free-fall collapse 2.4 Collapse of an isothermal sphere of gas 2.5 Collapse of a slowly rotating core 3 Observable properties of protostars 3.1 Evidence of infall from molecular line profiles 3.2 SEDs of protostars 3.3 The line spectrumof a protostar 4 Protostellar and pre-main-sequence evolution 4.1 The protostellar phase 4.2 Pre-main-sequence evolution 4.3 The birthline 5 Circumstellar disks 5.1 Accretion disks 5.2 Properties of steady accretion disks 5.3 Reprocessing disks 5.4 Disk-star interaction 6 SEDs of disks 6.1 Power-law disks 6.2 Long-wavelength flux and disk mass 6.3 Comparison with TTS observations: Heating mechanism 7 Disk properties from observations 7.1 Mass accretion rate 7.2 Inner radius 7.3 Masses 7.4 Sizes 8 Disk lifetimes 8.1 Ground-based near and mid-infrared surveys 8.2 Mid-infrared ISOCAMsurveys 8.3 ISOPHOT 60 microm survey 8.4 Surveys at millimeter wavelengths 9 Disk evolution 9.1 Can we observe the early planet formation phase? 9.2 Evidence for grain growth 9.3 Evidence of planetesimals 9.4 Where is the diskmass? 10 Secondary or debris disks 11 Summary

Theoretical predictions of properties and gas-phase chromatography behaviour of bromides of group-5 elements Nb, Ta, and element 105, Db.

PubMed

Pershina, V; Anton, J

2012-01-21

Fully relativistic, four-component density functional theory electronic structure calculations were performed for MBr(5), MOBr(3), MBr(6)(-), KMBr(6), and MBr(5)Cl(-) of group-5 elements Nb, Ta, and element 105, Db, with the aim to predict adsorption behaviour of the bromides in gas-phase chromatography experiments. It was shown that in the atmosphere of HBr/BBr(3), the pentabromides are rather stable, and their stability should increase in the row Nb < Db < Ta. Several mechanisms of adsorption were considered. In the case of adsorption by van der Waals forces, the sequence in volatility of the pentabromides should be Nb < Ta < Db, being in agreement with the sublimation enthalpies of the Nb and Ta pentabromides. In the case of adsorption by chemical forces (on a quartz surface modified with KBr∕KCl), formation of the MBr(5)L(-) (L = Cl, Br) complex should occur, so that the volatility should change in an opposite way, i.e., Nb > Ta > Db. This sequence is in agreement with the one observed in the "one-atom-at-a-time" chromatography experiments. Some other scenarios, such as surface oxide formation were also considered but found to be irrelevant. © 2012 American Institute of Physics

Reaction pathways towards the formation of dolomite-analogues at ambient conditions

NASA Astrophysics Data System (ADS)

Pimentel, Carlos; Pina, Carlos M.

2016-04-01

In this paper we present results of a study of the crystallisation behaviour of the dolomite-analogues norsethite and PbMg(CO3)2 at room temperature and atmospheric pressure. Whereas precipitation of norsethite was previously obtained by mixing solutions (Hood et al., 1974; Pimentel and Pina, 2014a,b), we report, for the first time, the synthesis of PbMg(CO3)2 by using the same method. The formation of both phases was promoted by ageing slurries for periods of time ranging from a few days (norsethite) up to 6 months (PbMg(CO3)2). The crystallisation of both norsethite and PbMg(CO3)2 occurs by sequences of dissolution-precipitation reactions involving several amorphous and crystalline precursor phases, which were identified and characterised by X-ray diffraction and scanning electron microscopy. Depending on the initial composition and Ba:Mg and Pb:Mg ratios in the slurries, different precursors and reaction kinetics were observed. This demonstrates the existence of different reaction pathways towards the formation of the investigated dolomite-analogues. Our experimental results provide new insights into the possible mechanisms of formation of dolomite and other double carbonates in nature.

Generic equilibration dynamics of planar defects in trapped atomic superfluids

DOE PAGES

Scherpelz, Peter; Padavić, Karmela; Murray, Andy; ...

2015-03-18

Here, we investigate equilibration processes shortly after sudden perturbations are applied to ultracold trapped superfluids. We show the similarity of phase imprinting and localized density depletion perturbations, both of which initially are found to produce “phase walls”. These planar defects are associated with a sharp gradient in the phase. Importantly they relax following a quite general sequence. Our studies, based on simulations of the complex time-dependent Ginzburg-Landau equation, address the challenge posed by these experiments: how a superfluid eventually eliminatesa spatially extended planar defect. The processes involved are necessarily more complex than equilibration involving simpler line vortices. An essential mechanismmore » form relaxation involves repeated formation and loss of vortex rings near the trap edge.« less

Kinetic manipulation of silicide phase formation in Si nanowire templates.

PubMed

Chen, Yu; Lin, Yung-Chen; Zhong, Xing; Cheng, Hung-Chieh; Duan, Xiangfeng; Huang, Yu

2013-08-14

The phase formation sequence of silicides in two-dimensional (2-D) structures has been well-investigated due to their significance in microelectronics. Applying high-quality silicides as contacts in nanoscale silicon (Si) devices has caught considerable attention recently for their potential in improving and introducing new functions in nanodevices. However, nucleation and diffusion mechanisms are found to be very different in one-dimensional (1-D) nanostructures, and thus the phase manipulation of silicides is yet to be achieved there. In this work, we report kinetic phase modulations to selectively enhance or hinder the growth rates of targeted nickel (Ni) silicides in a Si nanowire (NW) and demonstrate that Ni31Si12, δ-Ni2Si, θ-Ni2Si, NiSi, and NiSi2 can emerge as the first contacting phase at the silicide/Si interface through these modulations. First, the growth rates of silicides are selectively tuned through template structure modifications. It is demonstrated that the growth rate of diffusion limited phases can be enhanced in a porous Si NW due to a short diffusion path, which suppresses the formation of interface limited NiSi2. In addition, we show that a confining thick shell can be applied around the Si NW to hinder the growth of the silicides with large volume expansion during silicidation, including Ni31Si12, δ-Ni2Si, and θ-Ni2Si. Second, a platinum (Pt) interlayer between the Ni source and the Si NW is shown to effectively suppress the formation of the phases with low Pt solubility, including the dominating NiSi2. Lastly, we show that with the combined applications of the above-mentioned approaches, the lowest resistive NiSi phase can form as the first phase in a solid NW with a Pt interlayer to suppress NiSi2 and a thick shell to hinder Ni31Si12, δ-Ni2Si, and θ-Ni2Si simultaneously. The resistivity and maximum current density of NiSi agree reasonably to reported values.

Separation of multiphosphorylated peptide isomers by hydrophilic interaction chromatography on an aminopropyl phase.

PubMed

Singer, David; Kuhlmann, Julia; Muschket, Matthias; Hoffmann, Ralf

2010-08-01

The separation of isomeric phosphorylated peptides is challenging and often impossible for multiphosphorylated isomers using chromatographic and capillary electrophoretic methods. In this study we investigated the separation of a set of single-, double-, and triple-phosphorylated peptides (corresponding to the human tau protein) by ion-pair reversed-phase chromatography (IP-RPC) and hydrophilic interaction chromatography (HILIC). In HILIC both hydroxyl and aminopropyl stationary phases were tested with aqueous acetonitrile in order to assess their separation efficiency. The hydroxyl phase separated the phosphopeptides very well from the unphosphorylated analogue, while on the aminopropyl phase even isomeric phosphopeptides attained baseline separation. Thus, up to seven phosphorylated versions of a given tau domain were separated. Furthermore, the low concentration of an acidic ammonium formate buffer allowed an online analysis with electrospray ionization tandem mass spectrometry (ESI-MS/MS) to be conducted, enabling peptide sequencing and identification of phosphorylation sites.

Reentrant equilibrium disordering in nanoparticle–polymer mixtures

DOE PAGES

Meng, Dong; Kumar, Sanat K.; Grest, Gary S.; ...

2017-01-31

A large body of experimental work has established that athermal colloid/polymer mixtures undergo a sequence of transitions from a disordered fluid state to a colloidal crystal to a second disordered phase with increasing polymer concentration. These transitions are driven by polymer-mediated interparticle attraction, which is a function of both the polymer density and size. It has been posited that the disordered state at high polymer density is a consequence of strong interparticle attractions that kinetically inhibit the formation of the colloidal crystal, i.e., the formation of a non-equilibrium gel phase interferes with crystallization. Here we use molecular dynamics simulations andmore » density functional theory on polymers and nanoparticles (NPs) of comparable size and show that the crystal-disordered phase coexistence at high polymer density for sufficiently long chains corresponds to an equilibrium thermodynamic phase transition. While the crystal is, indeed, stabilized at intermediate polymer density by polymer-induced intercolloid attractions, it is destabilized at higher densities because long chains lose significant configurational entropy when they are forced to occupy all of the crystal voids. Finally, our results are in quantitative agreement with existing experimental data and show that, at least in the nanoparticle limit of sufficiently small colloidal particles, the crystal phase only has a modest range of thermodynamic stability.« less

The origins of post-starburst galaxies at z < 0.05

NASA Astrophysics Data System (ADS)

Pawlik, M. M.; Taj Aldeen, L.; Wild, V.; Mendez-Abreu, J.; Lahén, N.; Johansson, P. H.; Jimenez, N.; Lucas, W.; Zheng, Y.; Walcher, C. J.; Rowlands, K.

2018-06-01

Post-starburst galaxies can be identified via the presence of prominent Hydrogen Balmer absorption lines in their spectra. We present a comprehensive study of the origin of strong Balmer lines in a volume-limited sample of 189 galaxies with 0.01 < z < 0.05, log ({M}_{\\star }/{M}_{⊙})>9.5 and projected axial ratio b/a > 0.32. We explore their structural properties, environments, emission lines, and star formation histories, and compare them to control samples of star-forming and quiescent galaxies, and simulated galaxy mergers. Excluding contaminants, in which the strong Balmer lines are most likely caused by dust-star geometry, we find evidence for three different pathways through the post-starburst phase, with most events occurring in intermediate-density environments: (1) a significant disruptive event, such as a gas-rich major merger, causing a starburst and growth of a spheroidal component, followed by quenching of the star formation (70 per cent of post-starburst galaxies at 9.5< log ({M}_{\\star}/{M}_{⊙})<10.5 and 60 per cent at log ({M}_{\\star}/{M}_{⊙})>10.5); (2) at 9.5< log ({M}_{\\star}/{M}_{⊙})<10.5, stochastic star formation in blue-sequence galaxies, causing a weak burst and subsequent return to the blue sequence (30 per cent); (3) at log ({M}_{\\star}/{M}_{⊙})>10.5, cyclic evolution of quiescent galaxies which gradually move towards the high-mass end of the red sequence through weak starbursts, possibly as a result of a merger with a smaller gas-rich companion (40 per cent). Our analysis suggests that active galactic nuclei (AGNs) are 'on' for 50 per cent of the duration of the post-starburst phase, meaning that traditional samples of post-starburst galaxies with strict emission-line cuts will be at least 50 per cent incomplete due to the exclusion of narrow-line AGNs.

(S, C, O, Sr) isotopic constraints on the diagenetic evolution of the COX clay formations at the Bure URL site, Paris Basin)

NASA Astrophysics Data System (ADS)

Lerouge, C.; Gaucher, E. C.; Tournassat, C.; Agrinier, P.; Widory, D.; Guerrot, C.; Buschaert, S.

2009-04-01

The Underground Research Laboratory of Bure, located in the Eastern part of the Paris Basin, was selected by ANDRA (French Agency for Nuclear Management) in order to study the feasibility of a nuclear waste disposal in the Callovian-Oxfordian thick clayey formation at 400 meters depth. Since 1994's, numerous investigations have been initiated to understand and predict the behaviour of the clay formation in time and in space, by constraining its stability, the chemical evolution of the porewaters, and solution transfers between the clayey formation and its adjacent limestone sequences during geological times (ANDRA, 2005). In that way, this study presents combined new mineralogical and isotopic data of the diagenetic mineral sequence to constrain the porewater chemistry of the rock at different stages of the sedimentary then burial history of the clayey formation. The petrological study of Callovian-Oxfordian claystones provided evidence of the following diagenetic mineral sequence: 1) Framboïdal pyrite ± micritic calcite in replacement of carbonate bioclasts and in bioturbations, 2) Iron-rich euhedral carbonates (ankerite, sideroplesite), Glauconite, 3) Sparry dolomite, celestite in residual porosity, 4) Chalcedony 5) quartz/calcite. Pyrite in bioturbations shows a wide range of δ34S (-38 to +74 permil/CDT), providing evidence of bacterial sulphate reduction processes. The lowest negative values (-38 to -22 permil) indicate precipitation of pyrite in a marine environment with a permanent recharge in sulphate, whereas the higher pyrite δ34S values (-14 up to +74 permil) show that pyrite precipitated in a system that closed for sulphate. Consequently the variations of pyrite δ34S in bioturbations along the lithostratigraphic profil indicate a change of sedimentation conditions from a deep marine environment to an environment with alternative recharge of marine sulphates; that is consistent with the transgression/regression cycle observed in the middle sequence of the formation. The δ34S values of celestite (+ 22 to +31 permil /CDT) reflect the last evolution stage of the system at which the bacterial activity ends, the celestite corresponding to the deposition of the residual dissolved sulphate anions in the diagenetic porewaters. The 87Sr/86Sr ratio of celestite (0.706872-0.707040) is consistent with a deposition from Jurassic marine-derived waters. Carbon and oxygen isotopic compositions of bulk calcite and dolomite are consistent with marine carbonates (δ13C= +0.2 to +2.3 permil/PDB, δ18O= +27.7 to +28.7 permil/SMOW) whereas late diagenetic siderite is slightly 13C- depleted. The 13C-depletion could be attributed to a partial contribution in diagenetic porewaters of carbonate ions derived partially from the degradation of organic matter issue of the bacterial sulphate reduction. The δ18O values of late diagenetic chalcedony range between +27 and +31 permil(/SMOW), suggesting precipitation from marine-derived porewaters at temperatures of maximum burial (~40-50°C). Late calcite in veinlet reworking with chalcedony and celestite, and late euhedral quartz in a limestone from the top of the formation have lower δ18O values (~+19 permil/SMOW), suggesting they precipitated from meteoric fluids (δ18O ~ -6 permil), whose signature is close to present-day porewaters of the formation. To conclude, combined mineralogical and isotopic data show that pyrite, sulfates, calcite cement, euhedral iron-bearing carbonates and probably chalcedony are diagenetic phases precipitated from marine-derived porewaters in conditions controlled by bacterial sulphate reduction. A calcite veinlet reworking chalcedony and celestite (in the middle sequence of the formation) and euhedral quartz encrusting a vug in a limestone from the top of the clayey formation are the only mineral records of the introduction of meteoric fluid in the clay formation, and the only phases at isotopic equilibrium with present-day porewaters.

Combined effect of Pt and W alloying elements on Ni-silicide formation

NASA Astrophysics Data System (ADS)

Luo, T.; Mangelinck, D.; Descoins, M.; Bertoglio, M.; Mouaici, N.; Hallén, A.; Girardeaux, C.

2018-03-01

A combinatorial study of the combined effect of Pt and W on Ni silicide formation is performed. Ni(Pt, W) films with thickness and composition gradients were prepared by a co-deposition composition spread technique using sputtering deposition from Pt, W, and Ni targets. The deposited Ni(Pt,W) films were characterized by X-ray diffraction, X-ray reflectivity, Rutherford backscattering, and atom probe tomography. The maximum content of alloying elements is close to 27 at. %. Simulations of the thickness and composition were carried out and compared with experimental results. In situ X-ray diffraction and atom probe tomography were used to study the phase formation. Both additive alloying elements (Pt + W) slow down the Ni consumption and the effect of W is more pronounced than the one of Pt. Regarding the effect of alloying elements on Ni silicides formation, three regions could be distinguished in the Ni(Pt,W)/Si wafer. For the region close to the Ni target, the low contents of alloying elements (Pt + W) have little impact on the phase sequence (δ-Ni2Si is the first silicide and NiSi forms when Ni is entirely consumed) but the kinetics of silicide formation slows down. The region close to the Pt target has high contents of (Pt + W) and is rich in Pt and a simultaneous phase formation of δ-Ni2Si and NiSi is observed. For the high (Pt + W) contents and W-rich region, NiSi forms unexpectedly before δ-Ni2Si and the subsequent growth of δ-Ni2Si is accompanied by the NiSi consumption. When Ni is entirely consumed, NiSi regrows at the expense of δ-Ni2Si.

Recognition of the DNA sequence by an inorganic crystal surface

PubMed Central

Sampaolese, Beatrice; Bergia, Anna; Scipioni, Anita; Zuccheri, Giampaolo; Savino, Maria; Samorì, Bruno; De Santis, Pasquale

2002-01-01

The sequence-dependent curvature is generally recognized as an important and biologically relevant property of DNA because it is involved in the formation and stability of association complexes with proteins. When a DNA tract, intrinsically curved for the periodical recurrence on the same strand of A-tracts phased with the B-DNA periodicity, is deposited on a flat surface, it exposes to that surface either a T- or an A-rich face. The surface of a freshly cleaved mica crystal recognizes those two faces and preferentially interacts with the former one. Statistical analysis of scanning force microscopy (SFM) images provides evidence of this recognition between an inorganic crystal surface and nanoscale structures of double-stranded DNA. This finding could open the way toward the use of the sequence-dependent adhesion to specific crystal faces for nanotechnological purposes. PMID:12361979

Cosmic Accretion and Galaxy Co-Evolution: Lessons from the Extended Chandra Deep Field South

NASA Astrophysics Data System (ADS)

Urry, C. Megan

2011-05-01

The Chandra deep fields reveal that most cosmic accretion onto supermassive black holes is obscured by gas and dust. The GOODS and MUSYC multiwavelength data show that many X-ray-detected AGN are faint and red (or even undetectable) in the optical but bright in the infrared, as is characteristic of obscured sources. (N.B. The ECDFS is most sensitive to the AGN that constitute the X-ray background, namely, moderate luminosity AGN, with log Lx=43-44, at moderate redshifts, 0.5

Alignment of 1000 Genomes Project reads to reference assembly GRCh38.

PubMed

Zheng-Bradley, Xiangqun; Streeter, Ian; Fairley, Susan; Richardson, David; Clarke, Laura; Flicek, Paul

2017-07-01

The 1000 Genomes Project produced more than 100 trillion basepairs of short read sequence from more than 2600 samples in 26 populations over a period of five years. In its final phase, the project released over 85 million genotyped and phased variants on human reference genome assembly GRCh37. An updated reference assembly, GRCh38, was released in late 2013, but there was insufficient time for the final phase of the project analysis to change to the new assembly. Although it is possible to lift the coordinates of the 1000 Genomes Project variants to the new assembly, this is a potentially error-prone process as coordinate remapping is most appropriate only for non-repetitive regions of the genome and those that did not see significant change between the two assemblies. It will also miss variants in any region that was newly added to GRCh38. Thus, to produce the highest quality variants and genotypes on GRCh38, the best strategy is to realign the reads and recall the variants based on the new alignment. As the first step of variant calling for the 1000 Genomes Project data, we have finished remapping all of the 1000 Genomes sequence reads to GRCh38 with alternative scaffold-aware BWA-MEM. The resulting alignments are available as CRAM, a reference-based sequence compression format. The data have been released on our FTP site and are also available from European Nucleotide Archive to facilitate researchers discovering variants on the primary sequences and alternative contigs of GRCh38. © The Authors 2017. Published by Oxford University Press.

Paleoenvironmental reconstruction and evolution of an Upper Cretaceous lacustrine-fluvial-deltaic sequence in the Parecis Basin, Brazil

NASA Astrophysics Data System (ADS)

Rubert, Rogerio R.; Mizusaki, Ana Maria Pimentel; Martinelli, Agustín G.; Urban, Camile

2017-12-01

The Cretaceous in the Brazilian Platform records events of magmatism, tectonism and sedimentation coupled to the Gondwana breakup. Some of these events are registered as sedimentary sequences in interior basins, such as in the Cretaceous sequence of the Alto Xingu Sub-basin, Parecis Basin, Central Brazil. This article proposes the faciologic characterization and paleoenvironmental reconstruction of the Cretaceous sequence of the eastern portion of the Parecis Basin and its relation with some reactivated structures as, for instance, the Serra Formosa Arch. Based on both data from outcrops and core drillings a paleoenvironmental and evolutionary reconstruction of the sequence is herein presented. The base of the studied section is characterized by chemical and low energy clastic sedimentation of Lake Bottom and Shoreline, in a context of fast initial subsidence and low sedimentation rate. As the subsidence process decreased, a deltaic progradation became dominant with deposition in a prodelta environment, followed by a deltaic front and deltaic plain interbedded with fluvial plain, and aeolian deposition completing the sequence. The inferred Coniacian-Santonian age is based on vertebrate (fishes and notosuchians) and ostracod fossils with regional chrono-correlates in the Adamantina (Bauru Group), Capacete (Sanfranciscana Basin), and Bajo de la Carpa (Neuquén Group, in Argentina) formations. The formation of a Coniacian depocenter in the Alto Xingu Sub-basin is associated to the Turonian-Coniacian reactivation event in the Peruvian Orogenic Phase of the Andean Orogeny, with the transference of stresses to interplate setting, reactivating Proterozoic structures of the basement.

Comparison of the quality of different magnetic resonance image sequences of multiple myeloma.

PubMed

Sun, Zhao-yong; Zhang, Hai-bo; Li, Shuo; Wang, Yun; Xue, Hua-dan; Jin, Zheng-yu

2015-02-01

To compare the image quality of T1WI fat phase,T1WI water phase, short time inversion recovery (STIR) sequence, and diffusion weighted imaging (DWI) sequence in the evaluation of multiple myeloma (MM). Totally 20MM patients were enrolled in this study. All patients underwent scanning at coronal T1WI fat phase, coronal T1WI water phase, coronal STIR sequence, and axial DWI sequence. The image quality of the four different sequences was evaluated. The image was divided into seven sections(head and neck, chest, abdomen, pelvis, thigh, leg, and foot), and the signal-to-noise ratio (SNR) of each section was measured at 7 segments (skull, spine, pelvis, humerus, femur, tibia and fibula and ribs) were measured. In addition, 20 active MM lesions were selected, and the contrast-to-noise ratio (CNR) of each scan sequence was calculated. The average image quality scores of T1WI fat phase,T1WI water phase, STIR sequence, and DWI sequence were 4.19 ± 0.70,4.16 ± 0.73,3.89 ± 0.70, and 3.76 ± 0.68, respectively. The image quality at T1-fat phase and T1-water phase were significantly higher than those at STIR (P=0.000 and P=0.001) and DWI sequence (both P=0.000); however, there was no significant difference between T1-fat and T1-water phase (P=0.723)and between STIR and DWI sequence (P=0.167). The SNR of T1WI fat phase was significantly higher than those of the other three sequences (all P=0.000), and there was no significant difference among the other three sequences (all P>0.05). Although the CNR of DWI sequences was slightly higher than those of the other three sequences,there was no significant difference among all of them (all P>0.05). Imaging at T1WI fat phase,T1WI water phase, STIR sequence, and DWI sequence has certain advantages,and they should be combined in the diagnosis of MM.

Controllable synthesis and property of graphene-based magnetic metal nanostructures

NASA Astrophysics Data System (ADS)

Wu, Kong-Lin; Li, Xiang-Zi; Wei, Xian-Wen; Ding, Ting-Hui; Jiang, Miao; Zhang, Wen-Juan; Ye, Yin

2014-12-01

A facile and effective solution phase reduction method was developed to synthesize graphene-based magnetic metal nanocomposites. Metals (Co, and Ni) or alloys (Fe51Co49, Fe48Ni52, Ni49Co51, Co51Cu49, and Ni52Cu48)/reduced graphene oxide (RGO) nanocomposites were successfully prepared by reduction of the corresponding aqueous metal ions and ethylenediamine (EDA)-graphene oxide (GO) with hydrazine hydrate at 353 K for 1 h under N2 atmosphere. The effects of synthetic parameters such as metal ions concentration, adding sequence of NaOH and N2H4·H2O, linkage agent and reaction time on the formation of nanocomposites were investigated. The experimental results showed that using ethylenediamine and adding sequence played critical roles in the formation of metals or alloys/RGO nanocomposites. Magnetic hysteresis measurements revealed that the as-synthesized metals or alloys in nanocomposites showed excellent soft magnetic behavior with enhanced saturation magnetization, and could have promising applications in biotechnology, catalysis, and magnetic storage devices.

Examining the influence of formative assessment on conceptual accumulation and conceptual change

NASA Astrophysics Data System (ADS)

Tomita, Miki K.

This study explored the effect of formative assessment on student achievement in science. Research in science education has shown that students enter science classrooms with previously formed explanatory models of the natural world; these naive "mental models" have a substantial influence on their learning of scientific conceptions. In general, conceptual change describes the pathway from pre-instructional or prior conceptions to a post-instructional or desired conception. Conceptual change involves a fundamental restructuring of a network of concepts rather than fitting new concepts into an existing conceptual network or structure. Research has shown that conceptual change is difficult to promote; for example, students may accumulate multiple conceptions over the course of instruction, including both new misconceptions and more scientifically-sound conceptions. Hellden and Solomon (2004) found that although students tended to evoke the same, less-scientific conceptions over time, they could produce more scientifically-sound conceptions during interviews with appropriate prompting; thus, students undergo conceptual accumulation rather than conceptual change. Students can recall scientifically-sound conceptions they have learned and may use them to reason, but they do so in partnership or hybridization with their less-scientific prior conceptions. Formative assessment, which focuses on providing immediate feedback by acting upon student understanding during the course of instruction, and conceptual change have both been linked to increased student achievement. Formative assessment is an instructional strategy that helps teachers to assess students' current understanding, identify the gap between current understanding and expected understanding, and provide immediate and useful feedback to students on how to close the gap. Formative assessment ranges from formal (e.g. embedded, planned-for interactions between teacher and entire class) to informal (e.g. on-the-fly interactions between teacher and class or student). In this study, the links between formative assessment and conceptual accumulation and conceptual change were explored. Specifically, this study asked: (1) Does formative assessment promote conceptual accumulation, and (2) Does formative assessment promote conceptual change? It was hypothesized that conceptual change-focused formative assessment would foster conceptual change, in addition to supporting conceptual accumulation. It was further hypothesized that all students will show gains in conceptual accumulation as indicated by measures of declarative and procedural knowledge, but that students exposed to conceptual change-focused formative assessment would also show gains in conceptual change as indicated by measures of schematic knowledge or mental models. To research the effect of formative assessment on conceptual accumulation and conceptual change, a small randomized experiment involving 102 middle school students was conducted. In Phase I of the study, 52 6th graders were randomly assigned to a treatment or control group; in Phase II of this study, 50 7th graders were randomly assigned to a treatment or control group. Both the control and experimental groups in both phases were taught about sinking and floating by the same teacher (the author) with identical curriculum materials and activities. In addition, the experimental group received three sets of embedded formative assessments focused on conceptual change around the topic of why things sink and float during the course of instruction. In Phase I of this study, both groups were kept at the same pace through the entire sequence of investigations. The control condition spent more time on some of the more critical FAST lessons, gathering additional data to support the theories the curriculum expected they would develop at a particular juncture but not receiving structured experiences aimed at addressing misconceptions. In Phase II, students in the control condition spent roughly the same time on each FAST lesson as those in the experimental condition (e.g. they finished the sequence of activities earlier because they did not have class sessions devoted to the RLs inserted at critical junctures) but participated in the formal assessments as a block of activities after they finished the FAST investigations and posttest measures. In other words, in addition to replicating Phase I, Phase II included a Reflective Lesson section for the control group after the end of the experiment proper, followed by a post-posttest. Overall, it was found that embedding conceptual change-focused formative assessments in the FAST curriculum significantly influenced conceptual change. It was also found that all students experienced significant gains in terms of their conceptual accumulation, regardless of exposure to the formative assessments. This study connected two previously isolated but theoretically linked educational frameworks: conceptual change and formative assessment. It was found that formative assessments can be used to promote conceptual change. It was also found that conceptual change is different than conceptual accumulation, in that students who show gains on measures of declarative and procedural knowledge do not necessarily show gains on measures of schematic knowledge. (Abstract shortened by UMI.)

Observations of a hydrofracture induced earthquake sequence in Harrison County Ohio in 2014

NASA Astrophysics Data System (ADS)

Friberg, P. A.; Brudzinski, M. R.; Currie, B. S.; Skoumal, R.

2015-12-01

On October 7, 2014, a Mw 1.9 earthquake was detected and located using the IRIS Earthscope Transportable Array stations in Ohio. The earthquake was located at a depth of ~3 km near the interface of the Paleozoic sedimentary rocks with the crystalline Precambrian basement. The location is within a few kilometers laterally of a 2013 earthquake sequence that was linked to hydraulic fracturing (HF) operations on three wells in Harrison county (Friberg et al, 2014). Using the Mw 1.9 event as a template in a multi-component cross correlation detector on station O53A, over 1000 matching detections were revealed between September 26 - October 17, 2014. These detections were all coincident in time with HF operations on 3 nearby (< 1km away) horizontally drilled wells (Tarbert 1H, 3H, and 5H) in the Utica formation (~2.4 km depth). The HF operations at two of the wells (1H and 5H) were coincident with the majority of the detected events. The final well (3H) stimulated in the series, produced only about 20 identified events. In addition to the coincident timing with nearby HF operations, the time clustered nature of the detections were similar to the 2013 sequence and two other Ohio HF induced sequences in 2014 (Skoumal et al, 2015). All of the other HF induced earthquake sequences in Ohio were related to operations in the Utica formation. Interestingly, this sequence of earthquakes did not follow a simple Gutenberg-Richter magnitude frequency relationship and was deficient in positive magnitude events; the magnitude 1.9 was preceded by a magnitude 1.7, and only a ½ dozen events slightly above magnitude 0.0. The majority of the events detected were below magnitude 0.0, with some as low as magnitude -2.0. While the majority of detections are too small to locate, high similarity in waveform character indicate they are spatially near to the magnitude 1.9 event. Furthermore, gradual shifts in P phase arrival relative to S phases indicate events are moving away from the station with progressive HF stages. Given the orientation of the wells relative to the station, the migration of events away from the station with progressive stages is also supportive of this being an induced sequence.

Sedimentology of the Simmler and Vaqueros formations in the Caliente Range-Carrizo Plain area, California

USGS Publications Warehouse

Bartow, J. Alan

1974-01-01

The Simmler and Vaqueros Formations in the Caliente Range-Carrizo Plain area make up a large part of the thick Tertiary sedimentary sequence that was .deposited in a basin which lay along the southwest side of the present-day San Andreas fault. The evolution of this basin during Oligocene and early Miocene time and the relationship of its sedimentary record to the tectonic history is an important chapter in the Tertiary history of California. The Simmler Formation, of provincial Oligocene to early Miocene age, unconformably overlies basement rocks and an Upper Cretaceous-lower Tertiary marine sequence. It consists of a sandstone facies, which is mostly a variegated sequence of sandstone and mudstone occurring in fining-upward cycles, and a conglomerate facies, which occurs around the southwest and southeast margins of the basin. The conformably overlying Vaqueros Formation, of provincial early to middle Miocene age, is subdivided from base upward ,into the Quail Canyon Sandstone, Soda Lake Shale, and Painted Rock Sandstone Members. The Vaqueros intertongues eastward, southeastward, and northward with the continental Caliente Formation and is conformably overlain by the Monterey Shale. In the Caliente Range, northeast of major thrust faults, the Vaqueros may reach a thickness of 8,700 feet (2,650 m). Around the margin of the basin, the formation is much thinner--locally only 200 feet (60 m) thick--and is generally undivided. The Quail Canyon Sandstone Member is composed of cross-bedded or planar-stratified sandstone. The Soda Lake Shale Member consists mostly of siltstone and platy shale with a few thin sandstone interbeds. The Painted Rock Sandstone Member, the thickest and coarsest member, consists mostly of large lenticular bodies of thick-bedded coarse-grained sandstone and thinner units of siltstone. Petrology and paleocurrent studies indicate that, in a given subarea, the Simmler and Vaqueros Formations were derived from the same source terrane and that the sediments were usually transported in the same general direction. Crystalline basement terranes to the north and south were the primary sources, but the Upper Cretaceous-lower Tertiary marine sequence made substantial contributions along the southwest side of the basin. The sandstone facies of the Simmler Formation is interpreted as an alluvial plain depositional complex formed by through-flowing low-sinuosity streams, and the conglomerate facies is interpreted as alluvial fan deposits. The Vaqueros Formation in the Caliente Range forms a transgressive-regressive sequence. The Quail Canyon Sandstone and lowermost Soda Lake Shale Members represent the transgressive phase, are interpreted as beach-nearshore and offshore deposits, and are locally the marine equivalents of the upper part of the Simmler conglomerate facies. The remainder of the Soda Lake Shale Member and the Painted Rock Sandstone Member represent the regressive phase and are interpreted as a complex of deltaic and shelf-slope deposits that prograded over basinal shales and turbidites. The reconstructed basin history began in the Oligocene with alluvial plain sedimentation in an area of relatively low relief. This was interrupted in the early Miocene (ca. 25 m.y. B.P.) by the beginning of a period of crustal extension, probably related to the first interaction of the Pacific and North American plates, resulting in the formation of a rapidly subsiding marine basin. This crustal extension was followed by a period of north-south compression in the Pliocene and Pleistocene, which caused the thick accumulation of sediments in the basin to be folded and thrust over the thinner basin-margin section. The Red Hills-Chimineas-Russell fault trend, along which Cretaceous granitic and Precambrian(?) gneissic rocks had been juxtaposed in Cretaceous time, was reactivated in the Pliocene, when 8 to 9 miles (13-14.5 km) of additional right-lateral slip occurred, The pattern of north-south thrusting and rig

Decrease in gamma-band activity tracks sequence learning

PubMed Central

Madhavan, Radhika; Millman, Daniel; Tang, Hanlin; Crone, Nathan E.; Lenz, Fredrick A.; Tierney, Travis S.; Madsen, Joseph R.; Kreiman, Gabriel; Anderson, William S.

2015-01-01

Learning novel sequences constitutes an example of declarative memory formation, involving conscious recall of temporal events. Performance in sequence learning tasks improves with repetition and involves forming temporal associations over scales of seconds to minutes. To further understand the neural circuits underlying declarative sequence learning over trials, we tracked changes in intracranial field potentials (IFPs) recorded from 1142 electrodes implanted throughout temporal and frontal cortical areas in 14 human subjects, while they learned the temporal-order of multiple sequences of images over trials through repeated recall. We observed an increase in power in the gamma frequency band (30–100 Hz) in the recall phase, particularly in areas within the temporal lobe including the parahippocampal gyrus. The degree of this gamma power enhancement decreased over trials with improved sequence recall. Modulation of gamma power was directly correlated with the improvement in recall performance. When presenting new sequences, gamma power was reset to high values and decreased again after learning. These observations suggest that signals in the gamma frequency band may play a more prominent role during the early steps of the learning process rather than during the maintenance of memory traces. PMID:25653598

37 CFR 1.822 - Symbols and format to be used for nucleotide and/or amino acid sequence data.

Code of Federal Regulations, 2011 CFR

2011-07-01

... for nucleotide and/or amino acid sequence data. 1.822 Section 1.822 Patents, Trademarks, and... Amino Acid Sequences § 1.822 Symbols and format to be used for nucleotide and/or amino acid sequence data. (a) The symbols and format to be used for nucleotide and/or amino acid sequence data shall...

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

Zhang, Fan; Levine, Lyle E.; Allen, Andrew J.

The precipitate structure and precipitation kinetics in an Al-Cu-Mg alloy (AA2024) aged at 190 °C, 208 °C, and 226 °C have been studied using ex situ Transmission Electron Microscopy (TEM) and in situ synchrotron-based, combined ultra-small angle X-ray scattering, small angle X-ray scattering (SAXS), and wide angle X-ray scattering (WAXS) across a length scale from sub-Angstrom to several micrometers. TEM brings information concerning the nature, morphology, and size of the precipitates while SAXS and WAXS provide qualitative and quantitative information concerning the time-dependent size and volume fraction evolution of the precipitates at different stages of the precipitation sequence. Within themore » experimental time resolution, precipitation at these ageing temperatures involves dissolution of nanometer-sized small clusters and formation of the planar S phase precipitates. Using a three-parameter scattering model constructed on the basis of TEM results, we established the temperature-dependent kinetics for the cluster-dissolution and S-phase formation processes simultaneously. These two processes are shown to have different kinetic rates, with the cluster-dissolution rate approximately double the S-phase formation rate. We identified a dissolution activation energy at (149.5 ± 14.6) kJ mol-1, which translates to (1.55 ± 0.15) eV/atom, as well as an activation energy for the formation of S precipitates at (129.2 ± 5.4) kJ mol-1, i.e. (1.33 ± 0.06) eV/atom. Importantly, the SAXS/WAXS results show the absence of an intermediate Guinier-Preston Bagaryatsky 2 (GPB2)/S" phase in the samples under the experimental ageing conditions. These results are further validated by precipitation simulations that are based on Langer-Schwartz theory and a Kampmann-Wagner numerical method.« less

Oscillatory phase separation in giant lipid vesicles induced by transmembrane osmotic differentials

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

Oglęcka, Kamila; Rangamani, Padmini; Liedberg, Bo

Giant lipid vesicles are closed compartments consisting of semi-permeable shells, which isolate femto- to pico-liter quantities of aqueous core from the bulk. Although water permeates readily across vesicular walls, passive permeation of solutes is hindered. In this study, we show that, when subject to a hypotonic bath, giant vesicles consisting of phase separating lipid mixtures undergo osmotic relaxation exhibiting damped oscillations in phase behavior, which is synchronized with swell–burst lytic cycles: in the swelled state, osmotic pressure and elevated membrane tension due to the influx of water promote domain formation. During bursting, solute leakage through transient pores relaxes the pressuremore » and tension, replacing the domain texture by a uniform one. This isothermal phase transition—resulting from a well-coordinated sequence of mechanochemical events—suggests a complex emergent behavior allowing synthetic vesicles produced from simple components, namely, water, osmolytes, and lipids to sense and regulate their micro-environment.« less

Understanding the optics to aid microscopy image segmentation.

PubMed

Yin, Zhaozheng; Li, Kang; Kanade, Takeo; Chen, Mei

2010-01-01

Image segmentation is essential for many automated microscopy image analysis systems. Rather than treating microscopy images as general natural images and rushing into the image processing warehouse for solutions, we propose to study a microscope's optical properties to model its image formation process first using phase contrast microscopy as an exemplar. It turns out that the phase contrast imaging system can be relatively well explained by a linear imaging model. Using this model, we formulate a quadratic optimization function with sparseness and smoothness regularizations to restore the "authentic" phase contrast images that directly correspond to specimen's optical path length without phase contrast artifacts such as halo and shade-off. With artifacts removed, high quality segmentation can be achieved by simply thresholding the restored images. The imaging model and restoration method are quantitatively evaluated on two sequences with thousands of cells captured over several days.

Oscillatory phase separation in giant lipid vesicles induced by transmembrane osmotic differentials

DOE PAGES

Oglęcka, Kamila; Rangamani, Padmini; Liedberg, Bo; ...

2014-10-15

Giant lipid vesicles are closed compartments consisting of semi-permeable shells, which isolate femto- to pico-liter quantities of aqueous core from the bulk. Although water permeates readily across vesicular walls, passive permeation of solutes is hindered. In this study, we show that, when subject to a hypotonic bath, giant vesicles consisting of phase separating lipid mixtures undergo osmotic relaxation exhibiting damped oscillations in phase behavior, which is synchronized with swell–burst lytic cycles: in the swelled state, osmotic pressure and elevated membrane tension due to the influx of water promote domain formation. During bursting, solute leakage through transient pores relaxes the pressuremore » and tension, replacing the domain texture by a uniform one. This isothermal phase transition—resulting from a well-coordinated sequence of mechanochemical events—suggests a complex emergent behavior allowing synthetic vesicles produced from simple components, namely, water, osmolytes, and lipids to sense and regulate their micro-environment.« less

Phase transitions in biogenic amorphous calcium carbonate.

PubMed

Gong, Yutao U T; Killian, Christopher E; Olson, Ian C; Appathurai, Narayana P; Amasino, Audra L; Martin, Michael C; Holt, Liam J; Wilt, Fred H; Gilbert, P U P A

2012-04-17

Crystalline biominerals do not resemble faceted crystals. Current explanations for this property involve formation via amorphous phases. Using X-ray absorption near-edge structure (XANES) spectroscopy and photoelectron emission microscopy (PEEM), here we examine forming spicules in embryos of Strongylocentrotus purpuratus sea urchins, and observe a sequence of three mineral phases: hydrated amorphous calcium carbonate (ACC · H(2)O) → dehydrated amorphous calcium carbonate (ACC) → calcite. Unexpectedly, we find ACC · H(2)O-rich nanoparticles that persist after the surrounding mineral has dehydrated and crystallized. Protein matrix components occluded within the mineral must inhibit ACC · H(2)O dehydration. We devised an in vitro, also using XANES-PEEM, assay to identify spicule proteins that may play a role in stabilizing various mineral phases, and found that the most abundant occluded matrix protein in the sea urchin spicules, SM50, stabilizes ACC · H(2)O in vitro.

Phase transitions in biogenic amorphous calcium carbonate

PubMed Central

Gong, Yutao U. T.; Killian, Christopher E.; Olson, Ian C.; Appathurai, Narayana P.; Amasino, Audra L.; Martin, Michael C.; Holt, Liam J.; Wilt, Fred H.; Gilbert, P. U. P. A.

2012-01-01

Crystalline biominerals do not resemble faceted crystals. Current explanations for this property involve formation via amorphous phases. Using X-ray absorption near-edge structure (XANES) spectroscopy and photoelectron emission microscopy (PEEM), here we examine forming spicules in embryos of Strongylocentrotus purpuratus sea urchins, and observe a sequence of three mineral phases: hydrated amorphous calcium carbonate (ACC·H2O) → dehydrated amorphous calcium carbonate (ACC) → calcite. Unexpectedly, we find ACC·H2O-rich nanoparticles that persist after the surrounding mineral has dehydrated and crystallized. Protein matrix components occluded within the mineral must inhibit ACC·H2O dehydration. We devised an in vitro, also using XANES-PEEM, assay to identify spicule proteins that may play a role in stabilizing various mineral phases, and found that the most abundant occluded matrix protein in the sea urchin spicules, SM50, stabilizes ACC·H2O in vitro. PMID:22492931

Secondary Fe- and Mn-Oxides Associated with Faults Near Moab, Utah: Records of Past Fluid Flow

NASA Astrophysics Data System (ADS)

Garcia, V. H.; Reiners, P. W.

2015-12-01

Secondary Fe- and Mn-oxides are locally common near faults and fractures, and as cements within sandstones of the Colorado Plateau, and provide evidence of past fluid-flow. Here we describe textural, mineralogic, and geochronologic observations from fault-zone Fe- and Mn-oxide mineralization in Flat Iron Mesa, near Moab, Utah. Several hypotheses have been proposed for their origin, including reactions associated with the mixing of deep reduced and near-surface oxygenated waters. We integrate field observations, detailed SEM and petrographic observations, geochemical models, (U-Th)/He and Ar/Ar dating, and other data to develop interpretations of the formation of these deposits. SEM imaging shows that sandstone matrix cement adjacent to the faults follows two precipitation sequences: Fe-oxide followed by barite and Fe-oxide followed by Mn-oxide. Dense oxide layers also accumulated in cm-scale fractures near faults, and show the following precipitation sequence: Fe-oxide, barite, Ba rich Mn-oxide, and pure Mn-oxide. The latter sequence is observed at larger scale across faults in one site in Flat Iron Mesa. Our new He dates for Mn-oxides are 1.7-2.9 Ma while Fe-oxide dates are 2.7-3.0 Ma. If these dates represent formation ages, they are consistent with the interpreted precipitation sequence but would require protracted mineralization over Ma-timescales. Alternatively, they may represent varying degrees of He retentivity in earlier formed deposits. Previous Ar/Ar dates have been interpreted as a 20-25 Ma formation age. Ongoing Ar/Ar and He diffusion studies will resolve this discordance. Assuming the previous Ar dates do not reflect contamination by detrital K-bearing phases and do reflect oxide formation, potential interpretations for the younger He ages include recent U-Th addition, recrystallization, later oxide growth, or large diffusive He loss at low temperatures.

Reaction of azides and enolisable aldehydes under the catalysis of organic bases and Cinchona based quaternary ammonium salts.

PubMed

Destro, Dario; Sanchez, Sandra; Cortigiani, Mauro; Adamo, Mauro F A

2017-06-21

Herein we report a two-step sequence for the preparation of amides starting from azides and enolisable aldehydes. The reaction proceeded via the formation of triazoline intermediates that were converted into amides via Lewis acid catalysis. Preliminary studies on the preparation of triazolines under chiral phase transfer catalysis are also presented, demonstrating that enantioenriched amides could be prepared from achiral aldehydes in moderate to low enantioselectivity.

Digestibility of gluten proteins is reduced by baking and enhanced by starch digestion

PubMed Central

Pan, Xiaoyan; Bellido, Vincent; Toole, Geraldine A.; Gates, Fred K.; Wickham, Martin S. J.; Shewry, Peter R.; Bakalis, Serafim; Padfield, Philip; Mills, E. N. Clare

2015-01-01

Scope Resistance of proteins to gastrointestinal digestion may play a role in determining immune‐mediated adverse reactions to foods. However, digestion studies have largely been restricted to purified proteins and the impact of food processing and food matrices on protein digestibility is poorly understood. Methods and results Digestibility of a total gliadin fraction (TGF), flour (cv Hereward), and bread was assessed using in vitro batch digestion with simulated oral, gastric, and duodenal phases. Protein digestion was monitored by SDS‐PAGE and immunoblotting using monoclonal antibodies specific for celiac‐toxic sequences (QQSF, QPFP) and starch digestion by measuring undigested starch. Whereas the TGF was rapidly digested during the gastric phase the gluten proteins in bread were virtually undigested and digested rapidly during the duodenal phase only if amylase was included. Duodenal starch digestion was also slower in the absence of duodenal proteases. Conclusion The baking process reduces the digestibility of wheat gluten proteins, including those containing sequences active in celiac disease. Starch digestion affects the extent of protein digestion, probably because of gluten‐starch complex formation during baking. Digestion studies using purified protein fractions alone are therefore not predictive of digestion in complex food matrices. PMID:26202208

The Outer Planetary Mission Design Project

NASA Astrophysics Data System (ADS)

Benfield, Michael; Turner, M. W.

2010-10-01

With the recent focus from the planetary science community on the outer planets of the solar system, The University of Alabama in Huntsville Integrated Product Team program is embarking on a new challenge to develop an outer planetary mission for the academic year 2010-2011. Currently four bodies are of interest for this mission: Titan, Europa, Triton, and Enceledus, with one body being chosen by the instructors by the beginning of the fall semester. This project will use the 2010 Discovery Announcement of Opportunity as its Request for Proposal (RFP). All of the teams competing in this project will use the AO to respond with a proposal to the instructors for their proposed mission and spacecraft concept. The project employs the two-semester design sequence of the IPT program to provide a framework for the development of this mission. This sequence is divided into four phases. Phase 1 - Requirements Development - focuses on the development of both the scientific and engineering requirements of the mission. During this phase the teams work very closely with the PI organization, represented by the College of Charleston. Phase 2 - Team Formation and Architecture Development - concentrates on the assessment of the overall mission architecture from the launch vehicle to the ground operations of the proposed spacecraft. Phase 3 - System Definition - provides for spacecraft subsystem trade studies and further refinement of the specific spacecraft to meet the scientific requirements and objectives developed in Phase 1. Phase 4 - Design - is the phase where the engineers provide the spacecraft design that is required for the mission of interest. At the conclusion of Phases 2 and 4, an external review board evaluates the proposed designs and chooses one winner of the competition.

Phosphodiester-mediated reaction of cisplatin with guanine in oligodeoxyribonucleotides.

PubMed

Campbell, Meghan A; Miller, Paul S

2008-12-02

The cancer chemotherapeutic agent cis-diamminedichloroplatinum(II) or cisplatin reacts primarily with guanines in DNA to form 1,2-Pt-GG and 1,3-Pt-GNG intrastrand cross-links and, to a lesser extent, G-G interstrand cross-links. Recent NMR evidence has suggested that cisplatin can also form a coordination complex with the phosphodiester internucleotide linkage of DNA. We have examined the effects of the phosphodiester backbone on the reactions of cisplatin with oligodeoxyribonucleotides that lack or contain a GTG sequence. Cisplatin forms a stable adduct with TpT that can be isolated by reversed phase HPLC. The cis-Pt-TpT adduct contains a single Pt, as determined by atomic absorption spectroscopy (AAS) and by electrospray ionization mass spectrometry (ESI-MS), and is resistant to digestion by snake venom phosphodiesterase. Treatment of the adduct with sodium cyanide regenerates TpT. Similar adduct formation was observed when T(pT)(8) was treated with cisplatin, but not when the phosphodiester linkages of T(pT)(8) were replaced with methylphosphonate groups. These results suggest that the platinum may be coordinated with the oxygens of the thymine and possibly with those of the phosphodiester group. As expected, reaction of a 9-mer containing a GTG sequence with cisplatin yielded an adduct that contained a 1,3-Pt-GTG intrastrand cross-link. However, we found that the number and placement of phosphodiesters surrounding a GTG sequence significantly affected intrastrand cross-link formation. Increasing the number of negatively charged phosphodiesters in the oligonucleotide increased the amount of GTG platination. Surrounding the GTG sequence with nonionic methylphosphonate linkages inhibited or eliminated cross-link formation. These observations suggest that interactions between cisplatin and the negatively charged phosphodiester backbone may play an important role in facilitating platination of guanine nucleotides in DNA.

Modeling the formation of iron sulfide scales using thermodynamic simulation software

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

Anderko, A.; Shuler, P.J.

1998-12-31

A program has been developed for generating stability diagrams that concisely represent the thermodynamic state of multicomponent, multiphase aqueous systems in wide ranges of temperature and component concentrations. The diagrams are based on a thermodynamic model that combines the Helgeson-Kirkham-Flowers equation of state for standard-state properties with a solutions nonideality model based on the activity coefficient expressions developed by Bromley and Pitzer. The diagrams offer a flexible choice of independent variables, which include component concentrations in addition to the potential and pH. The stability diagrams are used to predict the conditions that favor the formation of stable and metastable ironmore » sulfide species, which are commonly deposited under oil field-related conditions. First, the diagrams have been applied to establish a sequence of transformations that iron sulfides undergo as they age. The predicted transformation sequences take into account environmental variables (e.g., hydrogen sulfide concentration, oxygen availability, etc.). The predictions are in agreement with experimental data on iron sulfide formation at the iron/solution interface and in bulk solution. The understanding of iron sulfide transformation sequences makes it possible to simulate experimental studies of H{sub 2}S/CO{sub 2} corrosion in the presence or absence of oxygen. A comparison with laboratory corrosion rate data under gas pipeline conditions indicates that the magnitude of corrosion rates can be correlated with the predicted stability of metastable iron sulfide phases.« less

Streptococcus mutans competence-stimulating peptide inhibits Candida albicans hypha formation.

PubMed

Jarosz, Lucja M; Deng, Dong Mei; van der Mei, Henny C; Crielaard, Wim; Krom, Bastiaan P

2009-11-01

The oral cavity is colonized by microorganisms growing in biofilms in which interspecies interactions take place. Streptococcus mutans grows in biofilms on enamel surfaces and is considered one of the main etiological agents of human dental caries. Candida albicans is also commonly found in the human oral cavity, where it interacts with S. mutans. C. albicans is a polymorphic fungus, and the yeast-to-hypha transition is involved in virulence and biofilm formation. The aim of this study was to investigate interkingdom communication between C. albicans and S. mutans based on the production of secreted molecules. S. mutans UA159 inhibited C. albicans germ tube (GT) formation in cocultures even when physically separated from C. albicans. Only S. mutans spent medium collected in the early exponential phase (4-h-old cultures) inhibited the GT formation of C. albicans. During this phase, S. mutans UA159 produces a quorum-sensing molecule, competence-stimulating peptide (CSP). The role of CSP in inhibiting GT formation was confirmed by using synthetic CSP and a comC deletion strain of S. mutans UA159, which lacks the ability to produce CSP. Other S. mutans strains and other Streptococcus spp. also inhibited GT formation but to different extents, possibly reflecting differences in CSP amino acid sequences among Streptococcus spp. or differences in CSP accumulation in the media. In conclusion, CSP, an S. mutans quorum-sensing molecule secreted during the early stages of growth, inhibits the C. albicans morphological switch.

Radiosensitivity in HeLa cervical cancer cells overexpressing glutathione S-transferase π 1

PubMed Central

YANG, LIANG; LIU, REN; MA, HONG-BIN; YING, MING-ZHEN; WANG, YA-JIE

2015-01-01

The aims of the present study were to investigate the effect of overexpressed exogenous glutathione S-transferase π 1 (GSTP1) gene on the radiosensitivity of the HeLa human cervical cancer cell line and conduct a preliminarily investigation into the underlying mechanisms of the effect. The full-length sequence of human GSTP1 was obtained by performing a polymerase chain reaction (PCR) using primers based on the GenBank sequence of GSTP1. Subsequently, the gene was cloned into a recombinant eukaryotic expression plasmid, and the resulting construct was confirmed by restriction analysis and DNA sequencing. A HeLa cell line that was stably expressing high levels of GSTP1 was obtained through stable transfection of the constructed plasmids using lipofectamine and screening for G418 resistance, as demonstrated by reverse transcription-PCR. Using the transfected HeLa cells, a colony formation assay was conducted to detect the influence of GSTP1 overexpression on the cell radiosensitivity. Furthermore, flow cytometry was used to investigate the effect of GSTP1 overexpression on cell cycle progression, with the protein expression levels of the cell cycle regulating factor cyclin B1 detected using western blot analysis. Colony formation and G2/M phase arrest in the GSTP1-expressing cells were significantly increased compared with the control group (P<0.01). In addition, the expression of cyclin B1 was significantly reduced in the GSTP1-expressing cells. These results demonstrated that increased expression of GSTP1 inhibits radiosensitivity in HeLa cells. The mechanism underlying this effect may be associated with the ability of the GSTP1 protein to reduce cyclin B1 expression, resulting in significant G2/M phase arrest. PMID:26622693

Radiosensitivity in HeLa cervical cancer cells overexpressing glutathione S-transferase π 1.

PubMed

Yang, Liang; Liu, Ren; Ma, Hong-Bin; Ying, Ming-Zhen; Wang, Ya-Jie

2015-09-01

The aims of the present study were to investigate the effect of overexpressed exogenous glutathione S-transferase π 1 ( GSTP1 ) gene on the radiosensitivity of the HeLa human cervical cancer cell line and conduct a preliminarily investigation into the underlying mechanisms of the effect. The full-length sequence of human GSTP1 was obtained by performing a polymerase chain reaction (PCR) using primers based on the GenBank sequence of GSTP1. Subsequently, the gene was cloned into a recombinant eukaryotic expression plasmid, and the resulting construct was confirmed by restriction analysis and DNA sequencing. A HeLa cell line that was stably expressing high levels of GSTP1 was obtained through stable transfection of the constructed plasmids using lipofectamine and screening for G418 resistance, as demonstrated by reverse transcription-PCR. Using the transfected HeLa cells, a colony formation assay was conducted to detect the influence of GSTP1 overexpression on the cell radiosensitivity. Furthermore, flow cytometry was used to investigate the effect of GSTP1 overexpression on cell cycle progression, with the protein expression levels of the cell cycle regulating factor cyclin B1 detected using western blot analysis. Colony formation and G 2 /M phase arrest in the GSTP1 -expressing cells were significantly increased compared with the control group (P<0.01). In addition, the expression of cyclin B1 was significantly reduced in the GSTP1 -expressing cells. These results demonstrated that increased expression of GSTP1 inhibits radiosensitivity in HeLa cells. The mechanism underlying this effect may be associated with the ability of the GSTP1 protein to reduce cyclin B1 expression, resulting in significant G 2 /M phase arrest.

Ternary eutectic dendrites: Pattern formation and scaling properties

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

Rátkai, László; Szállás, Attila; Pusztai, Tamás

2015-04-21

Extending previous work [Pusztai et al., Phys. Rev. E 87, 032401 (2013)], we have studied the formation of eutectic dendrites in a model ternary system within the framework of the phase-field theory. We have mapped out the domain in which two-phase dendritic structures grow. With increasing pulling velocity, the following sequence of growth morphologies is observed: flat front lamellae → eutectic colonies → eutectic dendrites → dendrites with target pattern → partitionless dendrites → partitionless flat front. We confirm that the two-phase and one-phase dendrites have similar forms and display a similar scaling of the dendrite tip radius with themore » interface free energy. It is also found that the possible eutectic patterns include the target pattern, and single- and multiarm spirals, of which the thermal fluctuations choose. The most probable number of spiral arms increases with increasing tip radius and with decreasing kinetic anisotropy. Our numerical simulations confirm that in agreement with the assumptions of a recent analysis of two-phase dendrites [Akamatsu et al., Phys. Rev. Lett. 112, 105502 (2014)], the Jackson-Hunt scaling of the eutectic wavelength with pulling velocity is obeyed in the parameter domain explored, and that the natural eutectic wavelength is proportional to the tip radius of the two-phase dendrites. Finally, we find that it is very difficult/virtually impossible to form spiraling two-phase dendrites without anisotropy, an observation that seems to contradict the expectations of Akamatsu et al. Yet, it cannot be excluded that in isotropic systems, two-phase dendrites are rare events difficult to observe in simulations.« less

Molecular dynamics studies of defect formation during heteroepitaxial growth of InGaN alloys on (0001) GaN surfaces

DOE PAGES

Gruber, J.; Zhou, X. W.; Jones, R. E.; ...

2017-05-15

Here, we investigate the formation of extended defects during molecular-dynamics (MD) simulations of GaN and InGaN growth on (0001) and (11more » $$\\bar{2}$$0) wurtzite-GaN surfaces. The simulated growths are conducted on an atypically large scale by sequentially injecting nearly a million individual vapor-phase atoms towards a fixed GaN surface; we apply time-and-position-dependent boundary constraints that vary the ensemble treatments of the vapor-phase, the near-surface solid-phase, and the bulk-like regions of the growing layer. The simulations employ newly optimized Stillinger-Weber In-Ga-N-system potentials, wherein multiple binary and ternary structures are included in the underlying density-functional-theory training sets, allowing improved treatment of In-Ga-related atomic interactions. To examine the effect of growth conditions, we study a matrix of >30 different MD-growth simulations for a range of InxGa1-xN-alloy compositions (0 ≤ x ≤ 0.4) and homologous growth temperatures [0.50 ≤ T/T* m(x) ≤ 0.90], where T* m(x) is the simulated melting point. Growths conducted on polar (0001) GaN substrates exhibit the formation of various extended defects including stacking faults/polymorphism, associated domain boundaries, surface roughness, dislocations, and voids. In contrast, selected growths conducted on semi-polar (11$$\\bar{2}$$0) GaN, where the wurtzite-phase stacking sequence is revealed at the surface, exhibit the formation of far fewer stacking faults. We discuss variations in the defect formation with the MD growth conditions, and we compare the resulting simulated films to existing experimental observations in InGaN/GaN. Finally, while the palette of defects observed by MD closely resembles those observed in the past experiments, further work is needed to achieve truly predictive large-scale simulations of InGaN/GaN crystal growth using MD methodologies.« less

Molecular dynamics studies of defect formation during heteroepitaxial growth of InGaN alloys on (0001) GaN surfaces

NASA Astrophysics Data System (ADS)

Gruber, J.; Zhou, X. W.; Jones, R. E.; Lee, S. R.; Tucker, G. J.

2017-05-01

We investigate the formation of extended defects during molecular-dynamics (MD) simulations of GaN and InGaN growth on (0001) and ( 11 2 ¯ 0 ) wurtzite-GaN surfaces. The simulated growths are conducted on an atypically large scale by sequentially injecting nearly a million individual vapor-phase atoms towards a fixed GaN surface; we apply time-and-position-dependent boundary constraints that vary the ensemble treatments of the vapor-phase, the near-surface solid-phase, and the bulk-like regions of the growing layer. The simulations employ newly optimized Stillinger-Weber In-Ga-N-system potentials, wherein multiple binary and ternary structures are included in the underlying density-functional-theory training sets, allowing improved treatment of In-Ga-related atomic interactions. To examine the effect of growth conditions, we study a matrix of >30 different MD-growth simulations for a range of InxGa1-xN-alloy compositions (0 ≤ x ≤ 0.4) and homologous growth temperatures [0.50 ≤ T/T*m(x) ≤ 0.90], where T*m(x) is the simulated melting point. Growths conducted on polar (0001) GaN substrates exhibit the formation of various extended defects including stacking faults/polymorphism, associated domain boundaries, surface roughness, dislocations, and voids. In contrast, selected growths conducted on semi-polar ( 11 2 ¯ 0 ) GaN, where the wurtzite-phase stacking sequence is revealed at the surface, exhibit the formation of far fewer stacking faults. We discuss variations in the defect formation with the MD growth conditions, and we compare the resulting simulated films to existing experimental observations in InGaN/GaN. While the palette of defects observed by MD closely resembles those observed in the past experiments, further work is needed to achieve truly predictive large-scale simulations of InGaN/GaN crystal growth using MD methodologies.

Molecular dynamics studies of defect formation during heteroepitaxial growth of InGaN alloys on (0001) GaN surfaces.

PubMed

Gruber, J; Zhou, X W; Jones, R E; Lee, S R; Tucker, G J

2017-05-21

We investigate the formation of extended defects during molecular-dynamics (MD) simulations of GaN and InGaN growth on (0001) and ([Formula: see text]) wurtzite-GaN surfaces. The simulated growths are conducted on an atypically large scale by sequentially injecting nearly a million individual vapor-phase atoms towards a fixed GaN surface; we apply time-and-position-dependent boundary constraints that vary the ensemble treatments of the vapor-phase, the near-surface solid-phase, and the bulk-like regions of the growing layer. The simulations employ newly optimized Stillinger-Weber In-Ga-N-system potentials, wherein multiple binary and ternary structures are included in the underlying density-functional-theory training sets, allowing improved treatment of In-Ga-related atomic interactions. To examine the effect of growth conditions, we study a matrix of >30 different MD-growth simulations for a range of In x Ga 1-x N-alloy compositions (0 ≤  x  ≤ 0.4) and homologous growth temperatures [0.50 ≤  T/T * m ( x ) ≤ 0.90], where T * m ( x ) is the simulated melting point. Growths conducted on polar (0001) GaN substrates exhibit the formation of various extended defects including stacking faults/polymorphism, associated domain boundaries, surface roughness, dislocations, and voids. In contrast, selected growths conducted on semi-polar ([Formula: see text]) GaN, where the wurtzite-phase stacking sequence is revealed at the surface, exhibit the formation of far fewer stacking faults. We discuss variations in the defect formation with the MD growth conditions, and we compare the resulting simulated films to existing experimental observations in InGaN/GaN. While the palette of defects observed by MD closely resembles those observed in the past experiments, further work is needed to achieve truly predictive large-scale simulations of InGaN/GaN crystal growth using MD methodologies.

Effect of substrate availability on nitrous oxide production by deammonification processes under anoxic conditions

PubMed Central

Schneider, Yvonne; Beier, Maike; Rosenwinkel, Karl‐Heinz

2012-01-01

Summary Due to its high global warming potential, nitrous oxide (N2O) emissions from wastewater treatment processes have recently received a high degree of attention. Nevertheless, there is still a lack of information regarding the microbiological processes leading to N2O production. In this study, two lab‐scale sequencing batch reactors were operated with deammonification biomass to investigate the role of denitrification and the influence of substrate availability regarding N2O formation during the anoxic phase of deammonification. Three different operational phases were established: within the first phase conversion by anammox was favoured and after a transition phase, denitrification activity was promoted. Low nitrous oxide production was observed during stable operation aiming for anammox conversion. Pulsed inflow of the wastewater containing ammonium (NH4+) and nitrite (NO2‐) led to increased N2O production rates. Within the period of denitrification as dominating nitrogen conversion process, the nitrous oxide concentration level was higher during continuous inflow conditions, but the reaction to pulsed inflow was less pronounced. The results indicated that denitrification was responsible for N2O formation from the deammonification biomass. Operational settings to achieve suppression of denitrification processes to a large extend were deducted from the results of the experiments. PMID:22296600

3D Micro-tomography on Aggregates from the 2014- 2015 Eruption of Hunga Tonga-Hunga Ha'apai Volcano

NASA Astrophysics Data System (ADS)

Colombier, M.; Scheu, B.; Cronin, S. J.; Tost, M.; Dobson, K. J.; Dingwell, D. B.

2016-12-01

In December 2014- January 2015, a surtseyan eruption at Hunga Tonga-Hunga Ha'apai volcano (Tonga) formed a new island. Three main eruptive phases were distinguished by observation and deposits: (i) mound and cone construction, involving collapse of 300-600 m-high wet tephra jets, grain flows, slope-remobilisation and energetic surges, with little or no convective plume (ii) The upper cone-building phase with lower jets (mainly <300 m) but greater ash production (weak, steam-rich plumes to 6 km) and weak surges, and (iii) final phase with weak surge, fall and ballistic deposits with more vesicular pyroclasts producing proximal capping deposits. Most sampled deposits contain ash, lapilli and bombs, and lapilli-sized aggregates are ubiquitous. We used high-resolution 3D X-ray microcomputed tomography (XCT) to quantify the grain size distribution (GSD) and porosity by sampling multiple stratigraphic units within the main eruptive sequences. We visualized and quantified the internal structure of the aggregates to understand the evolution of this surtseyan eruption. We present here an overview of the textural information: porosity, vesicle size distribution and morphology as well as the variability of the aggregation features. Aggregates from the fall deposits of the early wet phase are mostly loosely packed, poorly-structured ash clusters. Aggregates from the early surge sequence and the main cone building phase dominantly exhibit a central particle coated by ash cluster material. Vesicles in the particles from the early fall deposits tend to be smaller and more isolated than in the particles from the surge sequence and the main cone building phase. The GSD of aggregates obtained by XCT is highly valuable to correct the total GSD of volcaniclastic deposits. The strong variations in the aggregation features across the eruption suggest a range of different formation and deposition mechanisms related to varying degrees of magma-water-interaction, which changed the morphology and textural properties of the individual particles.

Mesoarchean Banded Iron Formation sequences in Dixon Island-Cleaverville Formation, Pilbara Australia: Oxygenic signal from DXCL project

NASA Astrophysics Data System (ADS)

Kiyokawa, S.; Ito, T.; Ikehara, M.; Yamaguchi, K. E.; Naraoka, H.; Onoue, T.; Horie, K.; Sakamoto, R.; Aihara, Y.; Miki, T.

2013-12-01

The 3.2-3.1 Ga Dixon island-Cleaverville formations are well-preserved Banded Iron Formation (BIF) within hydrothermal oceanic sequence at oceanic island arc setting (Kiyokawa et al., 2002, 2006, 2012). The stratigraphy of the Dixon Island (3195+15Ma) -Cleaverville (3108+13Ma) formations shows the well preserved environmental condition at the Mesoarchean ocean floor. The stratigraphy of these formations are formed about volcano-sedimentary sequences with hydrothermal chert, black shale and banded iron formation to the top. Based on the scientific drilling of DXCL project at 2007 and 2011, detail lithology between BIF sequence was clearly understood. Four drilling holes had been done at coastal sites; the Dixon Island Formation is DX site (100m) and the Cleaverville Formation is CL2 (40m), CL1 (60m) and CL3 (200m) sites and from stratigraphic bottom to top. Coarsening and thickening upward black shale-BIF sequences are well preserved of the stratigraphy form the core samples. The Dixon Island Formation consists komatiite-rhyolite sequences with many hydrothermal veins and very fine laminated cherty rocks above them. The Cleaverville Formation contains black shale, fragments-bearing pyroclastic beds, white chert, greenish shale and BIF. The CL3 core, which drilled through BIF, shows siderite-chert beds above black shale identified before magnetite lamination bed. U-Pb SHRIMP data of the tuff in lower Dixon Island Formation is 3195+15 Ma and the pyroclastic sequence below the Cleaverville BIF is 3108+13 Ma. Sedimentation rate of these sequence is 2-8 cm/ 1000year. The hole section of the organic carbon rich black shales below BIF are similar amount of organic content and 13C isotope (around -30per mill). There are very weak sulfur MIF signal (less 0.2%) in these black shale sequence. Our result show that thick organic rich sediments may be triggered to form iron rich siderite and magnetite iron beds. The stratigraphy in this sequence quite resemble to other Iron formation (eg. Hamersley BIF). So we investigate that the Cleaverville iron formation, which is one of the best well known Mesoarchean iron formation, was already started cyanobacteria oxygen production system to used pre-syn iron sedimentation at anoxic oceanic condition.

Formation of aerobic granular sludge and the influence of the pH on sludge characteristics in a SBR fed with brewery/bottling plant wastewater.

PubMed

Stes, Hannah; Aerts, Sven; Caluwé, Michel; Dobbeleers, Thomas; Wuyts, Sander; Kiekens, Filip; D'aes, Jolien; De Langhe, Piet; Dries, Jan

2018-05-01

A laboratory-scale sequencing batch reactor (SBR) was operated for 450 days to assess aerobic granule formation when treating brewery/bottling plant wastewater by consistent application of a feast/famine regime. The experiment was divided into three major periods according to the different operational conditions: (I) no pH control and strong fluctuations in organic loading rate (OLR) (1.18 ± 0.25 kgCOD·(m 3 ·day) -1 ), (II) pH control and aeration control strategy to reduce OLR fluctuations (1.45 ± 0.65 kgCOD·(m 3 ·day) -1 ) and (III) no pH control and stable OLR (1.42 ± 0.18 kgCOD·(m 3 ·day) -1 ). Aerobic granule formation was successful after 80 days and maintained during the subsequent 380 days. The aerobic granular sludge was characterized by SVI 5 and SVI 30 values below 60 mL.g -1 and dominated by granular, dense structures. An oxygen uptake rate based aeration control strategy insured endogenous respiration at the end of the aerobic phase, resulting in stable SBR operation when the influent composition fluctuated. The quantitative polymerase chain reaction results show no significant enrichment of Accumulibacter or Competibacter during the granulation process. The 16S rRNA sequencing results indicate enrichment of other, possibly important species during aerobic granule formation while treating brewery wastewaters.

Pressure-induced Structural Transformations in LanthanideTitanates: La2TiO5 and Nd2TiO5

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

F Zhang; J Wang; M Lang

The structure of orthorhombic rare earth titanates of La{sub 2}TiO{sub 5} and Nd{sub 2}TiO{sub 5}, where Ti cations are in five-fold coordination with oxygen, has been studied at high pressures by X-ray diffraction (XRD), Raman scattering measurements, and quantum mechanical calculations. Both XRD and Raman results indicated two pressure-induced phase transitions during the process. An orthorhombic super cell (a x b x 2c) formed at a pressure between 6 and 10 GPa, and then transformed to a hexagonal high-pressure phase accompanied by partial decomposition. The hexagonal high-pressure phase is quenchable. Detailed structural analysis indicated that the five-coordinated TiO{sub 5} polyhedramore » remain during the formation of super cell, but the orthorhombic-to-hexagonal phase transition at high pressures is a reconstructive process, and the five-fold Ti-O coordination increased to more than 6. This phase transition sequence was verified by quantum mechanical calculations.« less

Transformation and crystallization energetics of synthetic and biogenic amorphous calcium carbonate.

PubMed

Radha, A V; Forbes, Tori Z; Killian, Christopher E; Gilbert, P U P A; Navrotsky, Alexandra

2010-09-21

Amorphous calcium carbonate (ACC) is a metastable phase often observed during low temperature inorganic synthesis and biomineralization. ACC transforms with aging or heating into a less hydrated form, and with time crystallizes to calcite or aragonite. The energetics of transformation and crystallization of synthetic and biogenic (extracted from California purple sea urchin larval spicules, Strongylocentrotus purpuratus) ACC were studied using isothermal acid solution calorimetry and differential scanning calorimetry. Transformation and crystallization of ACC can follow an energetically downhill sequence: more metastable hydrated ACC → less metastable hydrated ACC ⇒ anhydrous ACC ∼ biogenic anhydrous ACC ⇒ vaterite → aragonite → calcite. In a given reaction sequence, not all these phases need to occur. The transformations involve a series of ordering, dehydration, and crystallization processes, each lowering the enthalpy (and free energy) of the system, with crystallization of the dehydrated amorphous material lowering the enthalpy the most. ACC is much more metastable with respect to calcite than the crystalline polymorphs vaterite or aragonite. The anhydrous ACC is less metastable than the hydrated, implying that the structural reorganization during dehydration is exothermic and irreversible. Dehydrated synthetic and anhydrous biogenic ACC are similar in enthalpy. The transformation sequence observed in biomineralization could be mainly energetically driven; the first phase deposited is hydrated ACC, which then converts to anhydrous ACC, and finally crystallizes to calcite. The initial formation of ACC may be a first step in the precipitation of calcite under a wide variety of conditions, including geological CO(2) sequestration.

Petrography and chemistry of SiO 2 filling phases in the amethyst geodes from the Serra Geral Formation deposit, Rio Grande do Sul, Brazil

NASA Astrophysics Data System (ADS)

Commin-Fischer, Adriane; Berger, Gilles; Polvé, Mireille; Dubois, Michel; Sardini, Paul; Beaufort, Daniel; Formoso, Milton

2010-04-01

The filling process of amethyst-bearing geodes from Serra Geral Formation basalts, Brazil, is investigated by different methods performed on the SiO 2 filling phases. Image analysis of quartz-amethyst deposits suggests a single growing mechanism ruled by geometric selection of randomly oriented crystals. Microthermometry of fluid inclusions reveals formation temperature lower than 100 °C, probably lower than 50 °C, and fluid salinity as high as 3 mass% NaCl eq. Composition in REE and trace-elements measured by ICP-MS on acid-digested or laser-ablated samples indicates a common genesis for amethyst, quartz and chalcedony, as well as the absence of significant variations from one geode to another. 87Sr/ 86Sr data on chalcedony shows that both the host basalt or the Botucatu sandstone are possible silica sources. These data, combined with thermo-kinetic considerations, permit us to discuss the filling process. We argue in favor of the contribution of a mineralized fluid of hydrothermal origin producing a regional silica source which decreased with time. The observed mineral sequence is related to the depletion of silica in the solution.

Nucleation and Growth of Tetrataenite (FeNi) in Meteorites

NASA Astrophysics Data System (ADS)

Goldstein, J. I.; Williams, D. B.; Zhang, J.

1992-07-01

The mineral tetrataenite (ordered FeNi) has been observed in chondrites, stony irons, and iron meteorites (1). FeNi is an equilibrium phase in the Fe-Ni phase diagram (Figure 1) and orders to tetrataenite at ~320 degrees C (2). The phase forms at temperatures at or below the eutectoid temperature (~400 degrees C) where taenite (gamma) transforms to kamacite (alpha) plus FeNi (gamma"). An understanding of the formation of tetrataenite can lead to a new method for determining cooling rates at low temperatures (<400 degrees C) for all types of meteorites. In a recent study of plessite in iron meteorites (3), two transformation sequences for the formation of tetrataenite were observed. In either sequence, during the cooling process, the taenite (gamma) phase initially undergoes a diffusionless transformation to a martensite (alpha, bcc) phase without a composition change. The martensite then decomposes either above or below the eutectoid temperature (~400 degrees C) during cooling or upon subsequent reheating. During martensite decomposition above the eutectoid, the taenite (gamma) phase nucleates by the reaction alpha(sub)2 ---> alpha + gamma and grows under volume diffusion control. The Ni composition of the taenite increases continuously following the equilibrium gamma/alpha + gamma boundary while the Ni composition of the kamacite matrix decreases following the alpha/alpha + gamma phase boundary (2), see Figure 1. Below the eutectoid temperature, the precipitate composition follows the equilibrium gamma"/alpha + gamma" boundary and reaches ~52 wt% Ni, the composition of FeNi, gamma". The kamacite (alpha) matrix composition approaches ~4 to 5 wt% Ni. The ordering transformation starts at ~320 degrees C forming the tetrataenite phase. During martensite decomposition below the eutectoid temperature, FeNi should form directly by the reaction alpha2 --> alpha + gamma" (FeNi). If this transformation sequence occurs, then the composition of kamacite and tetrataenite should also be given by the alpha/alpha + gamma" and gamma"/alpha + gamma" boundaries of the Fe-Ni phase diagram (Figure 1). However, the Ni content of kamacite and tetrataenite in black plessite, which forms below 400 degrees C, is ~10 wt% in kamacite and ~57 to 60 wt% in tetrataenite, much higher than the values given by the equilibrium phase diagram (3). It has been observed experimentally (4) that the Ni composition of the gamma phase formed by martensite decomposition below 400 degrees C lies along a metastable extension of the high temperature gamma/alpha + gamma phase boundary, Figure 2. Therefore, the FeNi phase formed by alpha(sub)2 decomposition below 400 degrees C has a non-equilibrium Ni content, >50 to 56 wt%. The growth or thickening of the FeNi phase occurs by some combination of interface and diffusion control (3). References: (1) Clarke R. S. and Scott E. R. D. (1980) Amer. Mineral. 65, 624-630. (2) Reuter K. B., Williams D. B., and Goldstein J. I. (1989) Met. Trans. 20A, 719-725. (3) Zhang J., Williams D. B. and Goldstein J. I. (1992) Submitted to Geochim. Cosmochim. Acta. (4) Zhang J., Williams L). B. and Goldstein J. I. (1992) Submitted to Met. Trans. Figure 1, which in the hard copy appears here, is an Fe-Ni phase diagram (2). Figure 2, which in the hard copy appears here, shows measured FeNi composition from heat-treated alloys (4).

Paleoweathering features in the Sergi Formation (Jurassic-Cretaceous), northeastern Brazil, and implications for hydrocarbon exploration

NASA Astrophysics Data System (ADS)

Pierini, Cristina; Mizusaki, Ana M.; Pimentel, Nuno; Faccini, Ubiratan F.; Scherer, Claiton M. S.

2010-03-01

Paleoweathering in the Sergi Formation has been classified and analyzed to ascertain its origin and relationship with stratigraphic evolution. The Sergi Formation belongs to the pre-rift sequence of the Recôncavo Basin (northeastern Brazil) and comprises a complex association of eolian and fluvial sandstones and lacustrine mudstones. This formation can be subdivided into three depositional sequences bounded by regional unconformities. Four paleoweathering types, each one related to a distinct origin, have been described in the Sergi Formation: (1) textural mottling, which is distinguished by alternating rock colors as a result of the iron oxide mobilization within mineral phases that evolved under alternating oxidation (yellowish, brownish and reddish shades) and reduction (grayish or greenish hues) conditions; (2) non-textural mottling, which displays a discoloration pattern that is independent of the original rock texture; (3) carbonate concentrations, usually related to carbonate nodule formation, which display a massive internal structure that reveals their origin through continuous growth or crystallization; and (4) banded carbonates (silicified), associated with the beginning of regular surface formation due to the chemical precipitation of carbonates within lacustrine environments. Both mottling color motifs and carbonate accumulation usually represent groundwater oscillation rather than pedogenesis. Only carbonate intraclasts and banded carbonate (silicified) have their origin ascribed to pedogenesis sensu stricto, although the carbonate intraclasts do not represent soil deposits in situ, but calcretes eroded from areas close to channels, and the banded carbonates (silicified) have strong diagenetic modifications. Therefore, it is reasonable to assume that fluvial and meteoric water have controlled paleoweathering evolution as well as deposition, yet both aspects are ruled by the same mechanisms (relief, sedimentation rate and, above all, climate).

Duplex Heterogeneous Nucleation Behavior of Precipitates in C-Mn Steel Containing Sn

NASA Astrophysics Data System (ADS)

Sun, Guilin; Tao, Sufen

2018-04-01

The two successive heterogeneous nucleation behaviors of FeSn2-MnS-Al2O3 complex precipitates in ultrahigh Sn-bearing steel were investigated. First, Al2O3 was the nucleation site of the MnS at the end of solidification. Then, FeSn2 nucleated heterogeneously on the MnS particles that nucleated on the Al2O3 particles. The formation sequence of the precipitated phase caused the duplex heterogeneous nucleation to occur consecutively at most twice.

Reaction paths in the system Al 2O 3-hBN-Y

NASA Astrophysics Data System (ADS)

Reichert, K.; Oreshina, O.; Cremer, R.; Neuschütz, D.

2001-07-01

As part of the investigations on the suitability of a new concept for a tailored fiber-matrix interface in sapphire fiber reinforced NiAl matrix composites for application as a high-temperature structural material, the interfacial reactions in the system alumina-hexagonal boron nitride-yttrium (Al 2O 3-hBN-Y) have been examined in the temperature range of 1100-1300°C. For this, alumina substrates were coated with hBN by means of CVD and subsequently with sputter deposited yttrium. Afterwards the samples were annealed for up to 16 h under inert atmosphere. Grazing incidence X-ray diffraction (GIXRD) served to analyze the phases formed by diffusion processes in the reaction zone. The peak intensities in these diffraction patterns were used to evaluate the sequence of phases formed due to diffusion and reaction. After the initial formation of YN and YB 2, the phases Y 2O 3, Al 2Y, and YB 4 were observed. Even longer annealing times or higher temperatures, respectively, led to the formation of the ternary oxides YAlO 3 and Y 3Al 5O 12 as well as metallic aluminum.

The physiological and pathological biophysics of phase separation and gelation of RNA binding proteins in amyotrophic lateral sclerosis and fronto-temporal lobar degeneration.

PubMed

St George-Hyslop, Peter; Lin, Julie Qiaojin; Miyashita, Akinori; Phillips, Emma C; Qamar, Seema; Randle, Suzanne J; Wang, GuoZhen

2018-04-30

Many RNA binding proteins, including FUS, contain moderately repetitive, low complexity, intrinsically disordered domains. These sequence motifs have recently been found to underpin reversible liquid: liquid phase separation and gelation of these proteins, permitting them to reversibly transition from a monodispersed state to liquid droplet- or hydrogel-like states. This function allows the proteins to serve as scaffolds for the formation of reversible membraneless intracellular organelles such as nucleoli, stress granules and neuronal transport granules. Using FUS as an example, this review examines the biophysics of this physiological process, and reports on how mutations and changes in post-translational state alter phase behaviour, and lead to neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Copyright © 2018. Published by Elsevier B.V.

Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

PubMed

Rehm, Charlotte; Wurmthaler, Lena A; Li, Yuanhao; Frickey, Tancred; Hartig, Jörg S

2015-01-01

In prokaryotes simple sequence repeats (SSRs) with unit sizes of 1-5 nucleotides (nt) are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6-9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4) structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type GGGNATC in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc), Xanthomonas axonopodis pv. citri str. 306 (Xac), and Nostoc sp. strain PCC7120 (Ana). In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs) and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria.

Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

PubMed Central

Rehm, Charlotte; Wurmthaler, Lena A.; Li, Yuanhao; Frickey, Tancred; Hartig, Jörg S.

2015-01-01

In prokaryotes simple sequence repeats (SSRs) with unit sizes of 1–5 nucleotides (nt) are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6–9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4) structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type GGGNATC in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc), Xanthomonas axonopodis pv. citri str. 306 (Xac), and Nostoc sp. strain PCC7120 (Ana). In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs) and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria. PMID:26695179

Inverted temperature sequences: role of deformation partitioning

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

37 CFR 1.824 - Form and format for nucleotide and/or amino acid sequence submissions in computer readable form.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Form and format for... And/or Amino Acid Sequences § 1.824 Form and format for nucleotide and/or amino acid sequence... Code for Information Interchange (ASCII) text. No other formats shall be allowed. (3) The computer...

SNMR pulse sequence phase cycling

DOEpatents

Walsh, David O; Grunewald, Elliot D

2013-11-12

Technologies applicable to SNMR pulse sequence phase cycling are disclosed, including SNMR acquisition apparatus and methods, SNMR processing apparatus and methods, and combinations thereof. SNMR acquisition may include transmitting two or more SNMR pulse sequences and applying a phase shift to a pulse in at least one of the pulse sequences, according to any of a variety cycling techniques. SNMR processing may include combining SNMR from a plurality of pulse sequences comprising pulses of different phases, so that desired signals are preserved and indesired signals are canceled.

Cooperation of phosphates and carboxylates controls calcium oxalate crystallization in ultrafiltered urine.

PubMed

Grohe, Bernd; Chan, Brian P H; Sørensen, Esben S; Lajoie, Gilles; Goldberg, Harvey A; Hunter, Graeme K

2011-10-01

Osteopontin (OPN) is one of a group of proteins found in urine that are believed to limit the formation of kidney stones. In the present study, we investigate the roles of phosphate and carboxylate groups in the OPN-mediated modulation of calcium oxalate (CaOx), the principal mineral phase found in kidney stones. To this end, crystallization was induced by addition of CaOx solution to ultrafiltered human urine containing either human kidney OPN (kOPN; 7 consecutive carboxylates, 8 phosphates) or synthesized peptides corresponding to residues 65-80 (pSHDHMDDDDDDDDDGD; pOPAR) or 220-235 (pSHEpSTEQSDAIDpSAEK; P3) of rat bone OPN. Sequence 65-80 was also synthesized without the phosphate group (OPAR). Effects on calcium oxalate monohydrate (COM) and dihydrate (COD) formation were studied by scanning electron microscopy. We found that controls form large, partly intergrown COM platelets; COD was never observed. Adding any of the polyelectrolytes was sufficient to prevent intergrowth of COM platelets entirely, inhibiting formation of these platelets strongly, and inducing formation of the COD phase. Strongest effects on COM formation were found for pOPAR and OPAR followed by kOPN and then P3, showing that acidity and hydrophilicity are crucial in polyelectrolyte-affected COM crystallization. At higher concentrations, OPAR also inhibited COD formation, while P3, kOPN and, in particular, pOPAR promoted COD, a difference explainable by the variations of carboxylate and phosphate groups present in the molecules. Thus, we conclude that carboxylate groups play a primary role in inhibiting COM formation, but phosphate and carboxylate groups are both important in initiating and promoting COD formation.

Analysis of xylem formation in pine by cDNA sequencing

NASA Technical Reports Server (NTRS)

Allona, I.; Quinn, M.; Shoop, E.; Swope, K.; St Cyr, S.; Carlis, J.; Riedl, J.; Retzel, E.; Campbell, M. M.; Sederoff, R.;

A High-Throughput Process for the Solid-Phase Purification of Synthetic DNA Sequences

PubMed Central

Grajkowski, Andrzej; Cieślak, Jacek; Beaucage, Serge L.

2017-01-01

An efficient process for the purification of synthetic phosphorothioate and native DNA sequences is presented. The process is based on the use of an aminopropylated silica gel support functionalized with aminooxyalkyl functions to enable capture of DNA sequences through an oximation reaction with the keto function of a linker conjugated to the 5′-terminus of DNA sequences. Deoxyribonucleoside phosphoramidites carrying this linker, as a 5′-hydroxyl protecting group, have been synthesized for incorporation into DNA sequences during the last coupling step of a standard solid-phase synthesis protocol executed on a controlled pore glass (CPG) support. Solid-phase capture of the nucleobase- and phosphate-deprotected DNA sequences released from the CPG support is demonstrated to proceed near quantitatively. Shorter than full-length DNA sequences are first washed away from the capture support; the solid-phase purified DNA sequences are then released from this support upon reaction with tetra-n-butylammonium fluoride in dry dimethylsulfoxide (DMSO) and precipitated in tetrahydrofuran (THF). The purity of solid-phase-purified DNA sequences exceeds 98%. The simulated high-throughput and scalability features of the solid-phase purification process are demonstrated without sacrificing purity of the DNA sequences. PMID:28628204

Reversed-phase ion-pair liquid chromatography method for purification of duplex DNA with single base pair resolution

PubMed Central

Wysoczynski, Christina L.; Roemer, Sarah C.; Dostal, Vishantie; Barkley, Robert M.; Churchill, Mair E. A.; Malarkey, Christopher S.

2013-01-01

Obtaining quantities of highly pure duplex DNA is a bottleneck in the biophysical analysis of protein–DNA complexes. In traditional DNA purification methods, the individual cognate DNA strands are purified separately before annealing to form DNA duplexes. This approach works well for palindromic sequences, in which top and bottom strands are identical and duplex formation is typically complete. However, in cases where the DNA is non-palindromic, excess of single-stranded DNA must be removed through additional purification steps to prevent it from interfering in further experiments. Here we describe and apply a novel reversed-phase ion-pair liquid chromatography purification method for double-stranded DNA ranging in lengths from 17 to 51 bp. Both palindromic and non-palindromic DNA can be readily purified. This method has the unique ability to separate blunt double-stranded DNA from pre-attenuated (n-1, n-2, etc) synthesis products, and from DNA duplexes with single base pair overhangs. Additionally, palindromic DNA sequences with only minor differences in the central spacer sequence of the DNA can be separated, and the purified DNA is suitable for co-crystallization of protein–DNA complexes. Thus, double-stranded ion-pair liquid chromatography is a useful approach for duplex DNA purification for many applications. PMID:24013567

Pulse sequences for efficient multi-cycle terahertz generation in periodically poled lithium niobate.

PubMed

Ravi, Koustuban; Schimpf, Damian N; Kärtner, Franz X

2016-10-31

The use of laser pulse sequences to drive the cascaded difference frequency generation of high energy, high peak-power and multi-cycle terahertz pulses in cryogenically cooled (100 K) periodically poled Lithium Niobate is proposed and studied. Detailed simulations considering the coupled nonlinear interaction of terahertz and optical waves (or pump depletion), show that unprecedented optical-to-terahertz energy conversion efficiencies > 5%, peak electric fields of hundred(s) of mega volts/meter at terahertz pulse durations of hundred(s) of picoseconds can be achieved. The proposed methods are shown to circumvent laser induced damage limitations at Joule-level pumping by 1µm lasers to enable multi-cycle terahertz sources with pulse energies > 10 milli-joules. Various pulse sequence formats are proposed and analyzed. Numerical calculations for periodically poled structures accounting for cascaded difference frequency generation, self-phase-modulation, cascaded second harmonic generation and laser induced damage are introduced. The physics governing terahertz generation using pulse sequences in this high conversion efficiency regime, limitations and practical considerations are discussed. It is shown that varying the poling period along the crystal length and further reduction of absorption can lead to even higher energy conversion efficiencies >10%. In addition to numerical calculations, an analytic formulation valid for arbitrary pulse formats and closed-form expressions for important cases are presented. Parameters optimizing conversion efficiency in the 0.1-1 THz range, the corresponding peak electric fields, crystal lengths and terahertz pulse properties are furnished.

Chirality- and sequence-selective successive self-sorting via specific homo- and complementary-duplex formations

PubMed Central

Makiguchi, Wataru; Tanabe, Junki; Yamada, Hidekazu; Iida, Hiroki; Taura, Daisuke; Ousaka, Naoki; Yashima, Eiji

2015-01-01

Self-recognition and self-discrimination within complex mixtures are of fundamental importance in biological systems, which entirely rely on the preprogrammed monomer sequences and homochirality of biological macromolecules. Here we report artificial chirality- and sequence-selective successive self-sorting of chiral dimeric strands bearing carboxylic acid or amidine groups joined by chiral amide linkers with different sequences through homo- and complementary-duplex formations. A mixture of carboxylic acid dimers linked by racemic-1,2-cyclohexane bis-amides with different amide sequences (NHCO or CONH) self-associate to form homoduplexes in a completely sequence-selective way, the structures of which are different from each other depending on the linker amide sequences. The further addition of an enantiopure amide-linked amidine dimer to a mixture of the racemic carboxylic acid dimers resulted in the formation of a single optically pure complementary duplex with a 100% diastereoselectivity and complete sequence specificity stabilized by the amidinium–carboxylate salt bridges, leading to the perfect chirality- and sequence-selective duplex formation. PMID:26051291

Crystal grain growth at the α -uranium phase transformation in praseodymium

NASA Astrophysics Data System (ADS)

Cunningham, Nicholas C.; Velisavljevic, Nenad; Vohra, Yogesh K.

2005-01-01

Structural phase transformations under pressure are examined in praseodymium metal for the range 0-40GPa at ambient temperature. Pressure was generated with a diamond-anvil cell, and data were collected using high-resolution synchrotron x-ray diffraction and the image plate technique. The structural sequence double hexagonal close packed (dhcp)→face centered cubic (fcc)→distorted-fcc (d-fcc)→ α -uranium (α-U) is observed with increasing pressure. Rietveld refinement of all crystallographic phases provided confirmation of the hR24 structure for the d-fcc phase while the previously reported monoclinic phase between the d-fcc and the α-U phase was not confirmed. We observe dramatic crystal grain growth during the volume collapse concurrent with the symmetry-lowering transition to the α-U structure. No preferred orientation axis is observed, and the formation process for these large grains is expected to be via a nucleation and growth mechanism. An analogous effect in rare earth metal cerium suggests that the grain growth during transformation to the α-U structure is a common occurrence in f -electron metals at high pressures.

Mesoarchean black shale -iron sedimentary sequences in Cleaverville Formation, Pilbara Australia: drilling preliminary result of DXCL2

NASA Astrophysics Data System (ADS)

Kiyokawa, S.; Ito, T.; Ikehara, M.; Yamaguchi, K. E.; Onoue, T.; Horie, K.; Sakamoto, R.; Teraji, S.; Aihara, Y.

2012-12-01

The 3.2-3.1 Ga Dixon island-Cleaverville formations are well-preserved hydrothermal oceanic sequence at oceanic island arc setting (Kiyokawa et al., 2002, 2006, 2012). The Dixon Island (3195+15 Ma) - Cleaverville (3108+13 Ma) formations formed volcano-sedimentary sequences with hydrothermal chert, black shale and banded iron formation to the top. Based on the scientific drilling as DXCL1 at 2007 and DXCL2 at 2011, lithology was clearly understood. Four drilling holes had been done at coastal sites; the Dixon Island Formation is DX site (100m) and the Cleaverville Formation is CL2 (40m), CL1 (60m) and CL3 (200m) sites and from stratigraphic bottom to top. These sequences formed coarsening and thickening upward black shale-BIF sequences. The Dixon Island Formation consists komatiite-rhyolite sequences with many hydrothermal veins and very fine laminated cherty rocks above them. The Cleaverville Formation contains black shale, fragments-bearing pyroclastic beds, white chert, greenish shale and BIF. Especially, CL3 core, which drilled through the Iron formation, shows siderite-chert beds above black shale identified before magnetite lamination bed. The magnetite bed formed very thin laminated bed with siderite lamination. This magnetite bed was covered by black shale beds again. New U-Pb SHRIMP data of the pyroclastic in black shale is 3109Ma. Estimated 2-8 cm/1000year sedimentation rate are identified in these sequences. Our preliminary result show that siderite and chert layers formed before magnetite iron sedimentation. The lower-upper sequence of organic carbon rich black shales are similar amount of organic content and 13C isotope (around -30per mill). So we investigate that the Archean iron formation, especially Cleaverville iron formation, was highly related by hydrothermal input and started pre-syn iron sedimentation at anoxic oceanic condition.

Star formation with disc accretion and rotation. I. Stars between 2 and 22 M⊙ at solar metallicity

NASA Astrophysics Data System (ADS)

Haemmerlé, L.; Eggenberger, P.; Meynet, G.; Maeder, A.; Charbonnel, C.

2013-09-01

Context. The way angular momentum is built up in stars during their formation process may have an impact on their further evolution. Aims: In the framework of the cold disc accretion scenario, we study how angular momentum builds up inside the star during its formation for the first time and what the consequences are for its evolution on the main sequence (MS). Methods: Computation begins from a hydrostatic core on the Hayashi line of 0.7 M⊙ at solar metallicity (Z = 0.014) rotating as a solid body. Accretion rates depending on the luminosity of the accreting object are considered, which vary between 1.5 × 10-5 and 1.7 × 10-3 M⊙ yr-1. The accreted matter is assumed to have an angular velocity equal to that of the outer layer of the accreting star. Models are computed for a mass-range on the zero-age main sequence (ZAMS) between 2 and 22 M⊙. Results: We study how the internal and surface velocities vary as a function of time during the accretion phase and the evolution towards the ZAMS. Stellar models, whose evolution has been followed along the pre-MS phase, are found to exhibit a shallow gradient of angular velocity on the ZAMS. Typically, the 6 M⊙ model has a core that rotates 50% faster than the surface on the ZAMS. The degree of differential rotation on the ZAMS decreases when the mass increases (for a fixed value of vZAMS/vcrit). The MS evolution of our models with a pre-MS accreting phase show no significant differences with respect to those of corresponding models computed from the ZAMS with an initial solid-body rotation. Interestingly, there exists a maximum surface velocity that can be reached through the present scenario of formation for masses on the ZAMS larger than 8 M⊙. Typically, only stars with surface velocities on the ZAMS lower than about 45% of the critical velocity can be formed for 14 M⊙ models. Reaching higher velocities would require starting from cores that rotate above the critical limit. We find that this upper velocity limit is smaller for higher masses. In contrast, there is no restriction below 8 M⊙, and the whole domain of velocities to the critical point can be reached.

Conformation-Specific Infrared and Ultraviolet Spectroscopy of Cold [YAPAA+H]^{+} and [YGPAA+H]^{+} Ions: a Stereochemical "twist" on the β-HAIRPIN Turn

NASA Astrophysics Data System (ADS)

DeBlase, Andrew F.; Harrilal, Christopher P.; Lawler, John T.; Burke, Nicole L.; McLuckey, Scott A.; Zwier, Timothy S.

2017-06-01

Incorporation of the unnatural D-proline (^{D}P) stereoisomer into a polypeptide sequence is a typical strategy to encourage formation of β-hairpin loops because natural sequences are often unstructured in solution. Using conformation-specific IR and UV spectroscopy of cold (10 K) gas-phase ions, we probe the inherent conformational preferences of the ^{D}P and ^{L}P diastereomers in the protonated peptide [YAPAA+H]^{+}, where only intramolecular interactions are possible. Consistent with the solution phase studies, one of the conformers of [YADPAA+H]^{+} is folded into a charge-stabilized β-hairpin turn. However, a second predominant conformer family containing two sequential γ-turns is also identified, with similar energetic stability. A single conformational isomer of the ^{L}P diastereomer, [YALPAA+H]^{+}, is found and assigned to a structure that is not the anticipated "mirror image" β-turn. Instead, the ^{L}P stereo center promotes a cis alanine-proline amide bond. The assigned structures contain clues that the preference of the ^{D}P diastereomer to support a trans-amide bond and the proclivity of ^{L}P for a cis-amide bond is sterically driven and can be reversed by substituting glycine for alanine in position 2, forming [YGLPAA+H]^{+}. These results provide a basis for understanding the residue-specific and stereo-specific alterations in the potential energy surface that underlie these changing preferences, providing insights to the origin of β-hairpin formation.

Digestibility of gluten proteins is reduced by baking and enhanced by starch digestion.

PubMed

Smith, Frances; Pan, Xiaoyan; Bellido, Vincent; Toole, Geraldine A; Gates, Fred K; Wickham, Martin S J; Shewry, Peter R; Bakalis, Serafim; Padfield, Philip; Mills, E N Clare

2015-10-01

Resistance of proteins to gastrointestinal digestion may play a role in determining immune-mediated adverse reactions to foods. However, digestion studies have largely been restricted to purified proteins and the impact of food processing and food matrices on protein digestibility is poorly understood. Digestibility of a total gliadin fraction (TGF), flour (cv Hereward), and bread was assessed using in vitro batch digestion with simulated oral, gastric, and duodenal phases. Protein digestion was monitored by SDS-PAGE and immunoblotting using monoclonal antibodies specific for celiac-toxic sequences (QQSF, QPFP) and starch digestion by measuring undigested starch. Whereas the TGF was rapidly digested during the gastric phase the gluten proteins in bread were virtually undigested and digested rapidly during the duodenal phase only if amylase was included. Duodenal starch digestion was also slower in the absence of duodenal proteases. The baking process reduces the digestibility of wheat gluten proteins, including those containing sequences active in celiac disease. Starch digestion affects the extent of protein digestion, probably because of gluten-starch complex formation during baking. Digestion studies using purified protein fractions alone are therefore not predictive of digestion in complex food matrices. © 2015 The Authors. Molecular Nutrition & Food Research published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Lithium in lower-main-sequence stars of the Alpha Persei cluster

NASA Technical Reports Server (NTRS)

Balachandran, Suchitra; Lambert, David L.; Stauffer, John R.

1988-01-01

Lithium abundances are presented for main-sequence stars of spectral types F, G, and K in the young open cluster Alpha Per. For 46 cluster members, a correlation between Li abundance and projected rotational velocity v sin i is found: all of the Li-poor stars are slow rotators. Two explanations are proposed to account for the correlation: (1) that the Li depletion is introduced following a rapid spin-down phase experienced by young low-mass stars, and that this episode of Li depletion may be the dominant one determining the spread of Li abundances among young low-mass main-sequence stars, and (2) that star formation has occurred over a finite period such that the older stars have undergone a spin-down and depletion of Li by a means that may or may not depend on rotation. The Li abundance in the warm and rapidly rotating stars appears to be undepleted, as is predicted by recent models of pre-main-sequence stars. The depletion observed in the cool stars exceeds the level predicted by these models.

Some Physical Principles Governing Spatial and Temporal Organization in Living Systems

NASA Astrophysics Data System (ADS)

Ali, Md Zulfikar

Spatial and temporal organization in living organisms are crucial for a variety of biological functions and arise from the interplay of large number of interacting molecules. One of the central questions in systems biology is to understand how such an intricate organization emerges from the molecular biochemistry of the cell. In this dissertation we explore two projects. The first project relates to pattern formation in a cell membrane as an example of spatial organization, and the second project relates to the evolution of oscillatory networks as a simple example of temporal organization. For the first project, we introduce a model for pattern formation in a two-component lipid bilayer and study the interplay between membrane composition and membrane geometry, demonstrating the existence of a rich phase diagram. Pattern formation is governed by the interplay between phase separation driven by lipid-lipid interactions and tendency of lipid domains with high intrinsic curvature to deform the membrane away from its preferred position. Depending on membrane parameters, we find the formation of compact lipid micro-clusters or of striped domains. We calculate the stripe width analytically and find good agreement with stripe widths obtained from the simulations. For the second project, we introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm and apply it to study the following problems. Using the model, we study robustness and designabilty of a 2-component network that generate oscillations. We completely enumerate the sequence space and the phenotypic space, and discuss the relationship between designabilty, robustness and evolvability. We further apply the model to studies of neutral drift in networks that yield oscillatory dynamics, e.g. starting with a relatively simple network and allowing it to evolve by adding nodes and connections while requiring that oscillatory dynamics be preserved. Our studies demonstrate both the importance of employing a sequence-based evolutionary scheme and the relative rapidity (in evolutionary time) for the redistribution of function over new nodes via neutral drift. In addition we discovered another much slower timescale for network evolution, reflecting hidden order in sequence space that we interpret in terms of sparsely connected domains. Finally, we use the model to study the evolution of an oscillator from a non-oscillatory network under the influence of external periodic forcing as a model for evolution of circadian rhythm in living systems. We use a greedy algorithm based on optimizing biologically motivated fitness functions and find that the algorithm successfully produces oscillators. However, the distribution of free-period of evolved oscillators depends on the choice of fitness functions and the nature of forcing.

New Oxide Materials for an Ultra High Temperature Environment

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

Perepezko, John H.

In this project, a new oxide material, Hf 6Ta 2O 17 has been successfully synthesized by the controlled oxidization of Hf-Ta alloys. This oxide exhibits good oxidation resistance, high temperature phase stability up to more than 2000°C, low thermal conductivity and thus could serve as a component or a coating material in an ultrahigh temperature environment. We have examined the microstructure evolution and phase formation sequence during the oxidation exposure of Hf-Ta alloys at 1500°C and identified that the oxidation of a Hf-26.7atomic %Ta alloy leads to the formation of a single phase adherent Hf 6Ta 2O 17 with amore » complex atomic structure i.e. superstructure. The overall reactive diffusion pathway is consistent with the calculated Hf-Ta-O ternary phase diagram. Besides the synthesis of Hf 6Ta 2O 17 superstructure by oxidizing Hf-Ta alloys, we have also developed a synthesis method based upon the reactive sintering of the correct ratios of mixed powders of HfO 2 and Ta 2O 5 and verified the low thermal conductivity of Hf 6Ta 2O 17 superstructure on these samples. We have completed a preliminary analysis of the oxidation kinetics for Hf 6Ta 2O 17, which shows an initial parabolic oxidation kinetics.« less

Effect of substrate availability on nitrous oxide production by deammonification processes under anoxic conditions.

PubMed

Schneider, Yvonne; Beier, Maike; Rosenwinkel, Karl-Heinz

2012-05-01

Due to its high global warming potential, nitrous oxide (N(2)O) emissions from wastewater treatment processes have recently received a high degree of attention. Nevertheless, there is still a lack of information regarding the microbiological processes leading to N(2)O production. In this study, two lab-scale sequencing batch reactors were operated with deammonification biomass to investigate the role of denitrification and the influence of substrate availability regarding N(2)O formation during the anoxic phase of deammonification. Three different operational phases were established: within the first phase conversion by anammox was favoured and after a transition phase, denitrification activity was promoted. Low nitrous oxide production was observed during stable operation aiming for anammox conversion. Pulsed inflow of the wastewater containing ammonium (NH(4)(+)) and nitrite (NO(2)(-)) led to increased N(2)O production rates. Within the period of denitrification as dominating nitrogen conversion process, the nitrous oxide concentration level was higher during continuous inflow conditions, but the reaction to pulsed inflow was less pronounced. The results indicated that denitrification was responsible for N(2)O formation from the deammonification biomass. Operational settings to achieve suppression of denitrification processes to a large extend were deducted from the results of the experiments. © 2012 The Authors. Microbial Biotechnology © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Additives and solvents-induced phase and morphology modification of NaYF{sub 4} for improving up-conversion emission

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

Zhuang, Jianle, E-mail: zhuangjianle@126.com; MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275; Yang, Xianfeng

Both cubic and hexagonal NaYF{sub 4} were synthesized in different reaction systems via hydro/solvo-thermal route. The effects of reaction temperature, solvents, and additives on the synthesis of NaYF{sub 4} have been studied in detail. It has been shown that phase transformation from cubic NaYF{sub 4} to hexagonal NaYF{sub 4} always occurred. The sequence of the ability for inducing the phase transformation was ethanol>H{sub 2}O>acetic acid. It is found that ethanol can not only facilitate the formation of hexagonal NaYF{sub 4} but also control the growth of the crystal. This is quite unusual for the growth of H-NaYF{sub 4}. The up-conversionmore » emission properties of Yb/Er co-doped NaYF{sub 4} have also been investigated and the results demonstrated some general principles for improving up-conversion emission. - Graphical abstract: Additives and solvents can induce the phase transformation of NaYF{sub 4}, typically the use of organic sodium salt and ethanol. - Highlights: • The effect of additives and solvents on the synthesis of NaYF{sub 4} was studied in detail. • Ethanol can facilitate the formation of H-NaYF{sub 4} while acetic acid restrain it. • Three general principles for improving up-conversion emission were summarized.« less

The Use of Ammonium Formate as a Mobile-Phase Modifier for LC-MS/MS Analysis of Tryptic Digests

PubMed Central

Johnson, Darryl; Boyes, Barry; Orlando, Ron

2013-01-01

A major challenge facing current mass spectrometry (MS)-based proteomics research is the large concentration range displayed in biological systems, which far exceeds the dynamic range of commonly available mass spectrometers. One approach to overcome this limitation is to improve online reversed-phase liquid chromatography (RP-LC) separation methodologies. LC mobile-phase modifiers are used to improve peak shape and increase sample load tolerance. Trifluoroacetic acid (TFA) is a commonly used mobile-phase modifier, as it produces peptide separations that are far superior to other additives. However, TFA leads to signal suppression when incorporated with electrospray ionization (ESI), and thus, other modifiers, such as formic acid (FA), are used for LC-MS applications. FA exhibits significantly less signal suppression, but is not as effective of a modifier as TFA. An alternative mobile-phase modifier is the combination of FA and ammonium formate (AF), which has been shown to improve peptide separations. The ESI-MS compatibility of this modifier has not been investigated, particularly for proteomic applications. This work compares the separation metrics of mobile phases modified with FA and FA/AF and explores the use of FA/AF for the LC-MS analysis of tryptic digests. Standard tryptic-digest peptides were used for comparative analysis of peak capacity and sample load tolerance. The compatibility of FA/AF in proteomic applications was examined with the analysis of soluble proteins from canine prostate carcinoma tissue. Overall, the use of FA/AF improved online RP-LC separations and led to significant increases in peptide identifications with improved protein sequence coverage. PMID:24294112

The use of ammonium formate as a mobile-phase modifier for LC-MS/MS analysis of tryptic digests.

PubMed

Johnson, Darryl; Boyes, Barry; Orlando, Ron

2013-12-01

A major challenge facing current mass spectrometry (MS)-based proteomics research is the large concentration range displayed in biological systems, which far exceeds the dynamic range of commonly available mass spectrometers. One approach to overcome this limitation is to improve online reversed-phase liquid chromatography (RP-LC) separation methodologies. LC mobile-phase modifiers are used to improve peak shape and increase sample load tolerance. Trifluoroacetic acid (TFA) is a commonly used mobile-phase modifier, as it produces peptide separations that are far superior to other additives. However, TFA leads to signal suppression when incorporated with electrospray ionization (ESI), and thus, other modifiers, such as formic acid (FA), are used for LC-MS applications. FA exhibits significantly less signal suppression, but is not as effective of a modifier as TFA. An alternative mobile-phase modifier is the combination of FA and ammonium formate (AF), which has been shown to improve peptide separations. The ESI-MS compatibility of this modifier has not been investigated, particularly for proteomic applications. This work compares the separation metrics of mobile phases modified with FA and FA/AF and explores the use of FA/AF for the LC-MS analysis of tryptic digests. Standard tryptic-digest peptides were used for comparative analysis of peak capacity and sample load tolerance. The compatibility of FA/AF in proteomic applications was examined with the analysis of soluble proteins from canine prostate carcinoma tissue. Overall, the use of FA/AF improved online RP-LC separations and led to significant increases in peptide identifications with improved protein sequence coverage.

Microstructures, Martensitic Transformation, and Mechanical Behavior of Rapidly Solidified Ti-Ni-Hf and Ti-Ni-Si Shape Memory Alloys

NASA Astrophysics Data System (ADS)

Han, X. L.; Song, K. K.; Zhang, L. M.; Xing, H.; Sarac, B.; Spieckermann, F.; Maity, T.; Mühlbacher, M.; Wang, L.; Kaban, I.; Eckert, J.

2018-03-01

In this work, the microstructure and mechanical properties of rapidly solidified Ti50- x/2Ni50- x/2Hf x ( x = 0, 2, 4, 6, 8, 10, and 12 at.%) and Ti50- y/2Ni50- y/2Si y ( y = 1, 2, 3, 5, 7, and 10 at.%) shape memory alloys (SMAs) were investigated. The sequence of the phase formation and transformations in dependence on the chemical composition is established. Rapidly solidified Ti-Ni-Hf or Ti-Ni-Si SMAs are found to show relatively high yield strength and large ductility for specific Hf or Si concentrations, which is due to the gradual disappearance of the phase transformation from austenite to twinned martensite and the predominance of the phase transformation from twinned martensite to detwinned martensite during deformation as well as to the refinement of dendrites and the precipitation of brittle intermetallic compounds.

Swarm v2: highly-scalable and high-resolution amplicon clustering.

PubMed

Mahé, Frédéric; Rognes, Torbjørn; Quince, Christopher; de Vargas, Colomban; Dunthorn, Micah

2015-01-01

Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.

Sequence dependent aggregation of peptides and fibril formation

NASA Astrophysics Data System (ADS)

Hung, Nguyen Ba; Le, Duy-Manh; Hoang, Trinh X.

2017-09-01

Deciphering the links between amino acid sequence and amyloid fibril formation is key for understanding protein misfolding diseases. Here we use Monte Carlo simulations to study the aggregation of short peptides in a coarse-grained model with hydrophobic-polar (HP) amino acid sequences and correlated side chain orientations for hydrophobic contacts. A significant heterogeneity is observed in the aggregate structures and in the thermodynamics of aggregation for systems of different HP sequences and different numbers of peptides. Fibril-like ordered aggregates are found for several sequences that contain the common HPH pattern, while other sequences may form helix bundles or disordered aggregates. A wide variation of the aggregation transition temperatures among sequences, even among those of the same hydrophobic fraction, indicates that not all sequences undergo aggregation at a presumable physiological temperature. The transition is found to be the most cooperative for sequences forming fibril-like structures. For a fibril-prone sequence, it is shown that fibril formation follows the nucleation and growth mechanism. Interestingly, a binary mixture of peptides of an aggregation-prone and a non-aggregation-prone sequence shows the association and conversion of the latter to the fibrillar structure. Our study highlights the role of a sequence in selecting fibril-like aggregates and also the impact of a structural template on fibril formation by peptides of unrelated sequences.

On crystal versus fiber formation in dipeptide hydrogelator systems.

PubMed

Houton, Kelly A; Morris, Kyle L; Chen, Lin; Schmidtmann, Marc; Jones, James T A; Serpell, Louise C; Lloyd, Gareth O; Adams, Dave J

2012-06-26

Naphthalene dipeptides have been shown to be useful low-molecular-weight gelators. Here we have used a library to explore the relationship between the dipeptide sequence and the hydrogelation efficiency. A number of the naphthalene dipeptides are crystallizable from water, enabling us to investigate the comparison between the gel/fiber phase and the crystal phase. We succeeded in crystallizing one example directly from the gel phase. Using X-ray crystallography, molecular modeling, and X-ray fiber diffraction, we show that the molecular packing of this crystal structure differs from the structure of the gel/fiber phase. Although the crystal structures may provide important insights into stabilizing interactions, our analysis indicates a rearrangement of structural packing within the fibers. These observations are consistent with the fibrillar interactions and interatomic separations promoting 1D assembly whereas in the crystals the peptides are aligned along multiple axes, allowing 3D growth. This observation has an impact on the use of crystal structures to determine supramolecular synthons for gelators.

Oscillatory phase separation in giant lipid vesicles induced by transmembrane osmotic differentials

PubMed Central

Oglęcka, Kamila; Rangamani, Padmini; Liedberg, Bo; Kraut, Rachel S; Parikh, Atul N

2014-01-01

Giant lipid vesicles are closed compartments consisting of semi-permeable shells, which isolate femto- to pico-liter quantities of aqueous core from the bulk. Although water permeates readily across vesicular walls, passive permeation of solutes is hindered. In this study, we show that, when subject to a hypotonic bath, giant vesicles consisting of phase separating lipid mixtures undergo osmotic relaxation exhibiting damped oscillations in phase behavior, which is synchronized with swell–burst lytic cycles: in the swelled state, osmotic pressure and elevated membrane tension due to the influx of water promote domain formation. During bursting, solute leakage through transient pores relaxes the pressure and tension, replacing the domain texture by a uniform one. This isothermal phase transition—resulting from a well-coordinated sequence of mechanochemical events—suggests a complex emergent behavior allowing synthetic vesicles produced from simple components, namely, water, osmolytes, and lipids to sense and regulate their micro-environment. DOI: http://dx.doi.org/10.7554/eLife.03695.001 PMID:25318069

Synthetic peptides derived from salivary proteins and the control of surface charge densities of dental surfaces improve the inhibition of dental calculus formation.

PubMed

Grohe, Bernd

2017-08-01

Peptides descended from the salivary proteins statherin and histatin were recently identified in saliva and the acquired enamel pellicle (AEP), a proteomic layer coated on enamel. In particular, the statherin phosphopeptide DpSpSEEKFLR (DSS) was found to adsorb to enamel-like hydroxyapatite and inhibit plaque-related crystal formation. To determine the mechanism of these processes, we studied peptide-crystal interactions based on the sequences DSS and RKFHEKHHSHRGYR (RKF). The latter is a basic histatin sequence showing antimicrobial effects. To initiate crystallization we used calcium oxalate monohydrate (COM), a rather secondary phase in the oral environment, however highly amenable to experimental analyses of nucleation and growth processes. Using electron microscopy we found that the peptides DSS, DSS-RKF and DSS-DSS all inhibit crystal formation; with DSS-DSS showing the strongest effects while RKF showed no effect. In addition, using either enamel-like or mica substrates, we found that the ratio of the substrate's surface charge densities was directly correlated with the ratio of COM nucleation rates on theses surfaces. The findings suggest that mineralization processes on enamel/AEP-films are controllable by the degree of peptide phosphorylation/acidity and the level of the enamel surface charge density. Both parameters can, when well adjusted, help to overcome periodontal disease and dental calculus formation. In addition, the presence of antimicrobial RKF will reduce the buildup of bacterial plaque. Copyright © 2017 Elsevier B.V. All rights reserved.

Transformation and crystallization energetics of synthetic and biogenic amorphous calcium carbonate

PubMed Central

Radha, A. V.; Forbes, Tori Z.; Killian, Christopher E.; Gilbert, P. U. P. A.; Navrotsky, Alexandra

2010-01-01

Amorphous calcium carbonate (ACC) is a metastable phase often observed during low temperature inorganic synthesis and biomineralization. ACC transforms with aging or heating into a less hydrated form, and with time crystallizes to calcite or aragonite. The energetics of transformation and crystallization of synthetic and biogenic (extracted from California purple sea urchin larval spicules, Strongylocentrotus purpuratus) ACC were studied using isothermal acid solution calorimetry and differential scanning calorimetry. Transformation and crystallization of ACC can follow an energetically downhill sequence: more metastable hydrated ACC → less metastable hydrated ACC⇒anhydrous ACC ∼ biogenic anhydrous ACC⇒vaterite → aragonite → calcite. In a given reaction sequence, not all these phases need to occur. The transformations involve a series of ordering, dehydration, and crystallization processes, each lowering the enthalpy (and free energy) of the system, with crystallization of the dehydrated amorphous material lowering the enthalpy the most. ACC is much more metastable with respect to calcite than the crystalline polymorphs vaterite or aragonite. The anhydrous ACC is less metastable than the hydrated, implying that the structural reorganization during dehydration is exothermic and irreversible. Dehydrated synthetic and anhydrous biogenic ACC are similar in enthalpy. The transformation sequence observed in biomineralization could be mainly energetically driven; the first phase deposited is hydrated ACC, which then converts to anhydrous ACC, and finally crystallizes to calcite. The initial formation of ACC may be a first step in the precipitation of calcite under a wide variety of conditions, including geological CO2 sequestration. PMID:20810918

Relationships between palaeogeography and opal occurrence in Australia: A data-mining approach

NASA Astrophysics Data System (ADS)

Landgrebe, T. C. W.; Merdith, A.; Dutkiewicz, A.; Müller, R. D.

2013-07-01

Age-coded multi-layered geological datasets are becoming increasingly prevalent with the surge in open-access geodata, yet there are few methodologies for extracting geological information and knowledge from these data. We present a novel methodology, based on the open-source GPlates software in which age-coded digital palaeogeographic maps are used to “data-mine” spatio-temporal patterns related to the occurrence of Australian opal. Our aim is to test the concept that only a particular sequence of depositional/erosional environments may lead to conditions suitable for the formation of gem quality sedimentary opal. Time-varying geographic environment properties are extracted from a digital palaeogeographic dataset of the eastern Australian Great Artesian Basin (GAB) at 1036 opal localities. We obtain a total of 52 independent ordinal sequences sampling 19 time slices from the Early Cretaceous to the present-day. We find that 95% of the known opal deposits are tied to only 27 sequences all comprising fluvial and shallow marine depositional sequences followed by a prolonged phase of erosion. We then map the total area of the GAB that matches these 27 opal-specific sequences, resulting in an opal-prospective region of only about 10% of the total area of the basin. The key patterns underlying this association involve only a small number of key environmental transitions. We demonstrate that these key associations are generally absent at arbitrary locations in the basin. This new methodology allows for the simplification of a complex time-varying geological dataset into a single map view, enabling straightforward application for opal exploration and for future co-assessment with other datasets/geological criteria. This approach may help unravel the poorly understood opal formation process using an empirical spatio-temporal data-mining methodology and readily available datasets to aid hypothesis testing.

COSMIC-LAB: Double BSS sequences as signatures of the Core Collapse phenomenon in star clusters.

NASA Astrophysics Data System (ADS)

Ferraro, Francesco

2011-10-01

Globular Clusters {GCs} are old stellar systems tracing key stages of the star formation and chemical enrichment history of the early Universe and the galaxy assembly phase. As part of a project {COSMIC-LAB} aimed at using GCs as natural laboratories to study the complex interplay between dynamics and stellar evolution, here we present a proposal dealing with the role of Blue Straggler Stars {BSS}.BSS are core-hydrogen burning stars more massive than the main-sequence turnoff population. The canonical scenarios for BSS formation are either the mass transfer between binary companions, or stellar mergers induced by collisions. We have recently discovered two distinct and parallel sequences of BSS in the core of M30 {Ferraro et al. 2009, Nature 462, 1082}. We suggested that each of the two sequences is populated by BSS formed by one of the two processes, both triggered by the cluster core collapse, that, based on the observed BSS properties, must have occurred 1-2 Gyr ago. Following this scenario, we have identified a powerful "clock" to date the occurrence of this key event in the GC history.Here we propose to secure WFC3 images of 4 post-core collapse GCs, reaching S/N=200 at the BSS magnitude level, in order to determine the ubiquity of the BSS double sequence and calibrate the "dynamical clock". This requires very high spatial resolution and very high precision photometry capabilities that are unique to the HST. The modest amount of requested time will have a deep impact on the current and future generations of dynamical evolutionary models of collisional stellar systems.

Climate Proxy Signals in the Plio-Pleistocene Chemeron and Miocene Lukeino Formations, Baringo Basin, Kenya

NASA Astrophysics Data System (ADS)

Deino, A. L.; Kingston, J.; Hill, A.; Wilson, K. E.; Edgar, R.; Goble, E.

2009-12-01

The Chemeron Formation is a hominin-bearing, highly fossiliferous sequence of dominantly alluvial fan and fluvial sedimentary rocks, with climatically significant lacustrine intercalations, exposed within the Tugen Hills of the central Kenya Rift. As we have previously documented (Deino et al., 2006; Kingston et al., 2007), the formation contains a sequence of five 3-7 m thick diatomites in the interval 2.7-2.5 Ma that record, at precessional intervals, the repeated occurrence of deep-lake conditions in the Baringo Basin. These lakes appear abruptly, persist for only about 8,000 years of the ~23,000 year precessional cycle, and recede quickly. The oscillations have been tied to marine core and Mediterranean sapropel sections based on high-precision 40Ar/39Ar dating of K-feldspar in tuffs interspersed through the sequence, and paleomagnetic reversal stratigraphy. Ongoing paleontological investigations in the Tugen Hills are addressing the dynamics of high-resolution faunal and ecological change directly related to the fluctuating climatic background, including its effect on hominin evolution. This specific interval in the Baringo Basin/Tugen Hills has been identified by the Hominid Sites and Paleolakes Drilling Project Steering Committee as one of five target areas in East Africa for high-resolution coring studies. The drilling project is currently moving forward to the funding agency proposal development phase. Further exploration in the Tugen Hills has revealed a similar, older sequence of rhythmic alternating diatomites and non-lacustrine sediments in nearby drainages. These beds may represent a precessionally driven climate response possibly associated with the next older orbital eccentricity maximum from ~3.2-2.9 Ma. Characterization of the lithostratigraphy of this area is in progress, and samples of intercalated tuff beds suitable for high-precision single-crystal 40Ar/39Ar dating have been acquired. We have also extended our search for climate proxy records in the Tugen Hills to diatomaceous sequences between ~8-6 Ma that would specifically implicate precessional control as a pervasive factor in the formation of rift lake systems and by inference climate. Reconnaissance in summer ’09 of these older strata have revealed extensive lacustrine deposits indicating that this portion of the rift was inundated by major lake systems during the upper Miocene.

Late Proterozoic glacially controlled shelf sequences in western Mali (west Africa)

NASA Astrophysics Data System (ADS)

Deynoux, M.; Prousti, J. N.; Simon, B.

The Late Proterozoic deposits of the Bakoye Group (500 m) in western Mali constitute a remarkable example of a glacially influenced sedimentary record on an epicratonic platform. They are composed of alternating marine and continental formations which represent accumulation in a basin located in the vicinity of upland areas covered by ice sheets. One of these formations (the Ba4 Formation), which is the focus of this study, is composed of three major units. The basal Unit 1 is made up of carbonaceous coarse to fine grained sandstones which are organized in fining upward sequences and which comprise lenticular diamictite intercalations. This Unit is considered to represent the fore slope gravity flows of a subaqueous ice-cootact fan fed by meltwater streams (≪glacioturbidites≫). Unit 2 is made up of coarse to fine grained sandstones in a highly variable association of facies. This Unit is characterized by the abundance of wave ripples associated with convolute beddings. planar or wavy beddings and tabular or hummocky crossbeddings in a general shallowing upward trend. It also comprises evidence of gravity processes including debris flows and large slumped sandstone bodies. Unit 2 represents the progressive filling of the Ba4 basin and reflects the combined effect of glacially induced eustatism and isostacy during a phase of glacial retreat. The basal part of Unit 3 is made up of a succession (a few meters thick) of conglomerates, diamictites, sandstones, siltstones or carbonates lying on an erosional unconformity marked by periglacial frost wedges. The upper part of Unit 3 is thicker (100-150 m) and onlaps on these basal facies with a succession of sandstone bars exhibiting swaley and hummocky crossbeddings, large cut and fill structures, and planar laminations. Unit 3 is strongly transgressive, the lower shoreface and backshore deposits include algal mats and are onlapped by sand ridges emplaced in a high energy upper to middle shoreface environment. Overall, in tems of sequential stratigraphy, the deposits of the galcial Bakoya Groupe are organized in shallowing upward sequences limited by maximum flooding surfaces of regional extent. One of these sequences (the Ba4 Formation) is subdivided into parasequences generated in relation with local ice sheet fluctuation including glacioisostacy.

Two distinct sequences of blue straggler stars in the globular cluster M 30.

PubMed

Ferraro, F R; Beccari, G; Dalessandro, E; Lanzoni, B; Sills, A; Rood, R T; Pecci, F Fusi; Karakas, A I; Miocchi, P; Bovinelli, S

2009-12-24

Stars in globular clusters are generally believed to have all formed at the same time, early in the Galaxy's history. 'Blue stragglers' are stars massive enough that they should have evolved into white dwarfs long ago. Two possible mechanisms have been proposed for their formation: mass transfer between binary companions and stellar mergers resulting from direct collisions between two stars. Recently the binary explanation was claimed to be dominant. Here we report that there are two distinct parallel sequences of blue stragglers in M 30. This globular cluster is thought to have undergone 'core collapse', during which both the collision rate and the mass transfer activity in binary systems would have been enhanced. We suggest that the two observed sequences are a consequence of cluster core collapse, with the bluer population arising from direct stellar collisions and the redder one arising from the evolution of close binaries that are probably still experiencing an active phase of mass transfer.

Chromosome evolution with naked eye: Palindromic context of the life origin

NASA Astrophysics Data System (ADS)

Larionov, Sergei; Loskutov, Alexander; Ryadchenko, Eugeny

2008-03-01

Based on the representation of the DNA sequence as a two-dimensional (2D) plane walk, we consider the problem of identification and comparison of functional and structural organizations of chromosomes of different organisms. According to the characteristic design of 2D walks we identify telomere sites, palindromes of various sizes and complexity, areas of ribosomal RNA, transposons, as well as diverse satellite sequences. As an interesting result of the application of the 2D walk method, a new duplicated gigantic palindrome in the X human chromosome is detected. A schematic mechanism leading to the formation of such a duplicated palindrome is proposed. Analysis of a large number of the different genomes shows that some chromosomes (or their fragments) of various species appear as imperfect gigantic palindromes, which are disintegrated by many inversions and the mutation drift on different scales. A spread occurrence of these types of sequences in the numerous chromosomes allows us to develop a new insight of some accepted points of the genome evolution in the prebiotic phase.

Phase 2 of the Array Automated Assembly Task for the Low Cost Solar Array Project

NASA Technical Reports Server (NTRS)

Campbell, R. B.; Rai-Choundhury, P.; Seman, E. J.; Rohatgi, A.; Davis, J. R.; Ostroski, J. W.; Stapleton, R. E.

1979-01-01

Two process specifications supplied by contractors were tested. The aluminum silk screening process resulted in cells comparable to those from sputtered Al. The electroless plating of contacts specification could be used only with extensive modification. Several experiments suggest that there is some degradation of the front junction during the Al back surface field (BSF) fabrication. A revised process sequence was defined which incorporates Al BSF formation. A cost analysis of this process yielded a selling price of $0.75/watt peak in 1980.

Feasibility and systems definition study for Microwave Multi-Application Payload (MMAP)

NASA Technical Reports Server (NTRS)

Horton, J. B.; Allen, C. C.; Massaro, M. J.; Zemany, J. L.; Murrell, J. W.; Stanhouse, R. W.; Condon, G. P.; Stone, R. F.; Swana, J.; Afifi, M.

1977-01-01

Work completed on three Shuttle/Spacelab experiments is examined: the Adaptive Multibeam Phased Array Antenna (AMPA) Experiment, Electromagnetic Environment Experiment (EEE) and Millimeter Wave Communications Experiment (MWCE). Results included the definition of operating modes, sequence of operation, radii of operation about several ground stations, signal format, foot prints of typical orbits and preliminary definition of ground and user terminals. Conceptual hardware designs, Spacelab interfaces, data handling methods, experiment testing and verification studies were included. The MWCE-MOD I was defined conceptually for a steerable high gain antenna.

Toward direct pore-scale modeling of three-phase displacements

NASA Astrophysics Data System (ADS)

Mohammadmoradi, Peyman; Kantzas, Apostolos

2017-12-01

A stable spreading film between water and gas can extract a significant amount of bypassed non-aqueous phase liquid (NAPL) through immiscible three-phase gas/water injection cycles. In this study, the pore-scale displacement mechanisms by which NAPL is mobilized are incorporated into a three-dimensional pore morphology-based model under water-wet and capillary equilibrium conditions. The approach is pixel-based and the sequence of invasions is determined by the fluids' connectivity and the threshold capillary pressure of the advancing interfaces. In addition to the determination of three-phase spatial saturation profiles, residuals, and capillary pressure curves, dynamic finite element simulations are utilized to predict the effective permeabilities of the rock microtomographic images as reasonable representations of the geological formations under study. All the influential features during immiscible fluid flow in pore-level domains including wetting and spreading films, saturation hysteresis, capillary trapping, connectivity, and interface development strategies are taken into account. The capabilities of the model are demonstrated by the successful prediction of saturation functions for Berea sandstone and the accurate reconstruction of three-phase fluid occupancies through a micromodel.

A Nanohelicoidal Nematic Liquid Crystal Formed by a Non-Linear Duplexed Hexamer.

PubMed

Mandle, Richard J; Goodby, John W

2018-06-11

The twist-bend modulated nematic liquid-crystal phase exhibits formation of a nanometre-scale helical pitch in a fluid and spontaneous breaking of mirror symmetry, leading to a quasi-fluid state composed of chiral domains despite being composed of achiral materials. This phase was only observed for materials with two or more mesogenic units, the manner of attachment between which is always linear. Non-linear oligomers with a H-shaped hexamesogen are now found to exhibit both nematic and twist-bend modulated nematic phases. This shatters the assumption that a linear sequence of mesogenic units is a prerequisite for this phase, and points to this state of matter being exhibited by a wider range of self-assembling structures than was previously envisaged. These results support the double helix model of the TB phase as opposed to the simple heliconical model. This new class of materials could act as low-molecular-weight surrogates for cross-linked liquid-crystalline elastomers. © 2018 Die Autoren. Veröffentlicht von Wiley-VCH Verlag GmbH & Co. KGaA.

Conformation-Specific Infrared and Ultraviolet Spectroscopy of Cold [YAPAA +H]+ and [YGPAA +H]+ Ions

NASA Astrophysics Data System (ADS)

Deblase, Andrew; Harrilal, Christopher; Lawler, John; Burke, Nicole; McLuckey, Scott; Timothy, Zwier

Incorporation of the unnatural D-proline stereoisomer into a peptide sequence is a typical strategy to synthesize model β-hairpin loops. Using conformation-specific IR and UV spectroscopy of cold ( 10 K) gas-phase ions, we unravel the inherent conformational preferences of the DP and LP diastereomers in the protonated peptide [YAPAA +H]+ because only intramolecular interactions are possible in this isolated regime. Consistent with the solution phase studies, one of the conformers of [YADPAA +H]+ is folded into a β-hairpin turn. However, a second predominant γ-turn conformer family is identified. The [YALPAA +H]+ stereoisomer discourages β-hairpin formation. We show that the trans(DP) ->cis (LP) isomerization is sterically driven and can be reversed by substituting [YGLPAA +H]+ for [YALPAA +H]+. Therefore, we provide a basis for understanding residue-specific alterations in the potential energy surface and reveal new insights into the origin of β-hairpin formation from the bottom-up. National Science Foundation (NSF CHE 1213289) and the U.S. Department of Energy (Office of Basic Energy Sciences under Award Number FG02-00ER15105).

Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles

PubMed Central

Hennig, Sven; Kong, Geraldine; Mannen, Taro; Sadowska, Agata; Kobelke, Simon; Blythe, Amanda; Knott, Gavin J.; Iyer, K. Swaminathan; Ho, Diwei; Newcombe, Estella A.; Hosoki, Kana; Goshima, Naoki; Kawaguchi, Tetsuya; Hatters, Danny; Trinkle-Mulcahy, Laura; Hirose, Tetsuro; Bond, Charles S.

2015-01-01

Prion-like domains (PLDs) are low complexity sequences found in RNA binding proteins associated with the neurodegenerative disorder amyotrophic lateral sclerosis. Recently, PLDs have been implicated in mediating gene regulation via liquid-phase transitions that drive ribonucleoprotein granule assembly. In this paper, we report many PLDs in proteins associated with paraspeckles, subnuclear bodies that form around long noncoding RNA. We mapped the interactome network of paraspeckle proteins, finding enrichment of PLDs. We show that one protein, RBM14, connects key paraspeckle subcomplexes via interactions mediated by its PLD. We further show that the RBM14 PLD, as well as the PLD of another essential paraspeckle protein, FUS, is required to rescue paraspeckle formation in cells in which their endogenous counterpart has been knocked down. Similar to FUS, the RBM14 PLD also forms hydrogels with amyloid-like properties. These results suggest a role for PLD-mediated liquid-phase transitions in paraspeckle formation, highlighting this nuclear body as an excellent model system for understanding the perturbation of such processes in neurodegeneration. PMID:26283796

Time-Correlated Single-Photon Counting Fluorescence Imaging of Lipid Domains In Raft-Mimicking Giant Unilamellar Vesicles

NASA Astrophysics Data System (ADS)

Clarke, James; Cheng, Kwan; Shindell, Orrin; Wang, Exing

We have designed and constructed a high-throughput electrofusion chamber and an incubator to fabricate Giant Unilamellar Vesicles (GUVs) consisting of high-melting lipids, low-melting lipids, cholesterol and both ordered and disordered phase sensitive fluorescent probes (DiIC12, dehydroergosterol and BODIPY-Cholesterol). GUVs were formed in a 3 stage pulse sequence electrofusion process with voltages ranging from 50mVpp to 2.2Vpp and frequencies from 5Hz to 10Hz. Steady state and time-correlated single-photon counting (TCSPC) fluorescence lifetime (FLIM) based confocal and/or multi-photon microscopic techniques were used to characterize phase separated lipid domains in GUVs. Confocal imaging measures the probe concentration and the chemical environment of the system. TCSPC techniques determine the chemical environment through the perturbation of fluorescent lifetimes of the probes in the system. The above techniques will be applied to investigate the protein-lipid interactions involving domain formation. Specifically, the mechanisms governing lipid domain formations in the above systems that mimic the lipid rafts in cells will be explored. Murchison Fellowship at Trinity University.

A stationary-phase protein of Escherichia coli that affects the mode of association between the trp repressor protein and operator-bearing DNA.

PubMed

Yang, W; Ni, L; Somerville, R L

1993-06-15

Highly purified preparations of trp repressor (TrpR) protein derived from Escherichia coli strains that were engineered to overexpress this material were found to contain another protein, of 21 kDa. The second protein, designated WrbA [for tryptophan (W) repressor-binding protein] remained associated with its namesake through several sequential protein fractionation steps. The N-terminal amino acid sequence of the WrbA protein guided the design of two degenerate oligonucleotides that were used as probes in the cloning of the wrbA gene (198 codons). The WrbA protein, in purified form, was found by several criteria to enhance the formation and/or stability of noncovalent complexes between TrpR holorepressor and its primary operator targets. The formation of an operator-holorepressor-WrbA ternary complex was demonstrated by gel mobility-shift analysis. The WrbA protein alone does not interact with the trp operator. During the stationary phase, cells deficient in the WrbA protein were less efficient than wild type in their ability to repress the trp promoter. It is proposed that the WrbA protein functions as an accessory element in blocking TrpR-specific transcriptional processes that might be physiologically disadvantageous in the stationary phase of the bacterial life cycle.

An experimental study of entrainment and transport in the turbulent near wake of a circular cylinder

NASA Technical Reports Server (NTRS)

Cantwell, B.; Coles, D.

1983-01-01

Attention is given to an experimental investigation of transport processes in the near wake of a circular cylinder, for a Reynolds number of 140,000, in which an X-array of hot wire probes mounted on a pair of whirling arms was used for flow measurement. Rotation of the arms in a uniform flow applies a wide range of relative flow angles to these X-arrays, making them inherently self-calibrating in pitch. A phase signal synchronized with the vortex-shedding process allowed a sorting of the velocity data into 16 populations, each having essentially constant phase. An ensemble average for each population yielded a sequence of pictures of the instantaneous mean flow field in which the vortices are frozen, as they would be on a photograph. The measurements also yield nonsteady mean data for velocity, intermittency, vorticity, stress, and turbulent energy production, as a function of phase. Emphasis is given in a discussion of study results to the nonsteady mean flow, which emerges as a pattern of centers and saddles in a frame of reference that moves with the eddies. The kinematics of the vortex formation process are described in terms of the formation and evolution of saddle points between vortices in the first few diameters of the near wake.

Quantum memory receiver for superadditive communication using binary coherent states

NASA Astrophysics Data System (ADS)

Klimek, Aleksandra; Jachura, Michał; Wasilewski, Wojciech; Banaszek, Konrad

2016-11-01

We propose a simple architecture based on multimode quantum memories for collective readout of classical information keyed using a pair coherent states, exemplified by the well-known binary phase shift keying format. Such a configuration enables demonstration of the superadditivity effect in classical communication over quantum channels, where the transmission rate becomes enhanced through joint detection applied to multiple channel uses. The proposed scheme relies on the recently introduced idea to prepare Hadamard sequences of input symbols that are mapped by a linear optical transformation onto the pulse position modulation format [Guha, S. Phys. Rev. Lett. 2011, 106, 240502]. We analyze two versions of readout based on direct detection and an optional Dolinar receiver which implements the minimum-error measurement for individual detection of a binary coherent state alphabet.

Quantum memory receiver for superadditive communication using binary coherent states.

PubMed

Klimek, Aleksandra; Jachura, Michał; Wasilewski, Wojciech; Banaszek, Konrad

2016-11-12

We propose a simple architecture based on multimode quantum memories for collective readout of classical information keyed using a pair coherent states, exemplified by the well-known binary phase shift keying format. Such a configuration enables demonstration of the superadditivity effect in classical communication over quantum channels, where the transmission rate becomes enhanced through joint detection applied to multiple channel uses. The proposed scheme relies on the recently introduced idea to prepare Hadamard sequences of input symbols that are mapped by a linear optical transformation onto the pulse position modulation format [Guha, S. Phys. Rev. Lett. 2011 , 106 , 240502]. We analyze two versions of readout based on direct detection and an optional Dolinar receiver which implements the minimum-error measurement for individual detection of a binary coherent state alphabet.

POST-MAIN SEQUENCE EVOLUTION OF ICY MINOR PLANETS: IMPLICATIONS FOR WATER RETENTION AND WHITE DWARF POLLUTION

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

Malamud, Uri; Perets, Hagai B., E-mail: uri.mal@tx.technion.ac.il, E-mail: hperets@physics.technion.ac.il

Most observations of polluted white dwarf atmospheres are consistent with accretion of water-depleted planetary material. Among tens of known cases, merely two involve accretion of objects that contain a considerable mass fraction of water. The purpose of this study is to investigate the relative scarcity of these detections. Based on a new and highly detailed model, we evaluate the retention of water inside icy minor planets during the high-luminosity stellar evolution that follows the main sequence. Our model fully considers the thermal, physical, and chemical evolution of icy bodies, following their internal differentiation as well as water depletion, from themore » moment of their birth and through all stellar evolution phases preceding the formation of the white dwarf. We also account for different initial compositions and formation times. Our results differ from previous studies, which have either underestimated or overestimated water retention. We show that water can survive in a variety of circumstances and in great quantities, and therefore other possibilities are discussed in order to explain the infrequency of water detection. We predict that the sequence of accretion is such that water accretes earlier, and more rapidly, than the rest of the silicate disk, considerably reducing the chance of its detection in H-dominated atmospheres. In He-dominated atmospheres, the scarcity of water detections could be observationally biased. It implies that the accreted material is typically intrinsically dry, which may be the result of the inside-out depopulation sequence of minor planets.« less

Variable speed wind turbine generator with zero-sequence filter

DOEpatents

Muljadi, Eduard

1998-01-01

A variable speed wind turbine generator system to convert mechanical power into electrical power or energy and to recover the electrical power or energy in the form of three phase alternating current and return the power or energy to a utility or other load with single phase sinusoidal waveform at sixty (60) hertz and unity power factor includes an excitation controller for generating three phase commanded current, a generator, and a zero sequence filter. Each commanded current signal includes two components: a positive sequence variable frequency current signal to provide the balanced three phase excitation currents required in the stator windings of the generator to generate the rotating magnetic field needed to recover an optimum level of real power from the generator; and a zero frequency sixty (60) hertz current signal to allow the real power generated by the generator to be supplied to the utility. The positive sequence current signals are balanced three phase signals and are prevented from entering the utility by the zero sequence filter. The zero sequence current signals have zero phase displacement from each other and are prevented from entering the generator by the star connected stator windings. The zero sequence filter allows the zero sequence current signals to pass through to deliver power to the utility.

Variable Speed Wind Turbine Generator with Zero-sequence Filter

DOEpatents

Muljadi, Eduard

1998-08-25

A variable speed wind turbine generator system to convert mechanical power into electrical power or energy and to recover the electrical power or energy in the form of three phase alternating current and return the power or energy to a utility or other load with single phase sinusoidal waveform at sixty (60) hertz and unity power factor includes an excitation controller for generating three phase commanded current, a generator, and a zero sequence filter. Each commanded current signal includes two components: a positive sequence variable frequency current signal to provide the balanced three phase excitation currents required in the stator windings of the generator to generate the rotating magnetic field needed to recover an optimum level of real power from the generator; and a zero frequency sixty (60) hertz current signal to allow the real power generated by the generator to be supplied to the utility. The positive sequence current signals are balanced three phase signals and are prevented from entering the utility by the zero sequence filter. The zero sequence current signals have zero phase displacement from each other and are prevented from entering the generator by the star connected stator windings. The zero sequence filter allows the zero sequence current signals to pass through to deliver power to the utility.

Variable speed wind turbine generator with zero-sequence filter

DOEpatents

Muljadi, E.

1998-08-25

A variable speed wind turbine generator system to convert mechanical power into electrical power or energy and to recover the electrical power or energy in the form of three phase alternating current and return the power or energy to a utility or other load with single phase sinusoidal waveform at sixty (60) hertz and unity power factor includes an excitation controller for generating three phase commanded current, a generator, and a zero sequence filter. Each commanded current signal includes two components: a positive sequence variable frequency current signal to provide the balanced three phase excitation currents required in the stator windings of the generator to generate the rotating magnetic field needed to recover an optimum level of real power from the generator; and a zero frequency sixty (60) hertz current signal to allow the real power generated by the generator to be supplied to the utility. The positive sequence current signals are balanced three phase signals and are prevented from entering the utility by the zero sequence filter. The zero sequence current signals have zero phase displacement from each other and are prevented from entering the generator by the star connected stator windings. The zero sequence filter allows the zero sequence current signals to pass through to deliver power to the utility. 14 figs.

Geologic controls on the formation of lakes in north-central Florida

USGS Publications Warehouse

Kindinger, Jack G.; Davis, Jeffrey B.; Flocks, James G.; Pitman, Janet K.; Carroll, Alan R.

1998-01-01

Fluid exchange between surficial waters and groundwater, as well as the processes that control this exchange, are of critical concern to water management districts and planners. Digital high-resolution seismic systems were used to collect geophysical data from 30 lakes of north-central Florida. Although using seismic profile data in the past has been less than successful, the use of digital technology has increased the potential for success. Seismic profiles collected from the lakes of north-central Florida have shown the potential application of these techniques in understanding the formation of individual lakes. In each case study, lake structure and geomorphology were controlled by solution and/or mechanical processes. Processes that control lake development are twofold: 1) karstification or dissolution of the underlying limestone, and 2) me collapse, subsidence, or slumping of overburden to form sinkholes. Initial lake formation is directly related to the karst topography of the underlying host limestone. Lake size and shape are a factor of the thickness of overburden and size of the collapse or subsidence and/or clustering of depressions allowing for lake development. Lake development is through progressive sequence stages to maturity that can be delineated into geomorphic types. Case studies have shown that lakes can be divided by geomorphic types into progressive developmental phases: (1) active subsidence or collapse phase (young) - the open to partially filled collapse structures typically associated with sink holes; (2) transitional phase (middle age) - the sinkhole is plugged as the voids within the collapse are filled with sediment, periodic reactivation may occur; (3) baselevel phase (mature) - active sinkholes are progressively plugged by the continual erosion of material into the basin, and eventually sediment fills the basins; and (4) polje (drowned prairie) - broad flat-bottom basins located within the epiphreatic zone that are inundated at high stages of the water table and have one or all phases of sinkhole development and many types of karst and karren features. Most lakes in this study have a small diameter (

Solidification Sequence of Spray-Formed Steels

NASA Astrophysics Data System (ADS)

Zepon, Guilherme; Ellendt, Nils; Uhlenwinkel, Volker; Bolfarini, Claudemiro

2016-02-01

Solidification in spray-forming is still an open discussion in the atomization and deposition area. This paper proposes a solidification model based on the equilibrium solidification path of alloys. The main assumptions of the model are that the deposition zone temperature must be above the alloy's solidus temperature and that the equilibrium liquid fraction at this temperature is reached, which involves partial remelting and/or redissolution of completely solidified droplets. When the deposition zone is cooled, solidification of the remaining liquid takes place under near equilibrium conditions. Scanning electron microscopy (SEM) and optical microscopy (OM) were used to analyze the microstructures of two different spray-formed steel grades: (1) boron modified supermartensitic stainless steel (SMSS) and (2) D2 tool steel. The microstructures were analyzed to determine the sequence of phase formation during solidification. In both cases, the solidification model proposed was validated.

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.

PubMed

Samadian, Soroush; Bruce, Jeff P; Pugh, Trevor J

2018-03-01

Somatic copy number variations (CNVs) play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary Alignment Mapping (BAM) file, with a focus on targeted and exome sequencing experiments. As input, this tool requires a read alignment file (BAM format), lists of non-overlapping genome coordinates for introduction of gains and losses (bed file), and an optional file defining known haplotypes (vcf format). To improve runtime performance, Bamgineer introduces the desired CNVs in parallel using queuing and parallel processing on a local machine or on a high-performance computing cluster. As proof-of-principle, we applied Bamgineer to a single high-coverage (mean: 220X) exome sequence file from a blood sample to simulate copy number profiles of 3 exemplar tumors from each of 10 tumor types at 5 tumor cellularity levels (20-100%, 150 BAM files in total). To demonstrate feasibility beyond exome data, we introduced read alignments to a targeted 5-gene cell-free DNA sequencing library to simulate EGFR amplifications at frequencies consistent with circulating tumor DNA (10, 1, 0.1 and 0.01%) while retaining the multimodal insert size distribution of the original data. We expect Bamgineer to be of use for development and systematic benchmarking of CNV calling algorithms by users using locally-generated data for a variety of applications. The source code is freely available at http://github.com/pughlab/bamgineer.

Reaction process of {alpha} {yields} {gamma} massive transformation in Ti-rich TiAl alloy

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

Kumagai, T.; Abe, E.; Nakamura, M.

1995-08-01

Reaction sequence of the massive transformation from the high-temperature {alpha}-Ti phase to the {gamma}-TiAl phase ({gamma}{sub m}) in a Ti-48at.% Al alloy has been examined in terms of optical and transmission electron microscopes. Both transformed and untransformed regions were macroscopically observed in the sample quenched from the high-temperature {alpha} phase field, when the sample was held there for a extended period of time prior to quenching. The transformed region consists of randomly oriented fine {gamma} single phase grains, in which many thermal anti-phase domains (TAPDs), together with a number of stacking faults were observed. In contrast, the untransformed region comprisesmore » extremely fine lamellae of the {gamma} and {alpha}{sub 2}-Ti{sub 3}Al phases, and the {gamma} plates were found to run through the TAPDs caused by {alpha} {yields} {alpha}{sub 2} ordering. Subsequent aging at 1,273 K causes the microstructure change in the untransformed region from {alpha}{sub 2}/{gamma} lamellae to {gamma}/{gamma} lamellae spontaneously and expands the {gamma}{sub m} region. These observations suggest that the {alpha} {yields} {gamma}{sub m} transformation proceeds through formation of fine {gamma} plates.« less

Direct Visualisation of the Structural Transformation between the Lyotropic Liquid Crystalline Lamellar and Bicontinuous Cubic Mesophase.

PubMed

Tran, Nhiem; Zhai, Jiali; Conn, Charlotte E; Mulet, Xavier; Waddington, Lynne J; Drummond, Calum J

2018-05-29

The transition between the lyotropic liquid crystalline lamellar and the bicontinuous cubic mesophase drives multiple fundamental cellular processes involving changes in cell membrane topology including endocytosis and membrane budding. While several theoretical models have been proposed to explain this dynamic transformation, experimental validation of these models has been challenging due to the short lived nature of the intermediates present during the phase transition. Herein, we report the direct observation of a lamellar to bicontinuous cubic phase transition in nanoscale dispersions using a combination of cryogenic transmission electron microscopy and static small angle X-ray scattering. The results represent the first experimental confirmation of a theoretical model which proposed that the bicontinuous cubic phase originates from the centre of a lamellar vesicle, then propagates outward via the formation of inter-lamellar attachments and stalks. The observation was possible due to the precise control of the lipid composition to place the dispersion systems at the phase boundary of a lamellar and a cubic phase, allowing for the creation of long-lived structural intermediates. By surveying the nanoparticles using cryogenic transmission electron microscopy, a complete phase transition sequence was established.

Mineralogy, textures and mode of formation of a hibonite-bearing Allende inclusion

NASA Technical Reports Server (NTRS)

Allen, J. M.; Grossman, L.; Davis, A. M.; Hutcheon, I. D.

1978-01-01

The origin of a Type A, hibonite-rich, coarse-grained inclusion is investigated with the electron microprobe and petrographic and scanning electron microscopes. The primary phases are hibonite, rhonite, Ti-Al-pyroxene, spinel, perovskite and melilite. Evidence for the crystallization of the bulk of the primary phases, hibonite and melilite, from a melt is lacking, suggesting that they may have condensed directly from a solar nebular gas instead. Primary phases were intensely altered during a later condensation event which deposited grossular, anorthite, nepheline and wollastonite in veins and cavities. Four or five condensate rims were deposited as successive layers on the outside of the inclusion. From inside to outside, they consist of perovskite + spinel, nepheline + anorthite, Ti-Al-pyroxene + diopside, hedenbergite + or - wollastonite + or - andradite and, finally, prisms of diopside and hedenbergite with wollastonite and andradite. Reverse zoning in melilite; alteration phases and rim phases, which are not stable condensates from a gas of solar composition; and details of the sequence of rim condensates all suggest that the entire condensation history of this inclusion was interrupted by changes in pressure and/or temperature and/or gas phase composition.

Alternative end-joining repair pathways are the ultimate backup for abrogated classical non-homologous end-joining and homologous recombination repair: Implications for the formation of chromosome translocations.

PubMed

Iliakis, George; Murmann, Tamara; Soni, Aashish

2015-11-01

DNA double strand breaks (DSB) are the most deleterious lesions for the integrity of the genome, as their misrepair can lead to the formation of chromosome translocations. Cells have evolved two main repair pathways to suppress the formation of these genotoxic lesions: homology-dependent, error-free homologous recombination repair (HRR), and potentially error-prone, classical, DNA-PK-dependent non-homologous end-joining (c-NHEJ). The most salient feature of c-NHEJ, speed, will largely suppress chromosome translocation formation, while sequence alterations at the junction remain possible. It is now widely accepted that when c-NHEJ is inactivated, globally or locally, an alternative form of end-joining (alt-EJ) removes DSBs. Alt-EJ operates with speed and fidelity markedly lower than c-NHEJ, causing thus with higher probability chromosome translocations, and generating more extensive sequence alterations at the junction. Our working hypothesis is that alt-EJ operates as a backup to c-NHEJ. Recent results show that alt-EJ can also backup abrogated HRR in G2 phase cells, again at the cost of elevated formation of chromosome translocations. These observations raise alt-EJ to a global rescuing mechanism operating on ends that have lost their chromatin context in ways that compromise processing by HRR or c-NHEJ. While responsible for eliminating from the genome highly cytotoxic DNA ends, alt-EJ provides this function at the price of increased translocation formation. Here, we analyze recent literature on the mechanisms of chromosome translocation formation and propose a functional hierarchy among DSB processing pathways that makes alt-EJ the global backup pathway. We discuss possible ramifications of this model in cellular DSB management and pathway choice, and analyze its implications in radiation carcinogenesis and the design of novel therapeutic approaches. Copyright © 2015 Elsevier B.V. All rights reserved.

Evolved stars in the Local Group galaxies - II. AGB, RSG stars and dust production in IC10

NASA Astrophysics Data System (ADS)

Dell'Agli, F.; Di Criscienzo, M.; Ventura, P.; Limongi, M.; García-Hernández, D. A.; Marini, E.; Rossi, C.

2018-06-01

We study the evolved stellar population of the Local Group galaxy IC10, with the aim of characterizing the individual sources observed and to derive global information on the galaxy, primarily the star formation history and the dust production rate. To this aim, we use evolutionary sequences of low- and intermediate-mass (M < 8 M⊙) stars, evolved through the asymptotic giant branch phase, with the inclusion of the description of dust formation. We also use models of higher mass stars. From the analysis of the distribution of stars in the observational planes obtained with IR bands, we find that the reddening and distance of IC10 are E(B - V) = 1.85 mag and d = 0.77 Mpc, respectively. The evolved stellar population is dominated by carbon stars, that account for 40% of the sources brighter than the tip of the red giant branch. Most of these stars descend from ˜1.1 - 1.3 M⊙ progenitors, formed during the major epoch of star formation, which occurred ˜2.5 Gyr ago. The presence of a significant number of bright stars indicates that IC10 has been site of significant star formation in recent epochs and currently hosts a group of massive stars in the core helium-burning phase. Dust production in this galaxy is largely dominated by carbon stars; the overall dust production rate estimated is 7 × 10-6 M⊙/yr.

Sequence stratigraphic control on prolific HC reservoir development, Southwest Iran

USGS Publications Warehouse

Lasemi, Y.; Kondroud, K.N.

2008-01-01

An important carbonate formation in the Persian Gulf and the onshore oil fields of Southwest Iran is the Lowermost Cretaceous Fahliyan formation. The formation in Darkhowain field consists of unconformity-bounded depositional sequences containing prolific hydrocarbon reservoirs of contrasting origin. Located in the high stand systems tract (HST) of the lower sequence encompassing over 200m of oil column are the most prolific reservoir. Another reservoir is over 80m thick consisting of shallowing-upward cycles that are best developed within the transgressive systems tract of the upper sequence. Vertical facies distribution and their paleobathymetry and geophysical log signatures of the Fahliyan formation in the Darkhowain platform reveal the presence of two unconformity-bounded depositional sequences in Vail et al., Van Wagoner et al., and Sarg. The Fahliyan formation mainly consists of platform carbonates composed of restricted bioclastic lime mudstone to packstone of the platform interior, Lithocodium boundstone or ooid-intraclast-bioclast grainstone of the high energy platform margin and the bioclast packstone to lime mudstone related to the off-platform setting.

Reverse lyotropic liquid crystals from europium nitrate and P123 with enhanced luminescence efficiency.

PubMed

Yi, Sijing; Li, Qintang; Liu, Hongguo; Chen, Xiao

2014-10-02

Fabrication of lyotropic aggregates containing the lanthanide ions is becoming a preferable way to prepare novel functional materials. Here, the lyotropic liquid crystals (LLCs) of reverse hexagonal, reverse bicontinuous cubic, and lamellar phases have been constructed in sequence directly from the mixtures of Eu(NO3)3·6H2O and Pluronic P123 amphiphilc block copolymer with increasing the salt proportion. Their phase types and structural characteristics were analyzed using polarized optical microscopy (POM) and small-angle X-ray scattering (SAXS) measurements. The driving forces of reverse LLC phase formation were investigated using Fourier-transformed infrared spectroscopy (FTIR) and rheological measurements. The hydrated europium salt was found to act not only as a solvent here, but also as the bridge to form hydrogen bonding between coordinated water molecules and PEO blocks, which played a key role in the reverse LLCs formation. Compared to those in aqueous solutions and solid state, the enhanced luminescence quantum yields and prolonged excited state lifetimes were observed in two europium containing reverse mesophases. The luminescence quenching effect of lanthanide ions was efficiently suppressed, probably due to the substitution of coordinated water molecules by oxyethyl groups of P123 and ordered phase structures of LLCs, where the coordinated europium ions were confined and isolated by PEO blocks. The optimum luminescence performance was then found to exist in the reverse hexagonal phase. The obtained results on such lanthanide-induced reverse LLCs should be referable for designing new luminescent soft materials construction to expand their application fields.

Diagenetic Microcrystalline Opal Varieties from the Monterey Formation, CA: HRTEM Study of Structures and Phase Transformation Mechanisms

NASA Technical Reports Server (NTRS)

Cady, Sherry L.; Wenk, H.-R.; DeVincenzi, Don (Technical Monitor)

1994-01-01

Microcrystalline opal varieties form as intermediary precipitates during the diagenetic transformation of biogenically precipitated non-crystalline opal (opal-A) to microquartz. With regard to the Monterey Formation of California, X-ray powder diffraction studies have shown that a decrease in the primary d-spacing of opal-CT toward that of cristobalite occurs with increasing diagenesis. The initial timing of opal-CT/quartz formation and the value of the primary opal-CT d-spacing, are influenced by the sediment. lithology. Transmission electron microscopy methods (CTEM/HRTEM) were used to investigate the structure of the diagenetic phases and establish transformation mechanisms between the varieties of microcrystalline opals in charts and porcelanites from the Monterey Formation. HRTEM images revealed that the most common fibrous varieties of microcrystalline opals contain varying amounts of structural disorder. Finite lamellar units of cristobalite-and tridymite-type. layer sequences were found to be randomly stacked in a direction perpendicular to the fiber axis. Disordered and ordered fibers were found to have coprecipitated within the same radial fiber bundles that formed within the matrix of the Most siliceous samples. HRTEM images, which reveal that the fibers within radial and lepispheric fiber bundles branch non-crystallographically, support an earlier proposal that microspheres in chert grow via a spherulitic growth mechanism. A less common variety of opal-CT was found to be characterized by non-parallel (low-angle) stacking sequences that often contain twinned lamellae. Tabular-shaped crystals of orthorhombic tridymite (PO-2) were also identified in the porcelanite samples. A shift in the primary d-spacing of opal-CT has been interpreted as an indication of solid-state ordering g toward a predominantly cristobalite structure, (opal-C). Domains of opal-C were identified as topotactically-oriented overgrowths on discrete Sections of opal-CT fibers and as lamellar domains within relict opal-CT fibers. These findings indicate that the type of transformation mechanism depends upon the primary structural characteristics of the authigenic opaline. varieties that are in turn influenced by the sediment lithology.

Hot subdwarfs in (eclipsing) binaries with brown dwarf or low-mass main-sequence companions

NASA Astrophysics Data System (ADS)

Schaffenroth, Veronika; Geier, Stephan; Heber, Uli

2014-09-01

The formation of hot subdwarf stars (sdBs), which are core helium-burning stars located on the extended horizontal branch, is not yet understood. Many of the known hot subdwarf stars reside in close binary systems with short orbital periods of between a few hours and a few days, with either M-star or white-dwarf companions. Common-envelope ejection is the most probable formation channel. Among these, eclipsing systems are of special importance because it is possible to constrain the parameters of both components tightly by combining spectroscopic and light-curve analyses. They are called HW Virginis systems. Soker (1998) proposed that planetary or brown-dwarf companions could cause the mass loss necessary to form an sdB. Substellar objects with masses greater than >10 M_J were predicted to survive the common-envelope phase and end up in a close orbit around the stellar remnant, while planets with lower masses would entirely evaporate. This raises the question if planets can affect stellar evolution. Here we report on newly discovered eclipsing or not eclipsing hot subdwarf binaries with brown-dwarf or low-mass main-sequence companions and their spectral and photometric analysis to determine the fundamental parameters of both components.

Induction of trap formation in nematode-trapping fungi by bacteria-released ammonia.

PubMed

Su, H N; Xu, Y Y; Wang, X; Zhang, K Q; Li, G H

2016-04-01

A total of 11 bacterial strains were assayed for bacteria-induced trap formation in the nematode-trapping fungus Arthrobotrys oligospora YMF1·01883 with two-compartmented Petri dish. These strains were identified on the basis of their 16S rRNA gene sequences. Volatile organic compounds (VOCs) of eight isolates were extracted using solid-phase micro-extraction (SPME) and their structures were identified based on gas chromatography-mass spectrometry (GC-MS). At the same time, all isolates were used for quantitative measurement of ammonia by the indophenol blue method. The effects of pure commercial compounds on inducement of trap formation in A. oligospora were tested. Taken together, results demonstrated that the predominant bacterial volatile compound inducing trap formation was ammonia. Meanwhile, ammonia also played a role in other nematode-trapping fungi, including Arthrobotrys guizhouensis YMF1·00014, producing adhesive nets; Dactylellina phymatopaga YMF1·01474, producing adhesive knobs; Dactylellina cionopaga YMF1·01472, producing adhesive columns and Drechslerella brochopaga YMF1·01829, producing constricting rings. © 2016 The Society for Applied Microbiology.

On the nature of phase attraction in sensorimotor synchronization with interleaved auditory sequences.

PubMed

Repp, Bruno H

2004-10-01

In a task that requires in-phase synchronization of finger taps with an isochronous sequence of target tones that is interleaved with a sequence of distractor tones at various fixed phase relationships, the taps tend to be attracted to the distractor tones, especially when the distractor tones closely precede the target tones [Repp, B. H. (2003a). Phase attraction in sensorimotor synchronization with auditory sequences: Effects of single and periodic distractors on synchronization accuracy. Journal of Experimental Psychology: Human Perception and Performance, 29, 290-309]. The present research addressed two related questions about this distractor effect: (1) Is it a function of the absolute temporal separation or of the relative phase of the two stimulus sequences? (2) Is it the result of perceptual grouping (integration) of target and distractor tones or of simultaneous attraction to two independent sequences? In three experiments, distractor effects were compared across two different sequence rates. The results suggest that absolute temporal separation, not relative phase, is the critical variable. Experiment 3 also included an anti-phase tapping task that addressed the second question directly. The results suggest that the attraction of taps to distractor tones is caused mainly by temporal integration of target and distractor tones within a fixed window of 100-150 ms duration, with the earlier-occurring tone being weighted more strongly than the later-occurring one.

Evolution of the Alpine Tethys (Sava) suture zone in Fruška Gora Mountains (N Serbia): from orogenic building to tectonic omissions

NASA Astrophysics Data System (ADS)

Toljić, Marinko; Matenco, Liviu; ĐErić, Nevenka; Milivojević, Jelena; Gerzina, Nataša.; Stojadinović, Uros

2010-05-01

The Fru\\vska Gora Mountains in northern Serbia offers an unique opportunity to study the Cretaceous-Eocene evolution of the NE part of the Dinarides, which is largely covered elsewhere beneath the thick Miocene sediments of the Pannonian basin, deposited during the back-arc collapse associated with the subduction and roll-back recorded in the external Carpathians. The structural grain of the Fru\\vska Gora Mountains is the one of a large scale antiform, exposing a complex puzzle of highly deformed metamorphic rocks in its centre and Triassic-Miocene sequence of non-metamorphosed sediments, ophiolites and volcanics along its flanks. The metamorphic rocks were the target of structural investigations coupled with paleontological dating (conodonts, palynomorphs and radiolarians) in an effort to unravel the geodynamic evolution of an area thought to be located near the suture zone between the Tisza upper plate and the Adriatic lower plate, i.e. the Sava subduction zone of the Dinarides (e.g., Pamic, 2002; Schmid et al., 2008). The existence of this subduction zone was previously inferred here by local observations, such as metamorphosed Mesozoic sediments containing Middle Triassic conodonts (Đurđanović, 1971) or Early Cretaceous blue schists metamorphism (123±5 Ma, Milovanović et al., 1995). The metamorphic sequence is characterized by a Paleozoic age meta-sedimentary basement which contains palynomorphs of Upper Paleozoic - Carboniferous age and a meta-sedimentary and meta-volcanic sequence which contain a succession of contrasting metamorphosed lithologies such sandstones, black limestones, shallow water white limestones, basic volcanic sequences, deep nodular limestiones, radiolarites, meta-ophiolites and turbiditic sequences. The lower part of the sequence is contrastingly similar with the Triassic cover of the Drina-Ivanijca thrust sheet and its metamorphosed equivalent observed in the Kopaonik and Studenica series (Schefer et al., in press). This observation is supported by the newly found micro-fauna of Upper Triassic in age in the meta-sandstones associated with meta-volcanics on the SW slopes of the mountain. The upper part of the sequence display metamorphosed "flysh"-type of sequences and meta-basalts. In these deposits, slightly metamorphosed siliciclastics (lithic sandstones with volcanic-derived clasts) previously interpreted as Upper Jurassic mélange have proved to contain Upper Cretaceous palynomorphs. Among the rocks exposed in the metamorphic core of the mountains, the SW slope of Fru\\vska Gora offers the optimal locality for the study of the kinematic evolution. Here, four phases of folding have been mapped, being associated mainly with large-scale regional contraction. The first phase is characterized by isoclinal folding, with reconstructed SW vergence. The second generation of E-W oriented and coaxial folds is asymmetric and is up to metres in size, displaying a south vergence and has largely refolded the previous generation. The third event was responsible for the formation of upright folds, yet again E-W oriented, re-folding earlier structures. The first two phases of folding are associated with metamorphic conditions, while the third was apparently near the transition with the brittle domain. The relationship with a fourth folding event observed also in the non-metamorphosed clastic-carbonate rocks is rather uncertain, but is apparently associated with the present day antiformal structure of the Fuska Gora Mountains. Interestingly, the metamorphosed Triassic and Upper Cretaceous carbonatic-clastic sequence in the core of the antiform is in structural contact along the antiformal flanks with Lower-Middle Triassic and Upper Cretaceous-Paleogene sediments which display the same facies, but these are not metamorphosed. This demonstrates a large scale tectonic omission along the flanks of the Fru\\vska Gora antiform, 9-10km of rocks being removed by what we speculatively define as an extensional detachment exhuming the metamorphic core. This detachment has been subsequently folded into the present-day antiformal geometry of the Fru\\vska Gora Mountains. These findings demonstrate that the metamorphic and non-metamorphic Upper Cretaceous - Paleogene clastic-carbonate sediments belongs to the main Alpine Tethys (Sava) subduction zone of the Dinarides. The Paleozoic-Triassic metamorphic and non-metamorphic rocks belong to the distal Adriatic lower plate, or more precisely to the Jadar-Kopaonik composite thrust sheet (Schmid et al., 2008), while the layer of serpentinized peridotite found at their contact most probably belongs to the Western Vardar ophiolites obducted over the Adriatic plate during Late Jurassic - Earliest Cretaceous. The distal Jadar-Kopaonik composite unit was partly affected by strong contractional deformation and a Late Eocene greenschist facies metamorphism during the main phase of subduction and collision, similarly to what has been observed elsewhere in the Dinarides (Pamić, 2002; Schefer et al., in press). A Miocene phase of core-complex formation was responsible for the large tectonic omission observed, being probably followed by the formation of a wide open antiformal structure during the Pliocene-Quaternary inversion of the Pannonian basin.

Haplotype estimation using sequencing reads.

PubMed

Delaneau, Olivier; Howie, Bryan; Cox, Anthony J; Zagury, Jean-François; Marchini, Jonathan

2013-10-03

High-throughput sequencing technologies produce short sequence reads that can contain phase information if they span two or more heterozygote genotypes. This information is not routinely used by current methods that infer haplotypes from genotype data. We have extended the SHAPEIT2 method to use phase-informative sequencing reads to improve phasing accuracy. Our model incorporates the read information in a probabilistic model through base quality scores within each read. The method is primarily designed for high-coverage sequence data or data sets that already have genotypes called. One important application is phasing of single samples sequenced at high coverage for use in medical sequencing and studies of rare diseases. Our method can also use existing panels of reference haplotypes. We tested the method by using a mother-father-child trio sequenced at high-coverage by Illumina together with the low-coverage sequence data from the 1000 Genomes Project (1000GP). We found that use of phase-informative reads increases the mean distance between switch errors by 22% from 274.4 kb to 328.6 kb. We also used male chromosome X haplotypes from the 1000GP samples to simulate sequencing reads with varying insert size, read length, and base error rate. When using short 100 bp paired-end reads, we found that using mixtures of insert sizes produced the best results. When using longer reads with high error rates (5-20 kb read with 4%-15% error per base), phasing performance was substantially improved. Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Tectonic signatures on active margins

NASA Astrophysics Data System (ADS)

Hogarth, Leah Jolynn

High-resolution Compressed High-Intensity Radar Pulse (CHIRP) surveys offshore of La Jolla in southern California and the Eel River in northern California provide the opportunity to investigate the role of tectonics in the formation of stratigraphic architecture and margin morphology. Both study sites are characterized by shore-parallel tectonic deformation, which is largely observed in the structure of the prominent angular unconformity interpreted as the transgressive surface. Based on stratal geometry and acoustic character, we identify three sedimentary sequences offshore of La Jolla: an acoustically laminated estuarine unit deposited during early transgression, an infilling or "healing-phase" unit formed during the transgression, and an upper transparent unit. The estuarine unit is confined to the canyon edges in what may have been embayments during the last sea-level rise. The healing-phase unit appears to infill rough areas on the transgressive surface that may be related to relict fault structures. The upper transparent unit is largely controlled by long-wavelength tectonic deformation due to the Rose Canyon Fault. This unit is also characterized by a mid-shelf (˜40 m water depth) thickness high, which is likely a result of hydrodynamic forces and sediment grain size. On the Eel margin, we observe three distinct facies: a seaward-thinning unit truncated by the transgressive surface, a healing-phase unit confined to the edges of a broad structural high, and a highly laminated upper unit. The seaward-thinning wedge of sediment below the transgressive surface is marked by a number of channels that we interpret as distributary channels based on their morphology. Regional divergence of the sequence boundary and transgressive surface with up to ˜8 m of sediment preserved across the interfluves suggests the formation of subaerial accommodation during the lowstand. The healing-phase, much like that in southern California, appears to infill rough areas in the transgressive surface. Reflectors within the laminated upper unit exhibit divergence towards the Eel River Syncline, which suggests that deposition in the syncline is syntectonic. The transgressive surface is offset across the Eureka Anticline indicating deformation has occurred since ˜10 ka. The relief observed along the transgressive surface is consistent with deformation rates measured onshore.

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.

In situ spectroscopic study of the plastic deformation of amorphous silicon under non-hydrostatic conditions induced by indentation

PubMed Central

Gerbig, Y.B; Michaels, C.A.; Bradby, J.E.; Haberl, B.; Cook, R.F.

2016-01-01

Indentation-induced plastic deformation of amorphous silicon (a-Si) thin films was studied by in situ Raman imaging of the deformed contact region of an indented sample, employing a Raman spectroscopy-enhanced instrumented indentation technique. Quantitative analyses of the generated in situ Raman maps provide unique, new insight into the phase behavior of as-implanted a-Si. In particular, the occurrence and evolving spatial distribution of changes in the a-Si structure caused by processes, such as polyamorphization and crystallization, induced by indentation loading were measured. The experimental results are linked with previously published work on the plastic deformation of a-Si under hydrostatic compression and shear deformation to establish a sequence for the development of deformation of a-Si under indentation loading. The sequence involves three distinct deformation mechanisms of a-Si: (1) reversible deformation, (2) increase in coordination defects (onset of plastic deformation), and (3) phase transformation. Estimated conditions for the occurrence of these mechanisms are given with respect to relevant intrinsic and extrinsic parameters, such as indentation stress, volumetric strain, and bond angle distribution (a measure for the structural order of the amorphous network). The induced volumetric strains are accommodated solely by reversible deformation of the tetrahedral network when exposed to small indentation stresses. At greater indentation stresses, the increased volumetric strains in the tetrahedral network lead to the formation of predominately five-fold coordination defects, which seems to mark the onset of irreversible or plastic deformation of the a-Si thin film. Further increase in the indentation stress appears to initiate the formation of six-fold coordinated atomic arrangements. These six-fold coordinated arrangements may maintain their amorphous tetrahedral structure with a high density of coordination defects or nucleate as a new crystalline β-tin phase within the a-Si network. PMID:26924926

Steady state solutions to dynamically loaded periodic structures

NASA Technical Reports Server (NTRS)

Kalinowski, A. J.

1980-01-01

The general problem of solving for the steady state (time domain) dynamic response (i.e., NASTRAN rigid format-8) of a general elastic periodic structure subject to a phase difference loading of the type encountered in traveling wave propagation problems was studied. Two types of structural configurations were considered; in the first type, the structure has a repeating pattern over a span that is long enough to be considered, for all practical purposes, as infinite; in the second type, the structure has structural rotational symmetry in the circumferential direction. The theory and a corresponding set of DMAP instructions which permits the NASTRAN user to automatically alter the rigid format-8 sequence to solve the intended class of problems are presented. Final results are recovered as with any ordinary rigid format-8 solution, except that the results are only printed for the typical periodic segment of the structure. A simple demonstration problem having a known exact solution is used to illustrate the implementation of the procedure.

Willy: A prize noble Ur-Fremdling - Its history and implications for the formation of Fremdlinge and CAI

NASA Technical Reports Server (NTRS)

Armstrong, J. T.; El Goresy, A.; Wasserburg, G. J.

1985-01-01

The structure and composition of Willy, a 150-micron-diameter Fremdling in CAI 5241 from the Allende meteorite, are investigated using optical, secondary-electron, and electron-backscatter microscopy and electron-microprobe analysis. The results are presented in diagrams, maps, tables, graphs, and micrographs and compared with those for other Allende Fremdlinge. Willy is found to have a concentric-zone structure comprising a complex porous core of magnetite, metal, sulfide, scheelite, and other minor phases; a compact magnetite-apatite mantle; a thin (20 microns or less) reaction-assemblage zone; and a dense outer rim of fassaite with minor spinel. A multistage formation sequence involving changes in T and fO2 and preceding the introduction of Willy into the CAI (which itself preceded CAI spinel and silicate formation) is postulated, and it is inferred from the apparent lack of post-capture recrystallization that Willy has not been subjected to temperatures in excess of 600 C and may represent the precursor material for many other Fremdlinge.

Phase formation in the (1-y)BiFeO{sub 3}-yBiScO{sub 3} system under ambient and high pressure

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

Salak, A.N., E-mail: salak@ua.pt; Khalyavin, D.D., E-mail: dmitry.khalyavin@stfc.ac.uk; Pushkarev, A.V.

Formation and thermal stability of perovskite phases in the BiFe{sub 1-y}Sc{sub y}O{sub 3} system (0≤y≤0.70) were studied. When the iron-to-scandium substitution rate does not exceed about 15 at%, the single-phase perovskite ceramics with the rhombohedral R3c symmetry (as that of the parent compound, BiFeO{sub 3}) can be prepared from the stoichiometric mixture of the respective oxides at ambient pressure. Thermal treatment of the oxide mixtures with a higher content of scandium results in formation of two main phases, namely a BiFeO{sub 3}-like R3c phase and a cubic (I23) sillenite-type phase based on γ-Bi{sub 2}O{sub 3}. Single-phase perovskite ceramics of themore » BiFe{sub 1-y}Sc{sub y}O{sub 3} composition were synthesized under high pressure from the thermally treated oxide mixtures. When y is between 0 and 0.25 the high-pressure prepared phase is the rhombohedral R3c with the √2a{sub p}×√2a{sub p}×2√3a{sub p} superstructure (a{sub p} ~ 4 Å is the pseudocubic perovskite unit-cell parameter). The orthorhombic Pnma phase (√2a{sub p}×4a{sub p}×2√2a{sub p}) was obtained in the range of 0.30≤y≤0.60, while the monoclinic C2/c phase (√6a{sub p}×√2a{sub p}×√6a{sub p}) is formed when y=0.70. The normalized unit-cell volume drops at the crossover from the rhombohedral to the orthorhombic composition range. The perovskite BiFe{sub 1-y}Sc{sub y}O{sub 3} phases prepared under high pressure are metastable regardless of their symmetry. At ambient pressure, the phases with the compositions in the ranges of 0.20≤y≤0.25, 0.30≤y<0.50 and 0.50≤y≤0.70 start to decompose above 970, 920 and 870 K, respectively. - Graphical abstract: Formation of perovskite phases in the BiFe{sub 1-y}Sc{sub y}O{sub 3} system when y≥0.15 requires application of pressure of several GPa. The phases formed under high pressure: R3c (0.20≤y≤0.25), Pnma (0.30≤y≤0.60) and C2/c (y≥0.70) are metastable. - Highlights: • Maximal Fe-to-Sc substitution rate in BiFeO{sub 3} at ambient pressure is about 15 at%. • R3c → Pnma → C2/c phase sequence in high-pressure prepared BiFe{sub 1-y}Sc{sub y}O{sub 3} ceramics. • The perovskite BiFe{sub 1-y}Sc{sub y}O{sub 3} phases formed under high pressure are metastable.« less

ACTG: novel peptide mapping onto gene models.

PubMed

Choi, Seunghyuk; Kim, Hyunwoo; Paek, Eunok

2017-04-15

In many proteogenomic applications, mapping peptide sequences onto genome sequences can be very useful, because it allows us to understand origins of the gene products. Existing software tools either take the genomic position of a peptide start site as an input or assume that the peptide sequence exactly matches the coding sequence of a given gene model. In case of novel peptides resulting from genomic variations, especially structural variations such as alternative splicing, these existing tools cannot be directly applied unless users supply information about the variant, either its genomic position or its transcription model. Mapping potentially novel peptides to genome sequences, while allowing certain genomic variations, requires introducing novel gene models when aligning peptide sequences to gene structures. We have developed a new tool called ACTG (Amino aCids To Genome), which maps peptides to genome, assuming all possible single exon skipping, junction variation allowing three edit distances from the original splice sites, exon extension and frame shift. In addition, it can also consider SNVs (single nucleotide variations) during mapping phase if a user provides the VCF (variant call format) file as an input. Available at http://prix.hanyang.ac.kr/ACTG/search.jsp . eunokpaek@hanyang.ac.kr. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

O + ion conic and plasma sheet dynamics observed by Van Allen Probe satellites during the 1 June 2013 magnetic storm: Energetic Inner Magnetosphere O + Ions

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

Burke, W. J.; Erickson, P. J.; Yang, J.

The Van Allen Probe satellites were near apogee in the late evening local time sector during the 1 June 2013 magnetic storm's main phase. About an hour after crossing the ring current's “nose structure” into the plasma sheet, the satellites encountered a quasiperiodic sequence of 0.08–3 keV O + ions. Pitch angle distributions of this population consistently peaked nearly antiparallel to the local magnetic field. We then interpret this population as O + conics originating in the northern ionosphere. The sequences began as fairly steady state conic fluxes with energies in the ~ 80 to 100 eV range. Over aboutmore » a half hour buildup phase, O + energies peaked near 1 keV. During subsequent release phases lasting ~ 20 min, O + energies returned to low-energy starting points. We argue these observations reflect repeated formations and dissolutions of downward, magnetically aligned electric fields (ε||) layers trapping O + conics between mirror points within heating layers below and electrostatic barriers above. Nearly identical variations were observed at the locations of both satellites during 9 of these 13 conic cycles. Phase differences between cycles were observed at both spacecraft during the remaining events. Most “buildup” to “release” phase transitions coincided with AL index minima. But, in situ magnetometer measurements indicate only weak dipolarizations of tail-like magnetic fields. The lack of field-aligned reflected O + and tail-like magnetic fields suggest that both ionospheres may be active. However, Southern Hemisphere origin conics cannot be observed since they would be isotropized and accelerated during neutral sheet crossings.« less

O + ion conic and plasma sheet dynamics observed by Van Allen Probe satellites during the 1 June 2013 magnetic storm: Energetic Inner Magnetosphere O + Ions

DOE PAGES

Burke, W. J.; Erickson, P. J.; Yang, J.; ...

2016-05-07

The Van Allen Probe satellites were near apogee in the late evening local time sector during the 1 June 2013 magnetic storm's main phase. About an hour after crossing the ring current's “nose structure” into the plasma sheet, the satellites encountered a quasiperiodic sequence of 0.08–3 keV O + ions. Pitch angle distributions of this population consistently peaked nearly antiparallel to the local magnetic field. We then interpret this population as O + conics originating in the northern ionosphere. The sequences began as fairly steady state conic fluxes with energies in the ~ 80 to 100 eV range. Over aboutmore » a half hour buildup phase, O + energies peaked near 1 keV. During subsequent release phases lasting ~ 20 min, O + energies returned to low-energy starting points. We argue these observations reflect repeated formations and dissolutions of downward, magnetically aligned electric fields (ε||) layers trapping O + conics between mirror points within heating layers below and electrostatic barriers above. Nearly identical variations were observed at the locations of both satellites during 9 of these 13 conic cycles. Phase differences between cycles were observed at both spacecraft during the remaining events. Most “buildup” to “release” phase transitions coincided with AL index minima. But, in situ magnetometer measurements indicate only weak dipolarizations of tail-like magnetic fields. The lack of field-aligned reflected O + and tail-like magnetic fields suggest that both ionospheres may be active. However, Southern Hemisphere origin conics cannot be observed since they would be isotropized and accelerated during neutral sheet crossings.« less

Random sequences generation through optical measurements by phase-shifting interferometry

NASA Astrophysics Data System (ADS)

François, M.; Grosges, T.; Barchiesi, D.; Erra, R.; Cornet, A.

2012-04-01

The development of new techniques for producing random sequences with a high level of security is a challenging topic of research in modern cryptographics. The proposed method is based on the measurement by phase-shifting interferometry of the speckle signals of the interaction between light and structures. We show how the combination of amplitude and phase distributions (maps) under a numerical process can produce random sequences. The produced sequences satisfy all the statistical requirements of randomness and can be used in cryptographic schemes.

Nucleation, growth and evolution of calcium phosphate films on calcite.

PubMed

Naidu, Sonia; Scherer, George W

2014-12-01

Marble, a stone composed of the mineral calcite, is subject to chemically induced weathering in nature due to its relatively high dissolution rate in acid rain. To protect monuments and sculpture from corrosion, we are investigating the application of thin layers of hydroxyapatite (HAP) onto marble. The motivation for using HAP is its low dissolution rate and crystal and lattice compatibility with calcite. A mild, wet chemical synthesis route, in which diammonium hydrogen phosphate salt was reacted with marble, alone and with cationic and anionic precursors under different reaction conditions, was used to produce inorganic HAP layers on marble. Nucleation and growth on the calcite substrate was studied, as well as metastable phase evolution, using scanning electron microscopy, grazing incidence X-ray diffraction, and atomic force microscopy. Film nucleation was enhanced by surface roughness. The rate of nucleation and the growth rate of the film increased with cationic (calcium) and anionic (carbonate) precursor additions. Calcium additions also influenced phase formation, introducing a metastable phase (octacalcium phosphate) and a different phase evolution sequence. Copyright © 2014 Elsevier Inc. All rights reserved.

Effects of plant downtime on the microbial community composition in the highly saline brine of a geothermal plant in the North German Basin.

PubMed

Westphal, Anke; Lerm, Stephanie; Miethling-Graff, Rona; Seibt, Andrea; Wolfgramm, Markus; Würdemann, Hilke

2016-04-01

The microbial biocenosis in highly saline fluids produced from the cold well of a deep geothermal heat store located in the North German Basin was characterized during regular plant operation and immediately after plant downtime phases. Genetic fingerprinting revealed the dominance of sulfate-reducing bacteria (SRB) and fermentative Halanaerobiaceae during regular plant operation, whereas after shutdown phases, sequences of sulfur-oxidizing bacteria (SOB) were also detected. The detection of SOB indicated oxygen ingress into the well during the downtime phase. High 16S ribosomal RNA (rRNA) and dsrA gene copy numbers at the beginning of the restart process showed an enrichment of bacteria, SRB, and SOB during stagnant conditions consistent with higher concentrations of dissolved organic carbon (DOC), sulfate, and hydrogen sulfide in the produced fluids. The interaction of SRB and SOB during plant downtimes might have enhanced the corrosion processes occurring in the well. It was shown that scale content of fluids was significantly increased after stagnant phases. Moreover, the sulfur isotopic signature of the mineral scales indicated microbial influence on scale formation.

Viking Lander imaging investigation: Picture catalog of primary mission experiment data record

NASA Technical Reports Server (NTRS)

Tucker, R. B.

1978-01-01

All the images returned by the two Viking Landers during the primary phase of the Viking Mission are presented. Listings of supplemental information which described the conditions under which the images were acquired are included together with skyline drawings which show where the images are positioned in the field of view of the cameras. Subsets of the images are listed in a variety of sequences to aid in locating images of interest. The format and organization of the digital magnetic tape storage of the images are described. The mission and the camera system are briefly described.

Feasibility and systems definition study for microwave multi-application payload (MMAP)

NASA Technical Reports Server (NTRS)

Horton, J. B.; Allen, C. C.; Massaro, M. J.; Zemany, J. L.; Murrell, J. W.; Stanhouse, R. W.; Condon, G. P.; Stone, R. F.

1977-01-01

There were three Shuttle/Spacelab experiments: adaptive multibeam phased array antenna (AMPA) experiment, electromagnetic environment experiment (EEE), and millimeter wave communications experiment (MWCE). Work on the AMPA experiment was completed. Results included are definition of operating modes, sequence of operation, radii of operation about several ground stations, signal format, foot prints of typical orbits and preliminary definition of ground and user terminals. Definition of the MOD I EEE included conceptual hardware designs, spacelab interfaces, preliminary data handling methods, experiment tests and verification, and EMC studies. The MWCE was defined conceptually for a steerable high gain antenna.

Phase correction, phase resetting, and phase shifts after subliminal timing perturbations in sensorimotor synchronization.

PubMed

Repp, B H

2001-06-01

Recent studies of synchronized finger tapping have shown that perceptually subliminal phase shifts in an auditory sequence are rapidly compensated for in the motor activity (B. H. Repp, 2000a). Experiment 1 used a continuation-tapping task to confirm that this compensation is indeed a phase correction, not an adjustment of the central timekeeper period. Experiments 2-5 revealed that this phase correction occurs even when there is no ordinary sensorimotor asynchrony--when the finger taps are in antiphase or arbitrary phase relative to the auditory sequence (Experiments 2 and 3) or when the tap coinciding with the sequence phase shift is withheld (Experiments 4 and 5). The phase correction observed in the latter conditions was instantaneous, which suggests that phase resetting occurs when the motor activity is discontinuous. A prolonged phase shift suggestive of overcompensation was observed in some conditions, which poses a challenge to pure phase correction models.

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

NASA Astrophysics Data System (ADS)

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

2006-08-01

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

Reactive Desorption and Radiative Association as Possible Drivers of Complex Molecule Formation in the Cold Interstellar Medium

NASA Astrophysics Data System (ADS)

Vasyunin, A. I.; Herbst, Eric

2013-05-01

The recent discovery of terrestrial-type organic species such as methyl formate and dimethyl ether in the cold interstellar gas has proved that the formation of organic matter in the Galaxy begins at a much earlier stage of star formation than was previously thought. This discovery represents a challenge for astrochemical modelers. The abundances of these molecules cannot be explained by the previously developed "warm-up" scenario, in which organic molecules are formed via diffusive chemistry on surfaces of interstellar grains starting at 30 K, and then released to the gas at higher temperatures during later stages of star formation. In this article, we investigate an alternative scenario in which complex organic species are formed via a sequence of gas-phase reactions between precursor species formed on grain surfaces and then ejected into the gas via efficient reactive desorption, a process in which non-thermal desorption occurs as a result of conversion of the exothermicity of chemical reactions into the ejection of products from the surface. The proposed scenario leads to reasonable if somewhat mixed results at temperatures as low as 10 K and may be considered as a step toward the explanation of abundances of terrestrial-like organic species observed during the earliest stages of star formation.

Satellite RNA Increases DNA Damage and Accelerates Tumor Formation in Mouse Models of Pancreatic Cancer.

PubMed

Kishikawa, Takahiro; Otsuka, Motoyuki; Suzuki, Tatsunori; Seimiya, Takahiro; Sekiba, Kazuma; Ishibashi, Rei; Tanaka, Eri; Ohno, Motoko; Yamagami, Mari; Koike, Kazuhiko

2018-05-10

Highly repetitive tandem arrays such as satellite sequences in the centromeric and pericentromeric regions of chromosomes, which were previously considered to be silent, are actively transcribed in various biological processes, including cancers. In the pancreas, this aberrant expression occurs even in Kras-mutated pancreatic intraepithelial neoplasia (PanIN) tissues, which are precancerous lesions. To determine the biological role of satellite RNAs in carcinogenesis in vivo , we constructed mouse major satellite (MajSAT) RNA-expressing transgenic mice. However, these transgenic mice did not show spontaneous malignant tumor formation under normal breeding. Importantly, however, DNA damage was increased in pancreatic tissues induced by caerulein treatment or high-fat diet, which may be due to impaired nuclear localization of Y-Box Binding Protein 1 (YBX1), a component of the DNA damage repair machinery. In addition, when crossed with pancreas-specific Kras-mutant mice, MajSAT RNA expression resulted in an earlier increase in PanIN formation. These results suggest that aberrant MajSAT RNA expression accelerates oncogenesis by increasing the probability of a second driver mutation, thus accelerating cells to exit from the breakthrough phase to the expansion phase. Implications: Aberrant expression of satellite RNAs accelerates oncogenesis through a mechanism involving increased DNA damage. Mol Cancer Res; 1-8. ©2018 AACR. ©2018 American Association for Cancer Research.

Swarm v2: highly-scalable and high-resolution amplicon clustering

PubMed Central

Quince, Christopher; de Vargas, Colomban; Dunthorn, Micah

2015-01-01

Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks. PMID:26713226

Magnetic flux density measurement with balanced steady state free precession pulse sequence for MREIT: a simulation study.

PubMed

Minhas, Atul S; Woo, Eung Je; Lee, Soo Yeol

2009-01-01

Magnetic Resonance Electrical Impedance Tomography (MREIT) utilizes the magnetic flux density B(z), generated due to current injection, to find conductivity distribution inside an object. This B(z) can be measured from MR phase images using spin echo pulse sequence. The SNR of B(z) and the sensitivity of phase produced by B(z) in MR phase image are critical in deciding the resolution of MREIT conductivity images. The conventional spin echo based data acquisition has poor phase sensitivity to current injection. Longer scan time is needed to acquire data with higher SNR. We propose a balanced steady state free precession (b-SSFP) based pulse sequence which is highly sensitive to small off-resonance phase changes. A procedure to reconstruct B(z) from MR signal obtained with b-SSFP sequence is described. Phases for b-SSFP signals for two conductivity phantoms of TX 151 and Gelatin are simulated from the mathematical models of b-SSFP signal. It was observed that the phase changes obtained from b-SSFP pulse sequence are highly sensitive to current injection and hence would produce higher magnetic flux density. However, the b-SSFP signal is dependent on magnetic field inhomogeneity and the signal deteriorated highly for small offset from resonance frequency. The simulation results show that the b-SSFP sequence can be utilized for conductivity imaging of a local region where magnetic field inhomogeneity is small. A proper shimming of magnet is recommended before using the b-SSFP sequence.

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

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

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

1996-08-01

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

Quantitative comparison between a multiecho sequence and a single-echo sequence for susceptibility-weighted phase imaging.

PubMed

Gilbert, Guillaume; Savard, Geneviève; Bard, Céline; Beaudoin, Gilles

2012-06-01

The aim of this study was to investigate the benefits arising from the use of a multiecho sequence for susceptibility-weighted phase imaging using a quantitative comparison with a standard single-echo acquisition. Four healthy adult volunteers were imaged on a clinical 3-T system using a protocol comprising two different three-dimensional susceptibility-weighted gradient-echo sequences: a standard single-echo sequence and a multiecho sequence. Both sequences were repeated twice in order to evaluate the local noise contribution by a subtraction of the two acquisitions. For the multiecho sequence, the phase information from each echo was independently unwrapped, and the background field contribution was removed using either homodyne filtering or the projection onto dipole fields method. The phase information from all echoes was then combined using a weighted linear regression. R2 maps were also calculated from the multiecho acquisitions. The noise standard deviation in the reconstructed phase images was evaluated for six manually segmented regions of interest (frontal white matter, posterior white matter, globus pallidus, putamen, caudate nucleus and lateral ventricle). The use of the multiecho sequence for susceptibility-weighted phase imaging led to a reduction of the noise standard deviation for all subjects and all regions of interest investigated in comparison to the reference single-echo acquisition. On average, the noise reduction ranged from 18.4% for the globus pallidus to 47.9% for the lateral ventricle. In addition, the amount of noise reduction was found to be strongly inversely correlated to the estimated R2 value (R=-0.92). In conclusion, the use of a multiecho sequence is an effective way to decrease the noise contribution in susceptibility-weighted phase images, while preserving both contrast and acquisition time. The proposed approach additionally permits the calculation of R2 maps. Copyright © 2012 Elsevier Inc. All rights reserved.

Synthesis and monitored selection of nucleotide surrogates for binding T:A base pairs in homopurine-homopyrimidine DNA triple helices.

PubMed

Mokhir, A A; Connors, W H; Richert, C

2001-09-01

A total of 16 oligodeoxyribonucleotides of general sequence 5'-TCTTCTZTCTTTCT-3', where Z denotes an N-acyl-N-(2-hydroxyethyl)glycine residue, were prepared via solid phase synthesis. The ability of these oligonucleotides to form triplexes with the duplex 5'-AGAAGATAGAAAGA-HEG-TCTTTCTATCTTCT-3', where HEG is a hexaethylene glycol linker, was tested. In these triplexes, an 'interrupting' T:A base pair faces the Z residue in the third strand. Among the acyl moieties of Z tested, an anthraquinone carboxylic acid residue linked via a glycinyl group gave the most stable triplex, whose UV melting point was 8.4 degrees C higher than that of the triplex with 5'-TCTTCTGTCTTTCT-3' as the third strand. The results from exploratory nuclease selection experiments suggest that a combinatorial search for strands capable of recognizing mixed sequences by triple helix formation is feasible.

Finite element analysis when orthogonal cutting of hybrid composite CFRP/Ti

NASA Astrophysics Data System (ADS)

Xu, Jinyang; El Mansori, Mohamed

2015-07-01

Hybrid composite, especially CFRP/Ti stack, is usually considered as an innovative structural configuration for manufacturing the key load-bearing components in modern aerospace industry. This paper originally proposed an FE model to simulate the total chip formation process dominated the hybrid cutting operation. The hybrid composite model was established based on three physical constituents, i.e., Ti constituent, interface and CFRP constituent. Different constitutive models and damage criteria were introduced to replicate the interrelated cutting behaviour of the stack material. The CFRP/Ti interface was modelled as a third phase through the concept of cohesive zone (CZ). Particular attention was made on the comparative studies of the influence of different cutting-sequence strategies on the machining responses induced in hybrid stack cutting. The numerical results emphasized the pivotal role of cutting-sequence strategy on the various machining induced responses including cutting-force generation, machined surface quality and induced interface damage.

Chemical Evidence for Evolution of galaxies

NASA Astrophysics Data System (ADS)

Dutil, Yvan

I have compiled the very best data published on abundance gradients. From this sample of 29 galaxies, some information can be gained on the mecanism of morphological evolution in disk galaxies. From this sample, I find that early-type galaxies show an identical trend in the behavior of extrapolated central abundance versus morphological type to that shown by late-type galaxies with strong bars, even in the absence of bar! On a a diagram showing extrapolated central abundance versus morphological type, two sequences appear: late-type barred galaxies and early-type galaxies (barred or not barred) fall on sequence 0.5 dex below that of normal late-type galaxies. This behavior is consistent with a scenario of morphological evolution of disk galaxies by formation and dissolution of a bar over a period of a few 10^^9 yr, where later type galaxies (Sd,Sc,Sbc, evolve into earlier-type disk galaxies trough transitory SBc and SBb phases.

Post-Starburst Galaxies At The End of The E+A Phase

NASA Astrophysics Data System (ADS)

Liu, Charles; Marinelli, Mariarosa; Chang, Madeleine; Lyczko, Camilla; Vega Orozco, Cecilia; SDSS-IV Collaboration

2018-06-01

Post-starburst galaxies, once thought to be rare curiosities, are now recognized to represent a key phase in the galaxy evolution. The post-starburst, or E+A phase, should however not be considered as a single, short-lived phenomenon; rather, it is an extended evolutionary process that occurs a galaxy transitions from an actively star-forming system into a quiescent one. We present a study of nearby galaxies at or near the end of the E+A phase, wherein all star formation has been quenched, the fossilized stellar population of the most recent starburst is highly localized, and the remainder of the galaxy's stellar population is old and quiescent. The luminosity and stellar age distribution of these "end-phase E+As" can provide insights into the evolution of galaxies onto and within the red sequence, from active to passive systems. This work is supported by National Science Foundation grants to CUNY College of Staten Island and the American Museum of Natural History; the College of Staten Island Office of Academic Affairs; the Sherman Fairchild Science Pathways Scholars Program (SP^2) at Barnard College; and the Alfred P. Sloan Foundation.

Examination of Multiphase (Zr,Ti)(V,Cr,Mn,Ni)2 Ni-MH Electrode Alloys: Part I. Dendritic Solidification Structure

NASA Astrophysics Data System (ADS)

Boettinger, W. J.; Newbury, D. E.; Wang, K.; Bendersky, L. A.; Chiu, C.; Kattner, U. R.; Young, K.; Chao, B.

2010-08-01

The solidification microstructures of three nine-element Zr-Ni-based AB2 type C14/C15 Laves hydrogen storage alloys are determined. The selected compositions represent a class of alloys being examined for usage as an MH electrode in nickel metal-hydride batteries that often have their best properties in the cast state. Solidification is accomplished by dendritic growth of hexagonal C14 Laves phase, peritectic solidification of cubic C15 Laves phase, and formation of cubic B2 phase in the interdendritic regions. The B2 phase decomposes in the solid state into a complex multivariate platelike structure containing Zr-Ni-rich intermetallics. The observed sequence C14/C15 upon solidification agrees with predictions using effective compositions and thermodynamic assessments of the ternary systems, Ni-Cr-Zr and Cr-Ti-Zr. Experimentally, the closeness of the compositions of the C14 and C15 phases required the use of compositional mapping with an energy dispersive detector capable of processing a very high X-ray flux to locate regions in the microstructure for quantitative composition measurement and transmission electron microscope examination.

Metastable tantalum oxide formation during the devitrification of amorphous tantalum thin films

DOE PAGES

Donaldson, Olivia K.; Hattar, Khalid; Trelewicz, Jason R.

2016-07-04

Microstructural evolution during the devitrification of amorphous tantalum thin films synthesized via pulsed laser deposition was investigated using in situ transmission electron microscopy (TEM) combined with ex situ isothermal annealing, bright-field imaging, and electron-diffraction analysis. The phases formed during crystallization and their stability were characterized as a function of the chamber pressure during deposition, devitrification temperature, and annealing time. A range of metastable nanocrystalline tantalum oxides were identified following devitrification including multiple orthorhombic oxide phases, which often were present with, or evolved to, the tetragonal TaO 2 phase. While the appearance of these phases indicated the films were evolving tomore » the stable form of tantalum oxide—monoclinic tantalum pentoxide—it was likely not achieved for the conditions considered due to an insufficient amount of oxygen present in the films following deposition. Nevertheless, the collective in situ and ex situ TEM analysis applied to thin film samples enabled the isolation of a number of metastable tantalum oxides. As a result, new insights were gained into the transformation sequence and stability of these nanocrystalline phases, which presents opportunities for the development of advanced tantalum oxide-based dielectric materials for novel memristor designs.« less

Xenon-ion-induced and thermal mixing of Co/Si bilayers and their interplay

NASA Astrophysics Data System (ADS)

Novaković, M.; Zhang, K.; Popović, M.; Bibić, N.; Hofsäss, H.; Lieb, K. P.

2011-05-01

Studies on ion-irradiated transition-metal/silicon bilayers demonstrate that interface mixing and silicide phase formation depend sensitively on the ion and film parameters, including the structure of the metal/Si interface. Thin Co layers e-gun evaporated to a thickness of 50 nm on Si(1 0 0) wafers were bombarded at room temperature with 400-keV Xe + ions at fluences of up to 3 × 10 16 cm -2. We used either crystalline or pre-amorphized Si wafers the latter ones prepared by 1.0-keV Ar-ion implantation. The as-deposited or Xe-ion-irradiated samples were then isochronally annealed at temperatures up to 700 °C. Changes of the bilayer structures induced by ion irradiation and/or annealing were investigated with RBS, XRD and HRTEM. The mixing rate for the Co/c-Si couples, Δ σ2/ Φ = 3.0(4) nm 4, is higher than the value expected for ballistic mixing and about half the value typical for spike mixing. Mixing of pre-amorphized Si is much weaker relative to crystalline Si wafers, contrary to previous results obtained for Fe/Si bilayers. Annealing of irradiated samples produces very similar interdiffusion and phase formation patterns above 400 °C as in the non-irradiated Co/Si bilayers: the phase evolution follows the sequence Co 2Si → CoSi → CoSi 2.

A stationary-phase protein of Escherichia coli that affects the mode of association between the trp repressor protein and operator-bearing DNA.

PubMed Central

Yang, W; Ni, L; Somerville, R L

1993-01-01

Highly purified preparations of trp repressor (TrpR) protein derived from Escherichia coli strains that were engineered to overexpress this material were found to contain another protein, of 21 kDa. The second protein, designated WrbA [for tryptophan (W) repressor-binding protein] remained associated with its namesake through several sequential protein fractionation steps. The N-terminal amino acid sequence of the WrbA protein guided the design of two degenerate oligonucleotides that were used as probes in the cloning of the wrbA gene (198 codons). The WrbA protein, in purified form, was found by several criteria to enhance the formation and/or stability of noncovalent complexes between TrpR holorepressor and its primary operator targets. The formation of an operator-holorepressor-WrbA ternary complex was demonstrated by gel mobility-shift analysis. The WrbA protein alone does not interact with the trp operator. During the stationary phase, cells deficient in the WrbA protein were less efficient than wild type in their ability to repress the trp promoter. It is proposed that the WrbA protein functions as an accessory element in blocking TrpR-specific transcriptional processes that might be physiologically disadvantageous in the stationary phase of the bacterial life cycle. Images Fig. 1 Fig. 3 Fig. 4 Fig. 5 PMID:8516330

Depositional architecture and sequence stratigraphy of the Upper Jurassic Hanifa Formation, central Saudi Arabia

NASA Astrophysics Data System (ADS)

El-Sorogy, Abdelbaset; Al-Kahtany, Khaled; Almadani, Sattam; Tawfik, Mohamed

2018-03-01

To document the depositional architecture and sequence stratigraphy of the Upper Jurassic Hanifa Formation in central Saudi Arabia, three composite sections were examined, measured and thin section analysed at Al-Abakkayn, Sadous and Maashabah mountains. Fourteen microfacies types were identified, from wackestones to boundstones and which permits the recognition of five lithofacies associations in a carbonate platform. Lithofacies associations range from low energy, sponges, foraminifers and bioclastic burrowed offshoal deposits to moderate lithoclstic, peloidal and bioclastic foreshoal deposits in the lower part of the Hanifa while the upper part is dominated by corals, ooidal and peloidal high energy shoal deposits to moderate to low energy peloidal, stromatoporoids and other bioclastics back shoal deposits. The studied Hanifa Formation exhibits an obvious cyclicity, distinguishing from vertical variations in lithofacies types. These microfacies types are arranged in two third order sequences, the first sequence is equivalent to the lower part of the Hanifa Formation (Hawtah member) while the second one is equivalent to the upper part (Ulayyah member). Within these two sequences, there are three to six fourth-order high frequency sequences respectively in the studied sections.

Age dependent variation of magnetic fabric on dike swarms from Maio Island (Cape Verde)

NASA Astrophysics Data System (ADS)

Moreira, Mário; Madeira, José; Mata, João.; Represas, Patrícia

2010-05-01

Maio is one of the oldest and most eroded islands of Cape Verde Archipelago. It comprises three major geological units: (1) an old raised sea-floor sequence of MORB covered by Jurassic(?)-Cretaceous deep marine sediments; (2) an intrusive 'Central Igneous Complex' (CIC), forming a dome-like structure in the older rocks; and (3) a sequence of initially submarine, then subaerial, extrusive volcanic formations and sediments. Based on the trend distribution of 290 dikes, we performed magnetic sampling on 26 basic and one carbonatite dikes. Anisotropy of magnetic susceptibility (AMS) was measured to infer geometries of magmatic flow. Dikes were sampled in both chilled margins were larger shear acting on particles embedded in the magmatic flow is expected. Sampling involved 11 dikes (N=195) intruding MORB pillows from the Upper Jurassic 'Batalha Formation' (Bt fm); 6 dikes (N=95) intruding the Lower Cretaceous 'Carquejo Formation' (Cq fm), and 10 dikes (N=129) intruding the submarine sequence of the Neogene 'Casas Velhas Formation' (CV fm). The studied hypabissal rocks are usually porphyritic, with phenocrysts of clinopyroxene and/or olivine set on an aphanitic groundmass. Dikes intruding CV fm trend N-S to NE-SW and plunge to SW. In Bt fm, dikes make ≈ 99% of the outcrops, span all directions and include frequent low dip sills. Dikes intruding Cq fm are shallow (mostly parallel to the limestone strata), dip 30o- 40o to the E, and trend N-S to NE-SW. Bulk susceptibility of the 26 basic dikes presents an average value of k = 47 ± 26 (×10-3) SI. The carbonatite dike intruding Bt fm has lower susceptibility: k = 4.6 ± 1.2 (×10-3) SI. More than 80% of the dikes show normal and triaxial magnetic fabric. Anisotropy is usually low, with P' < 1.08, but in CV fm dikes the anisotropy is higher and grows (up to P' ≈ 1.5) towards the centre of the volcano. Dominant magnetic fabric in CV fm is planar but in dikes from Cq fm and Bt fm it varies between oblate and prolate. Carbonatite dike shows low anisotropy (1.01 < P' < 1.06) and a slightly dominant planar fabric. Magnetic foliation is parallel or slightly oblique to the respective margins. Usually, when magnetic imbrication is observed the dihedral angle is small or the imbrications in both margins are scissored relative to the dike axis. Magnetic lineation shows some interesting systematic behaviours. In CV fm, lineation changes from shallow or intermediate plunges (~45o) in southern dikes to more than 60o in northern dikes (close to CIC). In Cq fm, lineation of N-S dikes has intermediate plunge (~40o) to the NE, while NE-SW trending dikes intruding the same formation in the south show shallower inclinations (< 30o). Lineation always falls in E or NE sectors of the projections. In Bt fm, (southeast shore) lineations usually plunge more than 60o. Thermomagnetic magnetic behaviour of rocks from Cv fm dikes indicates the Ti-rich composition of the main oxide phase, while the rocks from Bt fm present either a single magnetite-rich phase, either two phases: titano-magnetite 300o < TC

A Census of Broad-line Active Galactic Nuclei in Nearby Galaxies: Coeval Star Formation and Rapid Black Hole Growth

NASA Astrophysics Data System (ADS)

Trump, Jonathan R.; Hsu, Alexander D.; Fang, Jerome J.; Faber, S. M.; Koo, David C.; Kocevski, Dale D.

2013-02-01

We present the first quantified, statistical map of broad-line active galactic nucleus (AGN) frequency with host galaxy color and stellar mass in nearby (0.01 < z < 0.11) galaxies. Aperture photometry and z-band concentration measurements from the Sloan Digital Sky Survey are used to disentangle AGN and galaxy emission, resulting in estimates of uncontaminated galaxy rest-frame color, luminosity, and stellar mass. Broad-line AGNs are distributed throughout the blue cloud and green valley at a given stellar mass, and are much rarer in quiescent (red sequence) galaxies. This is in contrast to the published host galaxy properties of weaker narrow-line AGNs, indicating that broad-line AGNs occur during a different phase in galaxy evolution. More luminous broad-line AGNs have bluer host galaxies, even at fixed mass, suggesting that the same processes that fuel nuclear activity also efficiently form stars. The data favor processes that simultaneously fuel both star formation activity and rapid supermassive black hole accretion. If AGNs cause feedback on their host galaxies in the nearby universe, the evidence of galaxy-wide quenching must be delayed until after the broad-line AGN phase.

On the gas-phase formation of the HCO radical: accurate quantum study of the H+CO radiative association

NASA Astrophysics Data System (ADS)

Stoecklin, Thierry; Halvick, Philippe; Yu, Hua-Gen; Nyman, Gunnar; Ellinger, Yves

2018-04-01

We present the first quantum study of the radiative association of H and CO to form the HCO molecule within a time-independent approach. We use a recently published 3D potential energy surface of spectroscopic accuracy and two 3D dipole moment surfaces, which were calculated for this study. We discuss the variation of the radiative association cross-section as a function of both the rotational angular momentum of CO and the total angular momentum and use the uniform J-shifting approach to obtain the global radiative association rate coefficient. The effect of the saddle point separating the HCO molecule from the H+CO reactants and the main features of the radiative association cross-sections are analysed and discussed. The calculated rate coefficient is below 10-23 cm3 molecule-1 s-1 for temperatures lower than 30 K, and increases up to 5 × 10-20 cm3 molecule-1 s-1 at T = 300 K. These results demonstrate that the gas-phase H+CO radiative association cannot be the process at the origin of the sequence leading to the formation of methanol in a cold interstellar medium.

The relation between high-density and very-high-density amorphous ice.

PubMed

Loerting, Thomas; Salzmann, Christoph G; Winkel, Katrin; Mayer, Erwin

2006-06-28

The exact nature of the relationship between high-density (HDA) and very-high-density (VHDA) amorphous ice is unknown at present. Here we review the relation between HDA and VHDA, concentrating on experimental aspects and discuss these with respect to the relation between low-density amorphous ice (LDA) and HDA. On compressing LDA at 125 K up to 1.5 GPa, two distinct density steps are observable in the pressure-density curves which correspond to the LDA --> HDA and HDA --> VHDA conversion. This stepwise formation process LDA --> HDA --> VHDA at 125 K is the first unambiguous observation of a stepwise amorphous-amorphous-amorphous transformation sequence. Density values of amorphous ice obtained in situ between 0.3 and 1.9 GPa on isobaric heating up to the temperatures of crystallization show a pronounced change of slope at ca. 0.8 GPa which could indicate formation of a distinct phase. We infer that the relation between HDA and VHDA is very similar to that between LDA and HDA except for a higher activation barrier between the former. We further discuss the two options of thermodynamic phase transition versus kinetic densification for the HDA --> VHDA conversion.

Atomisation and droplet formation mechanisms in a model two-phase mixing layer

NASA Astrophysics Data System (ADS)

Zaleski, Stephane; Ling, Yue; Fuster, Daniel; Tryggvason, Gretar

2017-11-01

We study atomization in a turbulent two-phase mixing layer inspired by the Grenoble air-water experiments. A planar gas jet of large velocity is emitted on top of a planar liquid jet of smaller velocity. The density ratio and momentum ratios are both set at 20 in the numerical simulation in order to ease the simulation. We use a Volume-Of-Fluid method with good parallelisation properties, implemented in our code http://parissimulator.sf.net. Our simulations show two distinct droplet formation mechanisms, one in which thin liquid sheets are punctured to form rapidly expanding holes and the other in which ligaments of irregular shape form and breakup in a manner similar but not identical to jets in Rayleigh-Plateau-Savart instabilities. Observed distributions of particle sizes are extracted for a sequence of ever more refined grids, the largest grid containing approximately eight billion points. Although their accuracy is limited at small sizes by the grid resolution and at large size by statistical effects, the distributions overlap in the central region. The observed distributions are much closer to log normal distributions than to gamma distributions as is also the case for experiments.

On-chip multiplexed solid-phase nucleic acid hybridization assay using spatial profiles of immobilized quantum dots and fluorescence resonance energy transfer.

PubMed

Noor, M Omair; Tavares, Anthony J; Krull, Ulrich J

2013-07-25

A microfluidic based solid-phase assay for the multiplexed detection of nucleic acid hybridization using quantum dot (QD) mediated fluorescence resonance energy transfer (FRET) is described herein. The glass surface of hybrid glass-polydimethylsiloxane (PDMS) microfluidic channels was chemically modified to assemble the biorecognition interface. Multiplexing was demonstrated using a detection system that was comprised of two colors of immobilized semi-conductor QDs and two different oligonucleotide probe sequences. Green-emitting and red-emitting QDs were paired with Cy3 and Alexa Fluor 647 (A647) labeled oligonucleotides, respectively. The QDs served as energy donors for the transduction of dye labeled oligonucleotide targets. The in-channel assembly of the biorecognition interface and the subsequent introduction of oligonucleotide targets was accomplished within minutes using a combination of electroosmotic flow and electrophoretic force. The concurrent quantification of femtomole quantities of two target sequences was possible by measuring the spatial coverage of FRET sensitized emission along the length of the channel. In previous reports, multiplexed QD-FRET hybridization assays that employed a ratiometric method for quantification had challenges associated with lower analytical sensitivity arising from both donor and acceptor dilution that resulted in reduced energy transfer pathways as compared to single-color hybridization assays. Herein, a spatial method for quantification that is based on in-channel QD-FRET profiles provided higher analytical sensitivity in the multiplexed assay format as compared to single-color hybridization assays. The selectivity of the multiplexed hybridization assays was demonstrated by discrimination between a fully-complementary sequence and a 3 base pair sequence at a contrast ratio of 8 to 1. Copyright © 2013 Elsevier B.V. All rights reserved.

Beta-keratins of differentiating epidermis of snake comprise glycine-proline-serine-rich proteins with an avian-like gene organization.

PubMed

Dalla Valle, Luisa; Nardi, Alessia; Belvedere, Paola; Toni, Mattia; Alibardi, Lorenzo

2007-07-01

Beta-keratins of reptilian scales have been recently cloned and characterized in some lizards. Here we report for the first time the sequence of some beta-keratins from the snake Elaphe guttata. Five different cDNAs were obtained using 5'- and 3'-RACE analyses. Four sequences differ by only few nucleotides in the coding region, whereas the last cDNA shows, in this region, only 84% of identity. The gene corresponding to one of the cDNA sequences has a single intron present in the 5'-untranslated region. This genomic organization is similar to that of birds' beta-keratins. Cloning and Southern blotting analysis suggest that snake beta-keratins belong to a family of high-related genes as for geckos. PCR analysis suggests a head-to-tail orientation of genes in the same chromosome. In situ hybridization detected beta-keratin transcripts almost exclusively in differentiating oberhautchen and beta-cells of the snake epidermis in renewal phase. This is confirmed by Northern blotting that showed, in this phase, a high expression of two different transcripts whereas only the longer transcript is expressed at a much lower level in resting skin. The cDNA coding sequences encoded putative glycine-proline-serine rich proteins containing 137-139 amino acids, with apparent isoelectric point at 7.5 and 8.2. A central region, rich in proline, shows over 50% homology with avian scale, claw, and feather keratins. The prediction of secondary structure shows mainly a random coil conformation and few beta-strand regions in the central region, likely involved in the formation of a fibrous framework of beta-keratins. This region was possibly present in basic reptiles that originated reptiles and birds. Copyright 2007 Wiley-Liss, Inc.

Geoscientific Characterization of the Bruce Site, Tiverton, Ontario

NASA Astrophysics Data System (ADS)

Raven, K.; Jackson, R.; Avis, J.; Clark, I.; Jensen, M.

2009-05-01

Ontario Power Generation is proposing a Deep Geologic Repository (DGR) for the long-term management of its Low and Intermediate Level Radioactive Waste (L&ILW) within a Paleozoic-age sedimentary sequence beneath the Bruce site near Tiverton, Ontario, Canada. The concept envisions that the DGR would be excavated at a depth of approximately 680 m within the Ordovician Cobourg Formation, a massive, dense, low- permeability, argillaceous limestone. Characterization of the Bruce site for waste disposal is being conducted in accordance with a four year multi-phase Geoscientific Site Characterization Plan (GSCP). The GSCP, initially developed in 2006 and later revised in 2008 to account for acquired site knowledge based on successful completion of Phase I investigations, describes the tools and methods selected for geological, hydrogeological and geomechanical site characterization. The GSCP was developed, in part, on an assessment of geoscience data needs and collection methods, review of the results of detailed geoscientific studies completed in the same bedrock formations found off the Bruce site, and recent international experience in geoscientific characterization of similar sedimentary rocks for long-term radioactive waste management purposes. Field and laboratory work related to Phase 1 and Phase 2A are nearing completion and have focused on the drilling, testing and monitoring of four continuously cored vertical boreholes through Devonian, Silurian, Ordovician and Cambrian bedrock to depths of about 860 mBGS. Work in 2009 will focus on drilling and testing of inclined boreholes to assess presence of vertical structure. The available geological, hydrogeological and hydrogeochemical data indicate the presence of remarkably uniform and predictable geology, physical hydrogeologic and geochemical properties over well separation distances exceeding 1 km. The current data set including 2-D seismic reflection surveys, field and lab hydraulic testing, lab petrophysical and diffusion testing, lab porewater and field groundwater characterization, and field head monitoring confirm the anticipated favourable characteristics of the Bruce site for long-term waste management. These favourable characteristics include a tight geomechanically stable host formation that is overlain and underlain by thick, massive, very low permeability shale and argillaceous limestone formations where radionuclide transport appears to be very limited and dominated by diffusion.

Sequence stratigraphy and sedimentary study on Mishrif formation of Fauqi Oilfield of Missan in south east Iraq

NASA Astrophysics Data System (ADS)

Sang, Hua; Lin, Changsong; Jiang, Yiming

2017-05-01

The reservoir of Mishrif formation has a large scale distribution of marine facies carbonate sediments in great thickness in central and south east Iraq. Rudist reef and shoal facies limestones of the Mishrif Formation (Late Cenomanian - Middle Turonian) form a great potential reservoir rocks at oilfields and structures of Iraq. Facies modelling was applied to predict the relationship between facies distribution and reservoir characteristics to construct a predictive geologic model which will assist future exploration and development in south east Iraq. Microfacies analysis and electrofacies identification and correlations indicate that the limestone of the Mishrif Formation were mainly deposited in open platform setting. Sequence stratigraphic analyses of the Mishrif Formation indicate 3 third order depositional sequences.

THE QUENCHING TIMESCALE AND QUENCHING RATE OF GALAXIES

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

Lian, Jianhui; Kong, Xu; Yan, Renbin

2016-11-20

The average star formation rate (SFR) in galaxies has been declining since the redshift of 2. A fraction of galaxies quench and become quiescent. We constrain two key properties of the quenching process: the quenching timescale and the quenching rate among galaxies. We achieve this by analyzing the galaxy number density profile in NUV- u color space and the distribution in NUV- u versus u - i color–color diagram with a simple toy-model framework. We focus on galaxies in three mass bins between 10{sup 10} and 10{sup 10.6} M {sub ⊙}. In the NUV- u versus u - i color–colormore » diagram, the red u - i galaxies exhibit a different slope from the slope traced by the star-forming galaxies. This angled distribution and the number density profile of galaxies in NUV- u space strongly suggest that the decline of the SFR in galaxies has to accelerate before they turn quiescent. We model this color–color distribution with a two-phase exponential decline star formation history. The models with an e-folding time in the second phase (the quenching phase) of 0.5 Gyr best fit the data. We further use the NUV- u number density profile to constrain the quenching rate among star-forming galaxies as a function of mass. Adopting an e-folding time of 0.5 Gyr in the second phase (or the quenching phase), we found the quenching rate to be 19%/Gyr, 25%/Gyr and 33%/Gyr for the three mass bins. These are upper limits of the quenching rate as the transition zone could also be populated by rejuvenated red-sequence galaxies.« less

Aqueous Biphasic Systems for the Synthesis of Formates by Catalytic CO2 Hydrogenation: Integrated Reaction and Catalyst Separation for CO2‐Scrubbing Solutions

PubMed Central

Scott, Martin; Blas Molinos, Beatriz; Westhues, Christian

2017-01-01

Abstract Aqueous biphasic systems were investigated for the production of formate–amine adducts by metal‐catalyzed CO2 hydrogenation, including typical scrubbing solutions as feedstocks. Different hydrophobic organic solvents and ionic liquids could be employed as the stationary phase for cis‐[Ru(dppm)2Cl2] (dppm=bis‐diphenylphosphinomethane) as prototypical catalyst without any modification or tagging of the complex. The amines were found to partition between the two phases depending on their structure, whereas the formate–amine adducts were nearly quantitatively extracted into the aqueous phase, providing a favorable phase behavior for the envisaged integrated reaction/separation sequence. The solvent pair of methyl isobutyl carbinol (MIBC) and water led to the most practical and productive system and repeated use of the catalyst phase was demonstrated. The highest single batch activity with a TOFav of approximately 35 000 h−1 and an initial TOF of approximately 180 000 h−1 was achieved in the presence of NEt3. Owing to higher stability, the highest productivities were obtained with methyl diethanolamine (Aminosol CST 115) and monoethanolamine (MEA), which are used in commercial scale CO2‐scrubbing processes. Saturated aqueous solutions (CO2 overpressure 5–10 bar) of MEA could be converted into the corresponding formate adducts with average turnover frequencies up to 14×103 h−1 with an overall yield of 70 % based on the amine, corresponding to a total turnover number of 150 000 over eleven recycling experiments. This opens the possibility for integrated approaches to carbon capture and utilization. PMID:28103428

Reconciling mass functions with the star-forming main sequence via mergers

NASA Astrophysics Data System (ADS)

Steinhardt, Charles L.; Yurk, Dominic; Capak, Peter

2017-06-01

We combine star formation along the 'main sequence', quiescence and clustering and merging to produce an empirical model for the evolution of individual galaxies. Main-sequence star formation alone would significantly steepen the stellar mass function towards low redshift, in sharp conflict with observation. However, a combination of star formation and merging produces a consistent result for correct choice of the merger rate function. As a result, we are motivated to propose a model in which hierarchical merging is disconnected from environmentally independent star formation. This model can be tested via correlation functions and would produce new constraints on clustering and merging.

Learning by observation: insights from Williams syndrome.

PubMed

Foti, Francesca; Menghini, Deny; Mandolesi, Laura; Federico, Francesca; Vicari, Stefano; Petrosini, Laura

2013-01-01

Observing another person performing a complex action accelerates the observer's acquisition of the same action and limits the time-consuming process of learning by trial and error. Observational learning makes an interesting and potentially important topic in the developmental domain, especially when disorders are considered. The implications of studies aimed at clarifying whether and how this form of learning is spared by pathology are manifold. We focused on a specific population with learning and intellectual disabilities, the individuals with Williams syndrome. The performance of twenty-eight individuals with Williams syndrome was compared with that of mental age- and gender-matched thirty-two typically developing children on tasks of learning of a visuo-motor sequence by observation or by trial and error. Regardless of the learning modality, acquiring the correct sequence involved three main phases: a detection phase, in which participants discovered the correct sequence and learned how to perform the task; an exercise phase, in which they reproduced the sequence until performance was error-free; an automatization phase, in which by repeating the error-free sequence they became accurate and speedy. Participants with Williams syndrome beneficiated of observational training (in which they observed an actor detecting the visuo-motor sequence) in the detection phase, while they performed worse than typically developing children in the exercise and automatization phases. Thus, by exploiting competencies learned by observation, individuals with Williams syndrome detected the visuo-motor sequence, putting into action the appropriate procedural strategies. Conversely, their impaired performances in the exercise phases appeared linked to impaired spatial working memory, while their deficits in automatization phases to deficits in processes increasing efficiency and speed of the response. Overall, observational experience was advantageous for acquiring competencies, since it primed subjects' interest in the actions to be performed and functioned as a catalyst for executed action.

In Situ Observation of Oxygen Vacancy Dynamics and Ordering in the Epitaxial LaCoO3 System.

PubMed

Jang, Jae Hyuck; Kim, Young-Min; He, Qian; Mishra, Rohan; Qiao, Liang; Biegalski, Michael D; Lupini, Andrew R; Pantelides, Sokrates T; Pennycook, Stephen J; Kalinin, Sergei V; Borisevich, Albina Y

2017-07-25

Vacancy dynamics and ordering underpin the electrochemical functionality of complex oxides and strongly couple to their physical properties. In the field of the epitaxial thin films, where connection between chemistry and film properties can be most clearly revealed, the effects related to oxygen vacancies are attracting increasing attention. In this article, we report a direct, real-time, atomic level observation of the formation of oxygen vacancies in the epitaxial LaCoO 3 thin films and heterostructures under the influence of the electron beam utilizing scanning transmission electron microscopy (STEM). In the case of LaCoO 3 /SrTiO 3 superlattice, the formation of the oxygen vacancies is shown to produce quantifiable changes in the interatomic distances, as well as qualitative changes in the symmetry of the Co sites manifested as off-center displacements. The onset of these changes was observed in both the [100] pc and [110] pc orientations in real time. Additionally, annular bright field images directly show the formation of oxygen vacancy channels along [110]pc direction. In the case of 15 u.c. LaCoO 3 thin film, we observe the sequence of events during beam-induced formation of oxygen vacancy ordered phases and find them consistent with similar processes in the bulk. Moreover, we record the dynamics of the nucleation, growth, and defect interaction at the atomic scale as these transformations happen. These results demonstrate that we can track dynamic oxygen vacancy behavior with STEM, generating atomic-level quantitative information on phase transformation and oxygen diffusion.

FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences.

PubMed

Waldmann, Jost; Gerken, Jan; Hankeln, Wolfgang; Schweer, Timmy; Glöckner, Frank Oliver

2014-06-14

Advances in sequencing technologies challenge the efficient importing and validation of FASTA formatted sequence data which is still a prerequisite for most bioinformatic tools and pipelines. Comparative analysis of commonly used Bio*-frameworks (BioPerl, BioJava and Biopython) shows that their scalability and accuracy is hampered. FastaValidator represents a platform-independent, standardized, light-weight software library written in the Java programming language. It targets computer scientists and bioinformaticians writing software which needs to parse quickly and accurately large amounts of sequence data. For end-users FastaValidator includes an interactive out-of-the-box validation of FASTA formatted files, as well as a non-interactive mode designed for high-throughput validation in software pipelines. The accuracy and performance of the FastaValidator library qualifies it for large data sets such as those commonly produced by massive parallel (NGS) technologies. It offers scientists a fast, accurate and standardized method for parsing and validating FASTA formatted sequence data.

Lithofacies and sequence stratigraphic description of the upper part of the Avon Park Formation and the Arcadia Formation in U.S. Geological Survey G–2984 test corehole, Broward County, Florida

USGS Publications Warehouse

Cunningham, Kevin J.; Robinson, Edward

2017-07-18

Rock core and sediment from U.S. Geological Survey test corehole G–2984 completed in 2011 in Broward County, Florida, provide an opportunity to improve the understanding of the lithostratigraphic, sequence stratigraphic, and hydrogeologic framework of the intermediate confining unit and Floridan aquifer system in southeastern Florida. A multidisciplinary approach including characterization of sequence stratigraphy, lithofacies, ichnology, foraminiferal paleontology, depositional environments, porosity, and permeability was used to describe the geologic samples from this test corehole. This information has produced a detailed characterization of the lithofacies and sequence stratigraphy of the upper part of the middle Eocene Avon Park Formation and Oligocene to middle Miocene Arcadia Formation. This enhancement of the knowledge of the sequence stratigraphic framework is especially important, because subaerial karst unconformities at the upper boundary of depositional cycles at various hierarchical scales are commonly associated with secondary porosity and enhanced permeability in the Floridan aquifer system.

Fluorescence, polarized fluorescence, and Brewster angle microscopy of palmitic acid and lung surfactant protein B monolayers.

PubMed Central

Lipp, M M; Lee, K Y; Waring, A; Zasadzinski, J A

1997-01-01

Fluorescence, polarized fluorescence, and Brewster angle microscopy reveal that human lung surfactant protein SP-B and its amino terminus (SP-B[1-25]) alter the phase behavior of palmitic acid monolayers by inhibiting the formation of condensed phases and creating a new fluid protein-rich phase. This fluid phase forms a network that separates condensed phase domains at coexistence and persists to high surface pressures. The network changes the monolayer collapse mechanism from heterogeneous nucleation/growth and fracturing processes to a more homogeneous process through isolating individual condensed phase domains. This results in higher surface pressures at collapse, and monolayers easier to respread on expansion, factors essential to the in vivo function of lung surfactant. The network is stabilized by a low-line tension between the coexisting phases, as confirmed by the observation of extended linear domains, or "stripe" phases, and a Gouy-Chapman analysis of protein-containing monolayers. Comparison of isotherm data and observed morphologies of monolayers containing SP-B(1-25) with those containing the full SP-B sequence show that the shortened peptide retains most of the native activity of the full-length protein, which may lead to cheaper and more effective synthetic replacement formulations. Images FIGURE 1 FIGURE 3 FIGURE 4 FIGURE 6 FIGURE 7 FIGURE 8 FIGURE 9 FIGURE 10 PMID:9168053

Phase I (Year 1) Summary of Research--Establishing the Relationship between Fracture-Related Dolomite and Primary Rock Fabric on the Distribution of Reservoirs in the Michigan Basin

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

G. Michael Grammer

2005-11-09

This topical report covers the first 12 months of the subject 3-year grant, evaluating the relationship between fracture-related dolomite and dolomite constrained by primary rock fabric in the 3 most prolific reservoir intervals in the Michigan Basin (Ordovician Trenton-Black River Formations; Silurian Niagara Group; and the Devonian Dundee Formation). Phase I tasks, including Developing a Reservoir Catalog for selected dolomite reservoirs in the Michigan Basin, Characterization of Dolomite Reservoirs in Representative Fields and Technology Transfer have all been initiated and progress is consistent with our original scheduling. The development of a reservoir catalog for the 3 subject formations in themore » Michigan Basin has been a primary focus of our efforts during Phase I. As part of this effort, we currently have scanned some 13,000 wireline logs, and compiled in excess of 940 key references and 275 reprints that cover reservoir aspects of the 3 intervals in the Michigan Basin. A summary evaluation of the data in these publications is currently ongoing, with the Silurian Niagara Group being handled as a first priority. In addition, full production and reservoir parameter data bases obtained from available data sources have been developed for the 3 intervals in Excel and Microsoft Access data bases. We currently have an excess of 25 million cells of data for wells in the Basin. All Task 2 objectives are on time and on target for Phase I per our original proposal. Our mapping efforts to date, which have focused in large part on the Devonian Dundee Formation, have important implications for both new exploration plays and improved enhanced recovery methods in the Dundee ''play'' in Michigan--i.e. the interpreted fracture-related dolomitization control on the distribution of hydrocarbon reservoirs. In an exploration context, high-resolution structure mapping using quality-controlled well data should provide leads to convergence zones of fault/fracture trends that are not necessarily related to structural elevation. Further work in Phase II will be focused on delineating the relative contribution to fracture-only dolomitization to that which occurs in conjunction with primary facies and/or sequence stratigraphic framework.« less

Polysaccharide intercellular adhesin in biofilm: structural and regulatory aspects

PubMed Central

Arciola, Carla Renata; Campoccia, Davide; Ravaioli, Stefano; Montanaro, Lucio

2015-01-01

Staphylococcus aureus and Staphylococcus epidermidis are the leading etiologic agents of implant-related infections. Biofilm formation is the main pathogenetic mechanism leading to the chronicity and irreducibility of infections. The extracellular polymeric substances of staphylococcal biofilms are the polysaccharide intercellular adhesin (PIA), extracellular-DNA, proteins, and amyloid fibrils. PIA is a poly-β(1-6)-N-acetylglucosamine (PNAG), partially deacetylated, positively charged, whose synthesis is mediated by the icaADBC locus. DNA sequences homologous to ica locus are present in many coagulase-negative staphylococcal species, among which S. lugdunensis, however, produces a biofilm prevalently consisting of proteins. The product of icaA is an N-acetylglucosaminyltransferase that synthetizes PIA oligomers from UDP-N-acetylglucosamine. The product of icaD gives optimal efficiency to IcaA. The product of icaC is involved in the externalization of the nascent polysaccharide. The product of icaB is an N-deacetylase responsible for the partial deacetylation of PIA. The expression of ica locus is affected by environmental conditions. In S. aureus and S. epidermidis ica-independent alternative mechanisms of biofilm production have been described. S. epidermidis and S. aureus undergo to a phase variation for the biofilm production that has been ascribed, in turn, to the transposition of an insertion sequence in the icaC gene or to the expansion/contraction of a tandem repeat naturally harbored within icaC. A role is played by the quorum sensing system, which negatively regulates biofilm formation, favoring the dispersal phase that disseminates bacteria to new infection sites. Interfering with the QS system is a much debated strategy to combat biofilm-related infections. In the search of vaccines against staphylococcal infections deacetylated PNAG retained on the surface of S. aureus favors opsonophagocytosis and is a potential candidate for immune-protection. PMID:25713785

NOGO-A induction and localization during chick brain development indicate a role disparate from neurite outgrowth inhibition

PubMed Central

Caltharp, Shelley A; Pira, Charmaine U; Mishima, Noboru; Youngdale, Erik N; McNeill, David S; Liwnicz, Boleslaw H; Oberg, Kerby C

2007-01-01

Background Nogo-A, a myelin-associated protein, inhibits neurite outgrowth and abates regeneration in the adult vertebrate central nervous system (CNS) and may play a role in maintaining neural pathways once established. However, the presence of Nogo-A during early CNS development is counterintuitive and hints at an additional role for Nogo-A beyond neurite inhibition. Results We isolated chicken NOGO-A and determined its sequence. A multiple alignment of the amino acid sequence across divergent species, identified five previously undescribed, Nogo-A specific conserved regions that may be relevant for development. NOGO gene transcripts (NOGO-A, NOGO-B and NOGO-C) were differentially expressed in the CNS during development and a second NOGO-A splice variant was identified. We further localized NOGO-A expression during key phases of CNS development by in situ hybridization. CNS-associated NOGO-A was induced coincident with neural plate formation and up-regulated by FGF in the transformation of non-neural ectoderm into neural precursors. NOGO-A expression was diffuse in the neuroectoderm during the early proliferative phase of development, and migration, but localized to large projection neurons of the optic tectum and tectal-associated nuclei during architectural differentiation, lamination and network establishment. Conclusion These data suggest Nogo-A plays a functional role in the determination of neural identity and/or differentiation and also appears to play a later role in the networking of large projection neurons during neurite formation and synaptogenesis. These data indicate that Nogo-A is a multifunctional protein with additional roles during CNS development that are disparate from its later role of neurite outgrowth inhibition in the adult CNS. PMID:17433109

Key Role of Alphaproteobacteria and Cyanobacteria in the Formation of Stromatolites of Lake Dziani Dzaha (Mayotte, Western Indian Ocean).

PubMed

Gérard, Emmanuelle; De Goeyse, Siham; Hugoni, Mylène; Agogué, Hélène; Richard, Laurent; Milesi, Vincent; Guyot, François; Lecourt, Léna; Borensztajn, Stephan; Joseph, Marie-Béatrice; Leclerc, Thomas; Sarazin, Gérard; Jézéquel, Didier; Leboulanger, Christophe; Ader, Magali

2018-01-01

Lake Dziani Dzaha is a thalassohaline tropical crater lake located on the "Petite Terre" Island of Mayotte (Comoros archipelago, Western Indian Ocean). Stromatolites are actively growing in the shallow waters of the lake shores. These stromatolites are mainly composed of aragonite with lesser proportions of hydromagnesite, calcite, dolomite, and phyllosilicates. They are morphologically and texturally diverse ranging from tabular covered by a cauliflower-like crust to columnar ones with a smooth surface. High-throughput sequencing of bacterial and archaeal 16S rRNA genes combined with confocal laser scanning microscopy (CLSM) analysis revealed that the microbial composition of the mats associated with the stromatolites was clearly distinct from that of the Arthrospira -dominated lake water. Unicellular-colonial Cyanobacteria belonging to the Xenococcus genus of the Pleurocapsales order were detected in the cauliflower crust mats, whereas filamentous Cyanobacteria belonging to the Leptolyngbya genus were found in the smooth surface mats. Observations using CLSM, scanning electron microscopy (SEM) and Raman spectroscopy indicated that the cauliflower texture consists of laminations of aragonite, magnesium-silicate phase and hydromagnesite. The associated microbial mat, as confirmed by laser microdissection and whole-genome amplification (WGA), is composed of Pleurocapsales coated by abundant filamentous and coccoid Alphaproteobacteria. These phototrophic Alphaproteobacteria promote the precipitation of aragonite in which they become incrusted. In contrast, the Pleurocapsales are not calcifying but instead accumulate silicon and magnesium in their sheaths, which may be responsible for the formation of the Mg-silicate phase found in the cauliflower crust. We therefore propose that Pleurocapsales and Alphaproteobacteria are involved in the formation of two distinct mineral phases present in the cauliflower texture: Mg-silicate and aragonite, respectively. These results point out the role of phototrophic Alphaproteobacteria in the formation of stromatolites, which may open new perspective for the analysis of the fossil record.

Ceramic surfaces, interfaces and solid-state reactions

NASA Astrophysics Data System (ADS)

Heffelfinger, Jason Roy

Faceting, the decomposition of a surface into two or more surfaces of different orientation, is studied as a function of annealing time for ceramic surfaces. Single-crystals of Alsb2Osb3\\ (alpha-Alsb2Osb3 or corundum structure) are carefully prepared and characterized by atomic force microscopy, scanning electron microscopy and transmission electron microscopy. The mechanisms by which the originally smooth vicinal surface transforms into either a hill-and-valley or a terrace-and-step structure have been characterized. The progression of faceting is found to have a series of stages: surface smoothing, nucleation and growth of individual facets, formation of facet domains, coalescence of individual and facet domains and facet coarsening. These stages provide a model for the mechanisms of how other ceramic surfaces may facet into hill-and-valley and terrace-and-step surface microstructures. The well characterized Alsb2Osb3 surfaces provide excellent substrates by which to study the effect of surface structure on thin-film growth. Pulsed-laser deposition was used to grow thin films of yttria stabilized zirconia (YSZ) and Ysb2Osb3 onto annealed Alsb2Osb3 substrates. The substrate surface structure, such as surface steps and terraces, was found to have several effects on thin-film growth. Thin-films grown onto single-crystal substrates serve as a model geometry for studying thin-film solid-state reactions. Here, the reaction sequence and orientation relationship between thin films of Ysb2Osb3 and an Alsb2Osb3 substrate were characterized for different reaction temperatures. In a system were multiple reaction phases can form, the yttria aluminum monoclinic phase (YAM) was found to form prior to formation of other phases in this system. In a second system, a titanium alloy was reacted with single crystal Alsb2Osb3 in order to study phase formation in an intermetallic system. Both Tisb3Al and TiAl were found to form as reaction products and their orientation relationships with the Alsb2Osb3 are discussed.

Rapid-mix and chemical quench studies of ferredoxin-reduced stearoyl-acyl carrier protein desaturase.

PubMed

Lyle, Karen S; Haas, Jeffrey A; Fox, Brian G

2003-05-20

Stearoyl-ACP Delta9 desaturase (Delta9D) catalyzes the NADPH- and O(2)-dependent insertion of a cis double bond between the C9 and C10 positions of stearoyl-ACP (18:0-ACP) to produce oleoyl-ACP (18:1-ACP). This work revealed the ability of reduced [2Fe-2S] ferredoxin (Fd) to act as a catalytically competent electron donor during the rapid conversion of 18:0-ACP into 18:1-ACP. Experiments on the order of addition for substrate and reduced Fd showed high conversion of 18:0-ACP to 18:1-ACP (approximately 95% per Delta9D active site in a single turnover) when 18:0-ACP was added prior to reduced Fd. Reactions of the prereduced enzyme-substrate complex with O(2) and the oxidized enzyme-substrate complex with reduced Fd were studied by rapid-mix and chemical quench methods. For reaction of the prereduced enzyme-substrate complex, an exponential burst phase (k(burst) = 95 s(-1)) of product formation accounted for approximately 90% of the turnover expected for one subunit in the dimeric protein. This rapid phase was followed by a slower phase (k(linear) = 4.0 s(-1)) of product formation corresponding to the turnover expected from the second subunit. For reaction of the oxidized enzyme-substrate complex with excess reduced Fd, a slower, linear rate (k(obsd) = 3.4 s(-1)) of product formation was observed over approximately 1.5 turnovers per Delta9D active site potentially corresponding to a third phase of reaction. An analysis of the deuterium isotope effect on the two rapid-mix reaction sequences revealed only a modest effect on k(burst) ((D)k(burst) approximately 1.5) and k(linear) (D)k(linear) approximately 1.4), indicating C-H bond cleavage does not contribute significantly to the rate-limiting steps of pre-steady-state catalysis. These results were used to assemble and evaluate a minimal kinetic model for Delta9D catalysis.

Robust sensorimotor representation to physical interaction changes in humanoid motion learning.

PubMed

Shimizu, Toshihiko; Saegusa, Ryo; Ikemoto, Shuhei; Ishiguro, Hiroshi; Metta, Giorgio

2015-05-01

This paper proposes a learning from demonstration system based on a motion feature, called phase transfer sequence. The system aims to synthesize the knowledge on humanoid whole body motions learned during teacher-supported interactions, and apply this knowledge during different physical interactions between a robot and its surroundings. The phase transfer sequence represents the temporal order of the changing points in multiple time sequences. It encodes the dynamical aspects of the sequences so as to absorb the gaps in timing and amplitude derived from interaction changes. The phase transfer sequence was evaluated in reinforcement learning of sitting-up and walking motions conducted by a real humanoid robot and compatible simulator. In both tasks, the robotic motions were less dependent on physical interactions when learned by the proposed feature than by conventional similarity measurements. Phase transfer sequence also enhanced the convergence speed of motion learning. Our proposed feature is original primarily because it absorbs the gaps caused by changes of the originally acquired physical interactions, thereby enhancing the learning speed in subsequent interactions.

Depositional sequences and facies in the Torok Formation, National Petroleum Reserve, Alaska (NPRA)

USGS Publications Warehouse

Houseknecht, David W.; Schenk, Christopher J.

2002-01-01

Brookian turbidites (Cretaceous through Tertiary) have become oil exploration objectives on the NorthSlope of Alaska during the past decade, and it is likely this focus will extend into the National Petroleum Reserve-Alaska (NPRA). A regional grid of 2-D seismic data, sparse well control, and field work in the Brooks Range foothills provide constraints for an ongoing effort to establish a sequence stratigraphic framework for Brookian turbidites in the Torok Formation across NPRA. The Torok Formation and overlying Nanushuk Formation (both mostly Albian) display the overall seismic geometry of bottomset-clinoform-topset strata indicating northeastward migration of a shelf margin. Within bottomset and clinoform strata of the Torok, depositional sequences have been identified that represent four distinct phases of shelf-margin sedimentation. (1) Regression, representing low relative sea level, is characterized by the development of an erosional surface on the shelf and upper slope, and the deposition of turbidite channel deposits on the middle to lower slope and submarine fan deposits at the base of slope. These deposits constitute a lowstand systems tract (LST). (2) Transgression, representing rising relative sea level, is characterized by the deposition of a mudstone drape on the basin floor, slope, and outer shelf. This drape comprises relatively condensed facies that constitute a transgressive systems tract (TST). (3) Aggradation, representing high relative sea level, is characterized by the deposition of relatively thick strata on the outer shelf and moderately thick mudstones on the slope. (4) Progradation, also representing high relative sea level, is characterized by the deposition of relatively thin strata on the outer shelf and very thick mudstones on the slope. Together, deposits of the aggradation and progradation phases constitute a highstand systems tract (HST). Large scale geometries of Torok strata vary across the Colville basin. In southern NPRA, high rates of subsidence accommodated the deposition of a "foredeep clinoform wedge" that contains a high proportion of sand-rich LST deposits. In northern NPRA, lower rates of subsidence favored the accumulation of mud-rich HST deposits. The most favorable stratigraphic trapping geometries in the Torok Formation occur where amalgamated sandstones deposited in turbidite channels incised on the mid- to lower-slope and on the proximal parts of submarine fans during regression (LSTs) are capped by relatively condensed mudstone facies deposited during transgression (TSTs). Common successions observed in Torok cores include a spectrum of slope and turbidite facies. Upper slope facies comprise laminated mudstones and siltstones that locally display evidence of slumping, sliding, and chaotic failure. Lower slope facies comprise heterolithic turbidites at some locations and interlaminated mudstones and thin, very fine-grained sandstones at others. Torok turbidites include amalgamated sandstones deposited in channel systems as well as thin-bedded, widespread sandstones deposited by unconfined flows on lobes or in channel overbank settings. These turbidite facies likely occur in both channel-lobe systems and slope apron systems within the Torok.

P-MaNGA: GRADIENTS IN RECENT STAR FORMATION HISTORIES AS DIAGNOSTICS FOR GALAXY GROWTH AND DEATH

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

Li, Cheng; Wang, Enci; Lin, Lin

2015-05-10

We present an analysis of the data produced by the MaNGA prototype run (P-MaNGA), aiming to test how the radial gradients in recent star formation histories, as indicated by the 4000 Å break (D{sub n}(4000)), Hδ absorption (EW(Hδ{sub A})), and Hα emission (EW(Hα)) indices, can be useful for understanding disk growth and star formation cessation in local galaxies. We classify 12 galaxies observed on two P-MaNGA plates as either centrally quiescent (CQ) or centrally star-forming (CSF), according to whether D{sub n}(4000) measured in the central spaxel of each datacube exceeds 1.6. For each spaxel we generate both 2D maps and radialmore » profiles of D{sub n}(4000), EW(Hδ{sub A}), and EW(Hα). We find that CSF galaxies generally show very weak or no radial variation in these diagnostics. In contrast, CQ galaxies present significant radial gradients, in the sense that D{sub n}(4000) decreases, while both EW(Hδ{sub A}) and EW(Hα) increase from the galactic center outward. The outer regions of the galaxies show greater scatter on diagrams relating the three parameters than their central parts. In particular, the clear separation between centrally measured quiescent and star-forming galaxies in these diagnostic planes is largely filled in by the outer parts of galaxies whose global colors place them in the green valley, supporting the idea that the green valley represents a transition between blue-cloud and red-sequence phases, at least in our small sample. These results are consistent with a picture in which the cessation of star formation propagates from the center of a galaxy outward as it moves to the red sequence.« less

Characterization of an AGAMOUS-like MADS Box Protein, a Probable Constituent of Flowering and Fruit Ripening Regulatory System in Banana

PubMed Central

Roy Choudhury, Swarup; Roy, Sujit; Nag, Anish; Singh, Sanjay Kumar; Sengupta, Dibyendu N.

2012-01-01

The MADS-box family of genes has been shown to play a significant role in the development of reproductive organs, including dry and fleshy fruits. In this study, the molecular properties of an AGAMOUS like MADS box transcription factor in banana cultivar Giant governor (Musa sp, AAA group, subgroup Cavendish) has been elucidated. We have detected a CArG-box sequence binding AGAMOUS MADS-box protein in banana flower and fruit nuclear extracts in DNA-protein interaction assays. The protein fraction in the DNA-protein complex was analyzed by mass spectrometry and using this information we have obtained the full length cDNA of the corresponding protein. The deduced protein sequence showed ∼95% amino acid sequence homology with MA-MADS5, a MADS-box protein described previously from banana. We have characterized the domains of the identified AGAMOUS MADS-box protein involved in DNA binding and homodimer formation in vitro using full-length and truncated versions of affinity purified recombinant proteins. Furthermore, in order to gain insight about how DNA bending is achieved by this MADS-box factor, we performed circular permutation and phasing analysis using the wild type recombinant protein. The AGAMOUS MADS-box protein identified in this study has been found to predominantly accumulate in the climacteric fruit pulp and also in female flower ovary. In vivo and in vitro assays have revealed specific binding of the identified AGAMOUS MADS-box protein to CArG-box sequence in the promoters of major ripening genes in banana fruit. Overall, the expression patterns of this MADS-box protein in banana female flower ovary and during various phases of fruit ripening along with the interaction of the protein to the CArG-box sequence in the promoters of major ripening genes lead to interesting assumption about the possible involvement of this AGAMOUS MADS-box factor in banana fruit ripening and floral reproductive organ development. PMID:22984496

Characterization of an AGAMOUS-like MADS box protein, a probable constituent of flowering and fruit ripening regulatory system in banana.

PubMed

Roy Choudhury, Swarup; Roy, Sujit; Nag, Anish; Singh, Sanjay Kumar; Sengupta, Dibyendu N

2012-01-01

The MADS-box family of genes has been shown to play a significant role in the development of reproductive organs, including dry and fleshy fruits. In this study, the molecular properties of an AGAMOUS like MADS box transcription factor in banana cultivar Giant governor (Musa sp, AAA group, subgroup Cavendish) has been elucidated. We have detected a CArG-box sequence binding AGAMOUS MADS-box protein in banana flower and fruit nuclear extracts in DNA-protein interaction assays. The protein fraction in the DNA-protein complex was analyzed by mass spectrometry and using this information we have obtained the full length cDNA of the corresponding protein. The deduced protein sequence showed ~95% amino acid sequence homology with MA-MADS5, a MADS-box protein described previously from banana. We have characterized the domains of the identified AGAMOUS MADS-box protein involved in DNA binding and homodimer formation in vitro using full-length and truncated versions of affinity purified recombinant proteins. Furthermore, in order to gain insight about how DNA bending is achieved by this MADS-box factor, we performed circular permutation and phasing analysis using the wild type recombinant protein. The AGAMOUS MADS-box protein identified in this study has been found to predominantly accumulate in the climacteric fruit pulp and also in female flower ovary. In vivo and in vitro assays have revealed specific binding of the identified AGAMOUS MADS-box protein to CArG-box sequence in the promoters of major ripening genes in banana fruit. Overall, the expression patterns of this MADS-box protein in banana female flower ovary and during various phases of fruit ripening along with the interaction of the protein to the CArG-box sequence in the promoters of major ripening genes lead to interesting assumption about the possible involvement of this AGAMOUS MADS-box factor in banana fruit ripening and floral reproductive organ development.

Spectral and chemical characterization of jarosite in a palaeolacustrine depositional environment in Warkalli Formation in Kerala, South India and its implications

NASA Astrophysics Data System (ADS)

Singh, Mahima; Rajesh, V. J.; Sajinkumar, K. S.; Sajeev, K.; Kumar, S. N.

2016-11-01

Coastal cliffs fringing the Arabian Sea near Varkala exhibits the Warkalli Formation of the Tertiary sequence of Kerala, South India, with well-marked occurrence of jarosite associated with other hydrous mineral phases of phyllosilicate family in a palaeo-lacustrine depositional environment. Sandy phyllosilicates dominate the mineral assemblage, but jarosite occurs as a prominent secondary phase formed during acid-sulphate alteration of iron sulphide in this area. Here, we discuss about the potentiality of spectroscopic techniques to identify the possible mineral phases in the collected samples. The samples from the coastal cliffs have been characterized by hyperspectral analysis (VIS-NIR-SWIR), X-ray Diffraction (XRD), Fourier Transform Infra-red Reflectance (FTIR), Electron Probe Microanalysis (EPMA) and Laser Raman spectroscopy. The spectral and chemical analyses have confirmed the jarosite as natrojarosite and phyllosilicate as kaolinite. Other accessory phases have also been identified through XRD. FTIR spectroscopy has played a major role in identifying the major hydrous bonds between the minerals. VIS-NIR-SWIR spectra show several optimum spectral features at 910 nm, 1470 nm, 1849-1864 nm (in the form of a doublet), 1940 nm and 2270 nm, which could be utilised to locate jarosite in the remotely-sensed data. X-ray diffraction peaks helped in the identification of maximum number of minerals (kaolinite, smectite, quartz, feldspar, pyrite, marcasite and hematite) and the variation in jarosite content in the samples. We propose the formation of jarosite in the region by a seasonal, local and temporary development of acidic conditions. Abundance of organic matter in a fluvio-lacustrine environment has developed anaerobic conditions by removing available oxygen through decomposition of organic matter containing sulphur compounds. The sulphur thus liberated combines with hydrogen from water to develop acidic conditions and resulted in the formation of jarosite. The occurrence of jarosite in Warkalli Formation suggests on and off supply of water during diagenesis. Jarosite has been detected as a prominent deposit in several regions on Mars by Mars Exploration rover Opportunity and Mars Reconnaissance Orbiter-Compact Reconnaissance Imaging Spectrometer for Mars (CRISM). This study of jarosite formation in terrestrial environment will influence our understanding on the mineral precipitation, diagenesis and hydration processes on Mars. Additionally, it also shows the importance of spectroscopic techniques like Raman spectrometry to be used in future missions to Mars to further validate the results of orbital spectroscopy.

Plasmodium sporozoite motility is modulated by the turnover of discrete adhesion sites.

PubMed

Münter, Sylvia; Sabass, Benedikt; Selhuber-Unkel, Christine; Kudryashev, Mikhail; Hegge, Stephan; Engel, Ulrike; Spatz, Joachim P; Matuschewski, Kai; Schwarz, Ulrich S; Frischknecht, Friedrich

2009-12-17

Sporozoites are the highly motile stages of the malaria parasite injected into the host's skin during a mosquito bite. In order to navigate inside of the host, sporozoites rely on actin-dependent gliding motility. Although the major components of the gliding machinery are known, the spatiotemporal dynamics of the proteins and the underlying mechanism powering forward locomotion remain unclear. Here, we show that sporozoite motility is characterized by a continuous sequence of stick-and-slip phases. Reflection interference contrast and traction force microscopy identified the repeated turnover of discrete adhesion sites as the underlying mechanism of this substrate-dependent type of motility. Transient forces correlated with the formation and rupture of distinct substrate contact sites and were dependent on actin dynamics. Further, we show that the essential sporozoite surface protein TRAP is critical for the regulated formation and rupture of adhesion sites but is dispensable for retrograde capping.

Structure of the disturbed region of the atmosphere after the nuclear explosion in Hiroshima

NASA Astrophysics Data System (ADS)

Shcherbin, M. D.; Pavlyukov, K. V.; Salo, A. A.; Pertsev, S. F.; Rikunov, A. V.

2013-09-01

An attempt is undertaken to describe the development of the disturbed region of the atmosphere caused by the nuclear explosion over Hiroshima on August 6, 1945. Numerical simulation of the phenomenon is performed using the dynamic equations for a nonconducting inviscid gas taking into account the combustion of urban buildings, phase changes of water, electrification of ice particles, and removal of soot particles. The results of the numerical calculation of the development of the disturbed region indicate heavy rainfall, the formation of a storm cloud with lightning discharges, removal of soot particles, and the formation of vertical vortices. The temporal sequence of these meteorological phenomena is consistent with the data of observations. Because of the assumptions and approximations used in solving the problem, the results are of qualitative nature. Refinement of the results can be obtained by a more detailed study of the approximate initial and boundary conditions of the problem.

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

NASA Astrophysics Data System (ADS)

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

2015-05-01

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

The dark nemesis of galaxy formation: why hot haloes trigger black hole growth and bring star formation to an end

NASA Astrophysics Data System (ADS)

Bower, Richard G.; Schaye, Joop; Frenk, Carlos S.; Theuns, Tom; Schaller, Matthieu; Crain, Robert A.; McAlpine, Stuart

2017-02-01

Galaxies fall into two clearly distinct types: `blue-sequence' galaxies which are rapidly forming young stars, and `red-sequence' galaxies in which star formation has almost completely ceased. Most galaxies more massive than 3 × 1010 M⊙ follow the red sequence, while less massive central galaxies lie on the blue sequence. We show that these sequences are created by a competition between star formation-driven outflows and gas accretion on to the supermassive black hole at the galaxy's centre. We develop a simple analytic model for this interaction. In galaxies less massive than 3 × 1010 M⊙, young stars and supernovae drive a high-entropy outflow which is more buoyant than any tenuous corona. The outflow balances the rate of gas inflow, preventing high gas densities building up in the central regions. More massive galaxies, however, are surrounded by an increasingly hot corona. Above a halo mass of ˜1012 M⊙, the outflow ceases to be buoyant and star formation is unable to prevent the build-up of gas in the central regions. This triggers a strongly non-linear response from the black hole. Its accretion rate rises rapidly, heating the galaxy's corona, disrupting the incoming supply of cool gas and starving the galaxy of the fuel for star formation. The host galaxy makes a transition to the red sequence, and further growth predominantly occurs through galaxy mergers. We show that the analytic model provides a good description of galaxy evolution in the EAGLE hydrodynamic simulations. So long as star formation-driven outflows are present, the transition mass scale is almost independent of subgrid parameter choice.

Photo-catalytic oxidation of acetone on a TiO2 powder: An in situ FTIR investigation

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

Szanyi, János; Kwak, Ja Hun

2015-09-01

In situ transmission infrared spectroscopy was used to investigate the photo-oxidation of acetone on a commercial, oxidized TiO2 (P25) powder catalyst under UV irradiation at ambient temperature, in the absence and presence of gas phase O2. The photochemistry of a number of organic molecules (1-butanone, methanol and acetic acid,) under the same conditions was also studied in order to identify reaction intermediates and products formed in the photo-oxidation of acetone. Under anaerobic conditions (in the absence of gas phase oxygen) limited extent of photo-oxidation of acetone took place on the oxidized TiO2 sample. In the presence of O2 in themore » gas phase, however, acetone was completely converted to acetates and formates, and ultimately CO2. The initial step in the sequence of photo-induced reactions is the ejection of a methyl radical, resulting in the formation of surface acetates (from the acetyl group) and formates (from the methyl radicals). Acetate ions are also converted to formates, that, in turn, photo-oxidized to CO2. Under the experimental conditions applied the accumulation of carbonates and bicarbonates were observed on the TiO2 surface as the photo-oxidation of acetone proceeded (this was also observed during the course of photo-oxidation of all the other organics studied here). When the initial radical ejection step produced hydrocarbons containing more than one C atoms (as in the case in 2-butanone and mesytil oxide), the formation of aldehydes on the catalyst surface was also observed as a result of secondary reactions. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy. JHK also acknowledges the support of this work by the 2014 Research Fund of UNIST (Ulsan National Institute of Science and Technology, Ulsan, Korea). The authors thank M.A. Henderson for the fruitful discussions on the photo-oxidation of organic molecules on TiO2.« less

The SAMI Galaxy Survey: spatially resolving the main sequence of star formation

NASA Astrophysics Data System (ADS)

Medling, Anne M.; Cortese, Luca; Croom, Scott M.; Green, Andrew W.; Groves, Brent; Hampton, Elise; Ho, I.-Ting; Davies, Luke J. M.; Kewley, Lisa J.; Moffett, Amanda J.; Schaefer, Adam L.; Taylor, Edward; Zafar, Tayyaba; Bekki, Kenji; Bland-Hawthorn, Joss; Bloom, Jessica V.; Brough, Sarah; Bryant, Julia J.; Catinella, Barbara; Cecil, Gerald; Colless, Matthew; Couch, Warrick J.; Drinkwater, Michael J.; Driver, Simon P.; Federrath, Christoph; Foster, Caroline; Goldstein, Gregory; Goodwin, Michael; Hopkins, Andrew; Lawrence, J. S.; Leslie, Sarah K.; Lewis, Geraint F.; Lorente, Nuria P. F.; Owers, Matt S.; McDermid, Richard; Richards, Samuel N.; Sharp, Robert; Scott, Nicholas; Sweet, Sarah M.; Taranu, Dan S.; Tescari, Edoardo; Tonini, Chiara; van de Sande, Jesse; Walcher, C. Jakob; Wright, Angus

2018-04-01

We present the ˜800 star formation rate maps for the Sydney-AAO Multi-object Integral field spectrograph (SAMI) Galaxy Survey based on H α emission maps, corrected for dust attenuation via the Balmer decrement, that are included in the SAMI Public Data Release 1. We mask out spaxels contaminated by non-stellar emission using the [O III]/H β, [N II]/H α, [S II]/H α, and [O I]/H α line ratios. Using these maps, we examine the global and resolved star-forming main sequences of SAMI galaxies as a function of morphology, environmental density, and stellar mass. Galaxies further below the star-forming main sequence are more likely to have flatter star formation profiles. Early-type galaxies split into two populations with similar stellar masses and central stellar mass surface densities. The main-sequence population has centrally concentrated star formation similar to late-type galaxies, while galaxies >3σ below the main sequence show significantly reduced star formation most strikingly in the nuclear regions. The split populations support a two-step quenching mechanism, wherein halo mass first cuts off the gas supply and remaining gas continues to form stars until the local stellar mass surface density can stabilize the reduced remaining fuel against further star formation. Across all morphologies, galaxies in denser environments show a decreased specific star formation rate from the outside in, supporting an environmental cause for quenching, such as ram-pressure stripping or galaxy interactions.

Sedimentary environment and tectonic deformations of the Neoproterozoic Iron formation at the Wadi El-Dabbah greenstone sequence, Central Eastern Desert, Egypt

NASA Astrophysics Data System (ADS)

Kiyokawa, S.; Suzuki, T.; Ikehara, M.; Horie, K.; Takehara, M.; Abd-Elmonem, H.; Dawoud, A. D. M.; El-Hasan, M. M.

2017-12-01

El-Dabbah area Central Eastern Desert of the Nubia Shield preserved Neoproterozoic lower green schist faces volcaniclastics greenstone sequence and covered strike-slip deformation related subaerial sedimentary sequence (Hammamat Group). The volcaniclastics greenstone sequence (El-Dabbah Formation) preserved several iron beds bearing well stratified sequence. Four tectonic deformation identified as this area; thrust deformation (D1), strike-slip deformation with transtension normal fault and strong left-lateral shear (D2), subaerial pull apart sediments basin formed strike-slip deformations (D3), and extensional deformation after the Hammamat Group sedimentation (D4). New age data from intrusions identified about 638 Ma white granite and about 660 Ma quartz porphyry. Based on the detail mapping, we reconstruct more than 5000m thick volcano sedimentary succession. At least, 10 iron rich sections were identified within 3500m thick volcano-sedimentary sequence. There are 14 iron formation sequence identified in this greenstone sequence. Each Iron sequences are bedded with greenish-black shales within massive volcaniclastics and lava flow. Iron formation is formed mostly fine grain magnetite deposited within volcanic mudstone and siltstone with gradual distribution. Timing of this iron sediment is identified within Sturtian glaciation (730-700Ma). However, there is no geological direct support evidence in the Snowball earth event at this greenstone sequence. The volcanic activities at this ocean already produced many Fe2+ to ocean water. Repeated iron precipitation occur during volcanic activity interphase period which produced oxidation of iron and produce oxyhydroxide with mud-silt sediment at bottom of ocean.

Effect of solution annealing temperature on precipitation in 2205 duplex stainless steel

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

Kashiwar, A., E-mail: akashiwar@gmail.com; Vennela, N. Phani, E-mail: phanivennela@gmail.com; Kamath, S.L., E-mail: kamath@iitb.ac.in

2012-12-15

In the present study, effect of solution annealing temperature (1050 Degree-Sign C and 1100 Degree-Sign C) and isothermal ageing (700 Degree-Sign C: 15 min to 6 h) on the microstructural changes in 2205 duplex stainless steel has been investigated systematically. Scanning electron microscopy and X-ray diffraction were adopted to follow the microstructural evolution, while an energy dispersive spectrometer attached to scanning electron microscope was used to obtain localised chemical information of various phases. The ferritic matrix of the two phase 2205 duplex stainless steel ({approx} 45% ferrite and {approx} 55% austenite) undergoes a series of metallurgical transformations during ageing-formation ofmore » secondary austenite ({gamma}{sub 2}) and precipitation of Cr and Mo rich intermetallic (chi-{chi} and sigma-{sigma}) phases. For solution annealing at 1050 Degree-Sign C, significant amount of carbides were observed in the ferrite grains after 1 h of ageing at 700 Degree-Sign C. {chi} Phase precipitated after the precipitation of carbides-preferentially at the ferrite-ferrite and also at the ferrite-austenite boundaries. {sigma} Phase was not observed in significant quantity even after 6 h of ageing. The sequence of precipitation in samples solution annealed at 1050 Degree-Sign C was found to be carbides {yields} {chi} {yields} {sigma}. On the contrary, for samples solution annealed at 1100 Degree-Sign C, the precipitation of {chi} phase was negligible. {chi} Phase precipitated before {sigma} phase, preferentially along the ferrite-ferrite grain boundaries and was later consumed in the {sigma} phase precipitation. The {sigma} phase precipitated via the eutectoid transformation of ferrite to yield secondary austenite {gamma}{sub 2} and {sigma} phase in the ferrite and along the ferrite-austenite grain boundaries. An increase in the volume fraction of {gamma}{sub 2} and {sigma} phase with simultaneous decrease in the ferrite was evidenced with ageing. - Highlights: Black-Right-Pointing-Pointer Effect of solution annealing temperature on microstructural evolution is studied. Black-Right-Pointing-Pointer {chi} Phase precipitated preferentially in the samples solution annealed at 1050 Degree-Sign C. Black-Right-Pointing-Pointer {sigma} Phase precipitated preferentially in the samples solution annealed at 1100 Degree-Sign C. Black-Right-Pointing-Pointer For SA at 1050 Degree-Sign C, the sequence of precipitation was carbides {yields} {chi} phase {yields} {sigma} phase. Black-Right-Pointing-Pointer For SA at 1100 Degree-Sign C, {sigma} phase precipitated via the eutectoid reaction: ferrite (F) {yields} {sigma} + {gamma}{sub 2}.« less

Charge pattern matching as a ‘fuzzy’ mode of molecular recognition for the functional phase separations of intrinsically disordered proteins

NASA Astrophysics Data System (ADS)

Lin, Yi-Hsuan; Brady, Jacob P.; Forman-Kay, Julie D.; Chan, Hue Sun

2017-11-01

Biologically functional liquid-liquid phase separation of intrinsically disordered proteins (IDPs) is driven by interactions encoded by their amino acid sequences. Little is currently known about the molecular recognition mechanisms for distributing different IDP sequences into various cellular membraneless compartments. Pertinent physics was addressed recently by applying random-phase-approximation (RPA) polymer theory to electrostatics, which is a major energetic component governing IDP phase properties. RPA accounts for charge patterns and thus has advantages over Flory-Huggins (FH) and Overbeek-Voorn mean-field theories. To make progress toward deciphering the phase behaviors of multiple IDP sequences, the RPA formulation for one IDP species plus solvent is hereby extended to treat polyampholyte solutions containing two IDP species plus solvent. The new formulation generally allows for binary coexistence of two phases, each containing a different set of volume fractions ({φ }1,{φ }2) for the two different IDP sequences. The asymmetry between the two predicted coexisting phases with regard to their {φ }1/{φ }2 ratios for the two sequences increases with increasing mismatch between their charge patterns. This finding points to a multivalent, stochastic, ‘fuzzy’ mode of molecular recognition that helps populate various IDP sequences differentially into separate phase compartments. An intuitive illustration of this trend is provided by FH models, whereby a hypothetical case of ternary coexistence is also explored. Augmentations of the present RPA theory with a relative permittivity {ɛ }{{r}}(φ ) that depends on IDP volume fraction φ ={φ }1+{φ }2 lead to higher propensities to phase separate, in line with the case with one IDP species we studied previously. Notably, the cooperative, phase-separation-enhancing effects predicted by the prescriptions for {ɛ }{{r}}(φ ) we deem physically plausible are much more prominent than that entailed by common effective medium approximations based on Maxwell Garnett and Bruggeman mixing formulas. Ramifications of our findings on further theoretical development for IDP phase separation are discussed.

A novel mechanism for creating double pulsars

NASA Technical Reports Server (NTRS)

Sigurdsson, Steinn; Hernquist, Lars

1992-01-01

Simulations of encounters between pairs of hard binaries, each containing a neutron star and a main-sequence star, reveal a new formation mechanism for double pulsars in dense cores of globular clusters. In many cases, the two normal stars are disrupted to form a common envelope around the pair of neutron stars, both of which will be spun up to become millisecond pulsars. We predict that a new class of pulsars, double millisecond pulsars, will be discovered in the cores of dense globular clusters. The genesis proceeds through a short-lived double-core common envelope phase, with the envelope ejected in a fast wind. It is possible that the progenitor may also undergo a double X-ray binary phase. Any circular, short-period double pulsar found in the galaxy would necessarily come from disrupted disk clusters, unlike Hulse-Taylor class pulsars or low-mass X-ray binaries which may be ejected from clusters or formed in the galaxy.

Electronic and structural ground state of heavy alkali metals at high pressure

DOE PAGES

Fabbris, G.; Lim, J.; Veiga, L. S. I.; ...

2015-02-17

Here, alkali metals display unexpected properties at high pressure, including emergence of low symmetry crystal structures, that appear to occur due to enhanced electronic correlations among the otherwise nearly-free conduction electrons. We investigate the high pressure electronic and structural ground state of K, Rb, and Cs using x-ray absorption spectroscopy and x-ray diffraction measurements together with ab initio theoretical calculations. The sequence of phase transitions under pressure observed at low temperature is similar in all three heavy alkalis except for the absence of the oC84 phase in Cs. Both the experimental and theoretical results point to pressure-enhanced localization of themore » valence electrons characterized by pseudo-gap formation near the Fermi level and strong spd hybridization. Although the crystal structures predicted to host magnetic order in K are not observed, the localization process appears to drive these alkalis closer to a strongly correlated electron state.« less

Magnetotactic bacteria form magnetite from a phosphate-rich ferric hydroxide via nanometric ferric (oxyhydr)oxide intermediates.

PubMed

Baumgartner, Jens; Morin, Guillaume; Menguy, Nicolas; Perez Gonzalez, Teresa; Widdrat, Marc; Cosmidis, Julie; Faivre, Damien

2013-09-10

The iron oxide mineral magnetite (Fe3O4) is produced by various organisms to exploit magnetic and mechanical properties. Magnetotactic bacteria have become one of the best model organisms for studying magnetite biomineralization, as their genomes are sequenced and tools are available for their genetic manipulation. However, the chemical route by which magnetite is formed intracellularly within the so-called magnetosomes has remained a matter of debate. Here we used X-ray absorption spectroscopy at cryogenic temperatures and transmission electron microscopic imaging techniques to chemically characterize and spatially resolve the mechanism of biomineralization in those microorganisms. We show that magnetite forms through phase transformation from a highly disordered phosphate-rich ferric hydroxide phase, consistent with prokaryotic ferritins, via transient nanometric ferric (oxyhydr)oxide intermediates within the magnetosome organelle. This pathway remarkably resembles recent results on synthetic magnetite formation and bears a high similarity to suggested mineralization mechanisms in higher organisms.

Microstructure and antibacterial properties of microwave plasma nitrided layers on biomedical stainless steels

NASA Astrophysics Data System (ADS)

Lin, Li-Hsiang; Chen, Shih-Chung; Wu, Ching-Zong; Hung, Jing-Ming; Ou, Keng-Liang

2011-06-01

Nitriding of AISI 303 austenitic stainless steel using microwave plasma system at various temperatures was conducted in the present study. The nitrided layers were characterized via scanning electron microscopy, glancing angle X-ray diffraction, transmission electron microscopy and Vickers microhardness tester. The antibacterial properties of this nitrided layer were evaluated. During nitriding treatment between 350 °C and 550 °C, the phase transformation sequence on the nitrided layers of the alloys was found to be γ → (γ + γ N) → (γ + α + CrN). The analytical results revealed that the surface hardness of AISI 303 stainless steel could be enhanced with the formation of γ N phase in nitriding process. Antibacterial test also demonstrated the nitrided layer processed the excellent antibacterial properties. The enhanced surface hardness and antibacterial properties make the nitrided AISI 303 austenitic stainless steel to be one of the essential materials in the biomedical applications.

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.

New age constraints on the palaeoenvironmental evolution of the late Paleozoic back-arc basin along the western Gondwana margin of southern Peru

NASA Astrophysics Data System (ADS)

Boekhout, F.; Reitsma, M. J.; Spikings, R.; Rodriguez, R.; Ulianov, A.; Gerdes, A.; Schaltegger, U.

2018-03-01

The tectonic evolution of the western Gondwana margin during Pangaea amalgation is recorded in variations in the Permo-Carboniferous back-arc basin sedimentation of Peru. This study provides the first radiometric age constraints on the volcanic and sedimentary sequences of south-central eastern Peru up to the western-most tip of Bolivia, and now permits the correlation of lateral facies variations to the late Paleozoic pre-Andean orogenic cycle. The two phases of Gondwanide magmatism and metamorphism at c. 315 Ma and c. 260 Ma are reflected in two major changes in this sedimentary environment. Our detrital U-Pb zircon ages demonstrate that the timing of Ambo Formation deposition corroborates the Late Mississipian age estimates. The transition from the Ambo to the Tarma Formation around the Middle Pennsylvanian Early Gondwanide Orogeny (c. 315 Ma) represents a relative deepening of the basin. Throughout the shallow marine deposits of the Tarma Formation evidence for contemporaneous volcanism becomes gradually more pronounced and culminates around 312 - 309 Ma. Continuous basin subsidence resulted in a buildup of platform carbonates of the Copacabana Formation. Our data highlights the presence of a previously unrecognized phase of deposition of mainly fluvial sandstones and localized volcanism (281-270 Ma), which we named ´Oqoruro Formation'. This sedimentary succession was previously miss-assigned to the so-called Mitu Group, which has recently been dated to start deposition in the Middle Triassic (∼245-240 Ma). The emersion of this marine basin coincides with the onset of a major plutonic pulse related to the Late Gondwanide Orogeny (c. 260). Exhumation lead to the consequent retreat of the epeiric sea to the present-day sub-Andean region, and the coeval accumulation of the fluvial Oqoruro Formation in south eastern Peru. These late Paleozoic palaeoenvironmental changes in the back-arc basins along the western Gondwana margin of southern reflect changes in tectonic plate reorganization in a long-lived Paleozoic accretionary orogeny.

Sequence stratigraphy of the Raha Formation, Bakr Oil Field, Gulf of Suez, Egypt: Insights from electrical well log and palynological data

NASA Astrophysics Data System (ADS)

Mansour, Ahmed; Mohamed, Omar; Tahoun, Sameh S.; Elewa, Ashraf M. T.

2018-03-01

The current paper provides a high resolution sequence stratigraphic study of the Raha Formation from the productive Bakr Oil Field, central Gulf of Suez, Egypt. Sixty cutting rock samples spanning the Cenomanian from three wells (Bakr-114, B-115 and B-109) in the Bakr Basin, were palynologically investigated. The documented palynomorphs assemblage of either terrestrially-derived sporomorphs or marine inhabited dinocysts, allowed two palynological zones as well as their encompassing depositional palaeoenvironment to be recognized. These zones are Afropollis jardinus-Crybelosporites pannuceus Assemblage Zone (early-middle Cenomanian) and Classopollis brasiliensis-Tricolpites sagax Assemblage Zone (late Cenomanian). Detailed analysis of the particulate organic matter compositions suggested that the depositional palaeoenvironment of the Raha Formation was fluctuating between supratidal and distal-inner neritic conditions, due to successive oscillations of the Neo-Tethyan Ocean during the Cenomanian. The pronounced peaks of particulate organic matter versus gamma ray are markedly used in delineating the depositional sequences of the Raha Formation and their bounding surfaces. The Raha Formation probably corresponds to a second-order depositional sequence, which can be further subdivided into eight third-order depositional sequences, of which six are complete and two are incomplete ones. These depositional sequences are significantly synchronized based on a simple 2-D correlation model between the three wells. According to the hierarchical duration system, the Cenomanian herein was approximately attributed to 6 Myr, each of which has lower order depositional sequences that took approximately 0.9 Myr. Based on the sequence stratigraphic approach together with palynofacies analysis and gamma ray data, a condensed section was defined in the B-115.

Modeling of metastable phase formation diagrams for sputtered thin films.

PubMed

Chang, Keke; Music, Denis; To Baben, Moritz; Lange, Dennis; Bolvardi, Hamid; Schneider, Jochen M

2016-01-01

A method to model the metastable phase formation in the Cu-W system based on the critical surface diffusion distance has been developed. The driver for the formation of a second phase is the critical diffusion distance which is dependent on the solubility of W in Cu and on the solubility of Cu in W. Based on comparative theoretical and experimental data, we can describe the relationship between the solubilities and the critical diffusion distances in order to model the metastable phase formation. Metastable phase formation diagrams for Cu-W and Cu-V thin films are predicted and validated by combinatorial magnetron sputtering experiments. The correlative experimental and theoretical research strategy adopted here enables us to efficiently describe the relationship between the solubilities and the critical diffusion distances in order to model the metastable phase formation during magnetron sputtering.

A conformational switch is responsible for the reversal of the 6S RNA-dependent RNA polymerase inhibition in Escherichia coli.

PubMed

Steuten, Benedikt; Wagner, Rolf

2012-12-01

6S RNA is a bacterial transcriptional regulator,which accumulates during stationary phase and inhibits transcription from many promoters due to stable association with σ 70 -containing RNA polymerase. This inhibitory RNA polymerase ∼ 6S RNA complex dissociates during nutritional upshift, when cells undergo outgrowth from stationary phase, releasing active RNA polymerase ready for transcription. The release reaction depends on a characteristic property of 6S RNAs, namely to act as template for the de novo synthesis of small RNAs, termed pRNAs.Here, we used limited hydrolysis with structure-specific RNases and in-line probing of isolated 6S RNA and 6SRNA ∼ pRNA complexes to investigate the molecular details leading to the release reaction. Our results indicate that pRNA transcription induces the refolding of the 6S RNA secondary structure by disrupting part of the closing stem(conserved sequence regions CRI and CRIV) and formation of a new hairpin (conserved sequence regions CRIII and CRIV). Comparison of the dimethylsulfate modification pattern of 6S RNA in living cells at stationary growth and during outgrowth confirmed the conformational change observed in vitro. Based on our results, a model describing the individual steps of the release reaction is presented.

Motion-sensitized SPRITE measurements of hydrodynamic cavitation in fast pipe flow.

PubMed

Adair, Alexander; Mastikhin, Igor V; Newling, Benedict

2018-06-01

The pressure variations experienced by a liquid flowing through a pipe constriction can, in some cases, result in the formation of a bubble cloud (i.e., hydrodynamic cavitation). Due to the nature of the bubble cloud, it is ideally measured through the use of non-optical and non-invasive techniques; therefore, it is well-suited for study by magnetic resonance imaging. This paper demonstrates the use of Conical SPRITE (a 3D, centric-scan, pure phase-encoding pulse sequence) to acquire time-averaged void fraction and velocity information about hydrodynamic cavitation for water flowing through a pipe constriction. Copyright © 2018 Elsevier Inc. All rights reserved.

Automated Array Assembly, Phase 2

NASA Technical Reports Server (NTRS)

Daiello, R. V.

1978-01-01

The purpose of the overall program is to establish technological readiness and provide verification for the elements of a manufacturing sequence which would ultimately be suitable for the large-scale production of silicon solar-array modules at a selling price of less than $500/kW. A program and process plan for accomplishing this objective was developed and put into operation. Three junction-formation processes are shown; since cost analysis shows that they do not differ greatly in cost, each should be considered for technical merits and possible future cost reduction. The progress made in the various process steps of the plan is described, and conclusions are presented.

Viking lander imaging investigation during extended and continuation automatic missions. Volume 2: Lander 2 picture catalog of experiment data record

NASA Technical Reports Server (NTRS)

Jones, K. L.; Henshaw, M.; Mcmenomy, C.; Robles, A.; Scribner, P. C.; Wall, S. D.; Wilson, J. W.

1981-01-01

Images returned by the two Viking landers during the extended and continuation automatic phases of the Viking Mission are presented. Information describing the conditions under which the images were acquired is included with skyline drawings showing the images positioned in the field of view of the cameras. Subsets of the images are listed in a variety of sequences to aid in locating images of interest. The format and organization of the digital magnetic tape storage of the images are described. A brief description of the mission and the camera system is also included.

Viking lander imaging investigation during extended and continuation automatic missions. Volume 1: Lander 1 picture catalog of experiment data record

NASA Technical Reports Server (NTRS)

Jones, K. L.; Henshaw, M.; Mcmenomy, C.; Robles, A.; Scribner, P. C.; Wall, S. D.; Wilson, J. W.

1981-01-01

All images returned by Viking Lander 1 during the extended and continuation automatic phases of the Viking Mission are presented. Listings of supplemental information which describe the conditions under which the images were acquired are included together with skyline drawings which show where the images are positioned in the field of view of the cameras. Subsets of the images are listed in a variety of sequences to aid in locating images of interest. The format and organization of the digital magnetic tape storage of the images are described as well as the mission and the camera system.

Optimization of the β-Elimination/Michael Addition Chemistry on Reversed-Phase Supports for Mass Spectrometry Analysis of O-Linked Protein Modifications

PubMed Central

Nika, Heinz; Nieves, Edward; Hawke, David H.; Angeletti, Ruth Hogue

2013-01-01

We previously adapted the β-elimination/Michael addition chemistry to solid-phase derivatization on reversed-phase supports, and demonstrated the utility of this reaction format to prepare phosphoseryl peptides in unfractionated protein digests for mass spectrometric identification and facile phosphorylation-site determination. Here, we have expanded the use of this technique to β-N-acetylglucosamine peptides, modified at serine/threonine, phosphothreonyl peptides, and phosphoseryl/phosphothreonyl peptides, followed in sequence by proline. The consecutive β-elimination with Michael addition was adapted to optimize the solid-phase reaction conditions for throughput and completeness of derivatization. The analyte remained intact during derivatization and was recovered efficiently from the silica-based, reversed-phase support with minimal sample loss. The general use of the solid-phase approach for enzymatic dephosphorylation was demonstrated with phosphoseryl and phosphothreonyl peptides and was used as an orthogonal method to confirm the identity of phosphopeptides in proteolytic mixtures. The solid-phase approach proved highly suitable to prepare substrates from low-level amounts of protein digests for phosphorylation-site determination by chemical-targeted proteolysis. The solid-phase protocol provides for a simple, robust, and efficient tool to prepare samples for phosphopeptide identification in MALDI mass maps of unfractionated protein digests, using standard equipment available in most biological laboratories. The use of a solid-phase analytical platform is expected to be readily expanded to prepare digest from O-glycosylated- and O-sulfonated proteins for mass spectrometry-based structural characterization. PMID:23997661

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.

SDSS-IV MaNGA: Spatially Resolved Star Formation Main Sequence and LI(N)ER Sequence

NASA Astrophysics Data System (ADS)

Hsieh, B. C.; Lin, Lihwai; Lin, J. H.; Pan, H. A.; Hsu, C. H.; Sánchez, S. F.; Cano-Díaz, M.; Zhang, K.; Yan, R.; Barrera-Ballesteros, J. K.; Boquien, M.; Riffel, R.; Brownstein, J.; Cruz-González, I.; Hagen, A.; Ibarra, H.; Pan, K.; Bizyaev, D.; Oravetz, D.; Simmons, A.

2017-12-01

We present our study on the spatially resolved Hα and M * relation for 536 star-forming and 424 quiescent galaxies taken from the MaNGA survey. We show that the star formation rate surface density ({{{Σ }}}{SFR}), derived based on the Hα emissions, is strongly correlated with the M * surface density ({{{Σ }}}* ) on kiloparsec scales for star-forming galaxies and can be directly connected to the global star-forming sequence. This suggests that the global main sequence may be a consequence of a more fundamental relation on small scales. On the other hand, our result suggests that ∼20% of quiescent galaxies in our sample still have star formation activities in the outer region with lower specific star formation rate (SSFR) than typical star-forming galaxies. Meanwhile, we also find a tight correlation between {{{Σ }}}{{H}α } and {{{Σ }}}* for LI(N)ER regions, named the resolved “LI(N)ER” sequence, in quiescent galaxies, which is consistent with the scenario that LI(N)ER emissions are primarily powered by the hot, evolved stars as suggested in the literature.

On the determination of age and mass functions of stars in young open star clusters from the analysis of their luminosity functions

NASA Astrophysics Data System (ADS)

Piskunov, A. E.; Belikov, A. N.; Kharchenko, N. V.; Sagar, R.; Subramaniam, A.

2004-04-01

We construct the observed luminosity functions of the remote young open clusters NGC 2383, 2384, 4103, 4755, 7510 and Hogg 15 from CCD observations of them. The observed LFs are corrected for field star contamination determined with the help of a Galactic star count model. In the case of Hogg 15 and NGC 2383 we also consider the additional contamination from neighbouring clusters NGC 4609 and 2384, respectively. These corrections provide a realistic pattern of cluster LF in the vicinity of the main-sequence (MS) turn-on point and at fainter magnitudes reveal the so-called H-feature arising as a result of the transition of the pre-MS phase to the MS, which is dependent on the cluster age. The theoretical LFs are constructed representing a cluster population model with continuous star formation for a short time-scale and a power-law initial mass function (IMF), and these are fitted to the observed LF. As a result, we are able to determine for each cluster a set of parameters describing the cluster population (the age, duration of star formation, IMF slope and percentage of field star contamination). It is found that in spite of the non-monotonic behaviour of observed LFs, cluster IMFs can be described as power-law functions with slopes similar to Salpeter's value. The present main-sequence turn-on cluster ages are several times lower than those derived from the fitting of theoretical isochrones to the turn-off region of the upper main sequences.

Molecular Structure and Sequence in Complex Coacervates

NASA Astrophysics Data System (ADS)

Sing, Charles; Lytle, Tyler; Madinya, Jason; Radhakrishna, Mithun

Oppositely-charged polyelectrolytes in aqueous solution can undergo associative phase separation, in a process known as complex coacervation. This results in a polyelectrolyte-dense phase (coacervate) and polyelectrolyte-dilute phase (supernatant). There remain challenges in understanding this process, despite a long history in polymer physics. We use Monte Carlo simulation to demonstrate that molecular features (charge spacing, size) play a crucial role in governing the equilibrium in coacervates. We show how these molecular features give rise to strong monomer sequence effects, due to a combination of counterion condensation and correlation effects. We distinguish between structural and sequence-based correlations, which can be designed to tune the phase diagram of coacervation. Sequence effects further inform the physical understanding of coacervation, and provide the basis for new coacervation models that take monomer-level features into account.

Vanadium Oxide Thin Film Formation on Graphene Oxide by Microexplosive Decomposition of Ammonium Peroxovanadate and Its Application as a Sodium Ion Battery Anode.

PubMed

Mikhaylov, Alexey A; Medvedev, Alexander G; Grishanov, Dmitry A; Sladkevich, Sergey; Gun, Jenny; Prikhodchenko, Petr V; Xu, Zhichuan J; Nagasubramanian, Arun; Srinivasan, Madhavi; Lev, Ovadia

2018-02-27

Formation of vanadium oxide nanofilm-coated graphene oxide (GO) is achieved by thermally induced explosive disintegration of a microcrystalline ammonium peroxovanadate-GO composite. GO sheets isolate the microcrystalline grains and capture and contain the microexplosion products, resulting in the deposition of the nanoscale products on the GO. Thermal treatment of the supported nanofilm yields a sequence of nanocrystalline phases of vanadium oxide (V 3 O 7 , VO 2 ) as a function of temperature. This is the first demonstration of microexplosive disintegration of a crystalline peroxo compound to yield a nanocoating. The large number of recently reported peroxide-rich crystalline materials suggests that the process can be a useful general route for nanofilm formation. The V 3 O 7 @GO composite product was tested as a sodium ion battery anode and showed high charge capacity at high rate charge-discharge cycling (150 mAh g -1 at 3000 mA g -1 vs 300 mAh g -1 at 100 mA g -1 ) due to the nanomorphology of the vanadium oxide.

Formation of an Archean tectonic mélange in the Schreiber-Hemlo greenstone belt, Superior Province, Canada: Implications for Archean subduction-accretion process

NASA Astrophysics Data System (ADS)

Polat, Ali; Kerrich, Robert

1999-10-01

The late Archean (circa 2750-2670 Ma) Schreiber-Hemlo greenstone belt, Superior Province, Canada, is composed of tectonically juxtaposed fragments of oceanic plateaus (circa 2750-2700 Ma), oceanic island arcs (circa 2720-2695 Ma), and siliciclastic trench turbidites (circa 2705-2697 Ma). Following juxtaposition, these lithotectonic assemblages were collectively intruded by synkinematic tonalite-trondhjemite-granodiorite (TTG) plutons (circa 2720-2690 Ma) and ultramafic to felsic dikes and sills (circa 2690-2680 Ma), with subduction zone geochemical signatures. Overprinting relations between different sequences of structures suggest that the belt underwent at least three phases of deformation. During D1 (circa 2695-2685 Ma), oceanic plateau basalts and associated komatiites, arc-derived trench turbidites, and oceanic island arc sequences were all tectonically juxtaposed as they were incorporated into an accretionary complex. Fragmentation of these sequences resulted in broken formations and a tectonic mélange in the Schreiber assemblage of the belt. D2 (circa 2685-2680 Ma) is consistent with an intra-arc, right-lateral transpressional deformation. Fragmentation and mixing of D2 synkinematic dikes and sills suggest that mélange formation continued during D2. The D1 to D2 transition is interpreted in terms of a trenchward migration of the magmatic arc axis due to continued accretion and underplating. The D2 intra-arc strike-slip faults may have provided conduits for uprising melts from the descending slab, and they may have induced decompressional partial melting in the subarc mantle wedge, to yield synkinematic ultramafic to felsic intrusions. A similar close relationship between orogen-parallel strike-slip faulting and magmatism has recently been recognized in several Phanerozoic transpressional orogenic belts, suggesting that as in Phanerozoic counterparts, orogen-parallel strike-slip faulting in the Schreiber-Hemlo greenstone belt played an important role in magma emplacement.

Quantized phase coding and connected region labeling for absolute phase retrieval.

PubMed

Chen, Xiangcheng; Wang, Yuwei; Wang, Yajun; Ma, Mengchao; Zeng, Chunnian

2016-12-12

This paper proposes an absolute phase retrieval method for complex object measurement based on quantized phase-coding and connected region labeling. A specific code sequence is embedded into quantized phase of three coded fringes. Connected regions of different codes are labeled and assigned with 3-digit-codes combining the current period and its neighbors. Wrapped phase, more than 36 periods, can be restored with reference to the code sequence. Experimental results verify the capability of the proposed method to measure multiple isolated objects.

Formation of the molecular crystal structure during the vacuum sublimation of paracetamol

NASA Astrophysics Data System (ADS)

Belyaev, A. P.; Rubets, V. P.; Antipov, V. V.; Bordei, N. S.

2015-04-01

The results from structural and thermal studies on the formation of molecular crystals during the vacuum sublimation of paracetamol from its vapor phase are given. It is established that the vapor-crystal phase transition proceeds in a complicated way as the superposition of two phase transitions: a first-order phase transition with a change in density, and a second-order phase transition with a change in ordering. It is shown that the latter is a smeared phase transition that proceeds with the formation of a pretransitional phase that is irreversibly dissipated during phase transformation, leading to the formation of crystals of the rhombic syngony. Data from differential scanning calorimetry and X-ray diffraction analysis are presented along with microphotographs.

Functional Analysis of the Accessory Protein TapA in Bacillus subtilis Amyloid Fiber Assembly

PubMed Central

Romero, Diego; Vlamakis, Hera; Losick, Richard

2014-01-01

Bacillus subtilis biofilm formation relies on the assembly of a fibrous scaffold formed by the protein TasA. TasA polymerizes into highly stable fibers with biochemical and morphological features of functional amyloids. Previously, we showed that assembly of TasA fibers requires the auxiliary protein TapA. In this study, we investigated the roles of TapA sequences from the C-terminal and N-terminal ends and TapA cysteine residues in its ability to promote the assembly of TasA amyloid-like fibers. We found that the cysteine residues are not essential for the formation of TasA fibers, as their replacement by alanine residues resulted in only minor defects in biofilm formation. Mutating sequences in the C-terminal half had no effect on biofilm formation. However, we identified a sequence of 8 amino acids in the N terminus that is key for TasA fiber formation. Strains expressing TapA lacking these 8 residues were completely defective in biofilm formation. In addition, this TapA mutant protein exhibited a dominant negative effect on TasA fiber formation. Even in the presence of wild-type TapA, the mutant protein inhibited fiber assembly in vitro and delayed biofilm formation in vivo. We propose that this 8-residue sequence is crucial for the formation of amyloid-like fibers on the cell surface, perhaps by mediating the interaction between TapA or TapA and TasA molecules. PMID:24488317

Functional analysis of the accessory protein TapA in Bacillus subtilis amyloid fiber assembly.

PubMed

Romero, Diego; Vlamakis, Hera; Losick, Richard; Kolter, Roberto

2014-04-01

Bacillus subtilis biofilm formation relies on the assembly of a fibrous scaffold formed by the protein TasA. TasA polymerizes into highly stable fibers with biochemical and morphological features of functional amyloids. Previously, we showed that assembly of TasA fibers requires the auxiliary protein TapA. In this study, we investigated the roles of TapA sequences from the C-terminal and N-terminal ends and TapA cysteine residues in its ability to promote the assembly of TasA amyloid-like fibers. We found that the cysteine residues are not essential for the formation of TasA fibers, as their replacement by alanine residues resulted in only minor defects in biofilm formation. Mutating sequences in the C-terminal half had no effect on biofilm formation. However, we identified a sequence of 8 amino acids in the N terminus that is key for TasA fiber formation. Strains expressing TapA lacking these 8 residues were completely defective in biofilm formation. In addition, this TapA mutant protein exhibited a dominant negative effect on TasA fiber formation. Even in the presence of wild-type TapA, the mutant protein inhibited fiber assembly in vitro and delayed biofilm formation in vivo. We propose that this 8-residue sequence is crucial for the formation of amyloid-like fibers on the cell surface, perhaps by mediating the interaction between TapA or TapA and TasA molecules.

Reconstructing the flow pattern evolution in inner region of the Fennoscandian Ice Sheet by glacial landforms from Gausdal Vestfjell area, south-central Norway

NASA Astrophysics Data System (ADS)

Putniņš, Artūrs; Henriksen, Mona

2017-05-01

More than 17 000 landforms from detailed LiDAR data sets have been mapped in the Gausdal Vestfjell area, south-central Norway. The spatial distribution and relationships between the identified subglacial bedforms, mainly streamlined landforms and ribbed moraine ridges, have provided new insight on the glacial dynamics and the sequence of glacial events during the last glaciation. This established evolution of the Late Weichselian ice flow pattern at this inner region of the Fennoscandian Ice Sheet is stepwise where a topography independent ice flow (Phase I) are followed by a regional (Phase II) before a strongly channelized, topography driven ice flow (Phase III). The latter phase is divided into several substages where the flow sets are becoming increasingly confined into the valleys, likely separated by colder, less active ice before down-melting of ice took place. A migrating ice divide and lowering of the ice surface seems to be the main reasons for these changes in ice flow pattern. Formation of ribbed moraine can occur both when the ice flow slows down and speeds up, forming respectively broad fields and elongated belts of ribbed moraines.

Electrochemical detection of Piscirickettsia salmonis genomic DNA from salmon samples using solid-phase recombinase polymerase amplification.

PubMed

Del Río, Jonathan Sabaté; Svobodova, Marketa; Bustos, Paulina; Conejeros, Pablo; O'Sullivan, Ciara K

2016-12-01

Electrochemical detection of solid-phase isothermal recombinase polymerase amplification (RPA) of Piscirickettsia salmonis in salmon genomic DNA is reported. The electrochemical biosensor was constructed by surface functionalization of gold electrodes with a thiolated forward primer specific to the genomic region of interest. Solid-phase RPA and primer elongation were achieved in the presence of the specific target sequence and biotinylated reverse primers. The formation of the subsequent surface-tethered duplex amplicons was electrochemically monitored via addition of streptavidin-linked HRP upon completion of solid-phase RPA. Successful quantitative amplification and detection were achieved in less than 1 h at 37 °C, calibrating with PCR-amplified genomic DNA standards and achieving a limit of detection of 5 · 10 -8  μg ml -1 (3 · 10 3 copies in 10 μl). The presented system was applied to the analysis of eight real salmon samples, and the method was also compared to qPCR analysis, observing an excellent degree of correlation. Graphical abstract Schematic of use of electrochemical RPA for detection of Psiricketessia salmonis in salmon liver.

The effect of Fe-coverage on the structure, morphology and magnetic properties of α-FeSi2 nanoislands.

PubMed

Tripathi, J K; Garbrecht, M; Kaplan, W D; Markovich, G; Goldfarb, I

2012-12-14

Self-assembled α-FeSi(2) nanoislands were formed using solid-phase epitaxy of low (~1.2 ML) and high (~21 ML) Fe coverages onto vicinal Si(111) surfaces followed by thermal annealing. At a resulting low Fe-covered Si(111) surface, we observed in situ, by real-time scanning tunneling microscopy and surface electron diffraction, the entire sequence of Fe-silicide formation and transformation from the initially two-dimensional (2 × 2)-reconstructed layer at 300 °C into (2 × 2)-reconstructed nanoislands decorating the vicinal step-bunch edges in a self-ordered fashion at higher temperatures. In contrast, the silicide nanoislands at a high Fe-covered surface were noticeably larger, more three-dimensional, and randomly distributed all over the surface. Ex situ x-ray photoelectron spectroscopy and high-resolution transmission electron microscopy indicated the formation of an α-FeSi(2) island phase, in an α-FeSi(2){112} // Si{111} orientation. Superconducting quantum interference device magnetometry showed considerable superparamagnetism, with ~1.9 μ(B)/Fe atom at 4 K for the low Fe-coverage, indicating stronger ferromagnetic coupling of individual magnetic moments, as compared to high Fe-coverage, where the calculated moments were only ~0.8 μ(B)/Fe atom. Such anomalous magnetic behavior, particularly for the low Fe-coverage case, is radically different from the non-magnetic bulk α-FeSi(2) phase, and may open new pathways to high-density magnetic memory storage devices.

The statistical analysis of energy release in small-scale coronal structures

NASA Astrophysics Data System (ADS)

Ulyanov, Artyom; Kuzin, Sergey; Bogachev, Sergey

We present the results of statistical analysis of impulsive flare-like brightenings, which numerously occur in the quiet regions of solar corona. For our study, we utilized high-cadence observations performed with two EUV-telescopes - TESIS/Coronas-Photon and AIA/SDO. In total, we processed 6 sequences of images, registered throughout the period between 2009 and 2013, covering the rising phase of the 24th solar cycle. Based on high-speed DEM estimation method, we developed a new technique to evaluate the main parameters of detected events (geometrical sizes, duration, temperature and thermal energy). We then obtained the statistical distributions of these parameters and examined their variations depending on the level of solar activity. The results imply that near the minimum of the solar cycle the energy release in quiet corona is mainly provided by small-scale events (nanoflares), whereas larger events (microflares) prevail on the peak of activity. Furthermore, we investigated the coronal conditions that had specified the formation and triggering of registered flares. By means of photospheric magnetograms obtained with MDI/SoHO and HMI/SDO instruments, we examined the topology of local magnetic fields at different stages: the pre-flare phase, the peak of intensity and the ending phase. To do so, we introduced a number of topological parameters including the total magnetic flux, the distance between magnetic sources and their mutual arrangement. The found correlation between the change of these parameters and the formation of flares may offer an important tool for application of flare forecasting.

An EST dataset for Metasequoia glyptostroboides buds: the first EST resource for molecular genomics studies in Metasequoia.

PubMed

Zhao, Ying; Thammannagowda, Shivegowda; Staton, Margaret; Tang, Sha; Xia, Xinli; Yin, Weilun; Liang, Haiying

2013-03-01

The "living fossil" Metasequoia glyptostroboides Hu et Cheng, commonly known as dawn redwood or Chinese redwood, is the only living species in the genus and is valued for its essential oil and crude extracts that have great potential for anti-fungal activity. Despite its paleontological significance and economical value as a rare relict species, genomic resources of Metasequoia are very limited. In order to gain insight into the molecular mechanisms behind the formation of reproductive buds and the transition from vegetative phase to reproductive phase in Metasequoia, we performed sequencing of expressed sequence tags from Metasequoia vegetative buds and female buds. By using the 454 pyrosequencing technology, a total of 1,571,764 high-quality reads were generated, among which 733,128 were from vegetative buds and 775,636 were from female buds. These EST reads were clustered and assembled into 114,124 putative unique transcripts (PUTs) with an average length of 536 bp. The 97,565 PUTs that were at least 100 bp in length were functionally annotated by a similarity search against public databases and assigned with Gene Ontology (GO) terms. A total of 59 known floral gene families and 190 isotigs involved in hormone regulation were captured in the dataset. Furthermore, a set of PUTs differentially expressed in vegetative and reproductive buds, as well as SSR motifs and high confidence SNPs, were identified. This is the first large-scale expressed sequence tags ever generated in Metasequoia and the first evidence for floral genes in this critically endangered deciduous conifer species.

RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

PubMed Central

Shibata, Kazuhiro; Itoh, Masayoshi; Aizawa, Katsunori; Nagaoka, Sumiharu; Sasaki, Nobuya; Carninci, Piero; Konno, Hideaki; Akiyama, Junichi; Nishi, Katsuo; Kitsunai, Tokuji; Tashiro, Hideo; Itoh, Mari; Sumi, Noriko; Ishii, Yoshiyuki; Nakamura, Shin; Hazama, Makoto; Nishine, Tsutomu; Harada, Akira; Yamamoto, Rintaro; Matsumoto, Hiroyuki; Sakaguchi, Sumito; Ikegami, Takashi; Kashiwagi, Katsuya; Fujiwake, Syuji; Inoue, Kouji; Togawa, Yoshiyuki; Izawa, Masaki; Ohara, Eiji; Watahiki, Masanori; Yoneda, Yuko; Ishikawa, Tomokazu; Ozawa, Kaori; Tanaka, Takumi; Matsuura, Shuji; Kawai, Jun; Okazaki, Yasushi; Muramatsu, Masami; Inoue, Yorinao; Kira, Akira; Hayashizaki, Yoshihide

2000-01-01

The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3′ end and 5′ end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can be revealed by seven RISA systems within one month. PMID:11076861

The Herschel Virgo Cluster Survey. XIX. Physical properties of low luminosity FIR sources at z < 0.5

NASA Astrophysics Data System (ADS)

Pappalardo, Ciro; Bizzocchi, Luca; Fritz, Jacopo; Boselli, Alessandro; Boquien, Mederic; Boissier, Samuel; Baes, Maarten; Ciesla, Laure; Bianchi, Simone; Clemens, Marcel; Viaene, Sebastien; Bendo, George J.; De Looze, Ilse; Smith, Matthew W. L.; Davies, Jonathan

2016-05-01

Context. The star formation rate is a crucial parameter for the investigation galaxy evolution. At low redshift the cosmic star formation rate density declines smoothly, and massive active galaxies become passive, reducing their star formation activity. This implies that the bulk of the star formation rate density at low redshift is mainly driven by low mass objects. Aims: We investigate the properties of a sample of low luminosity far-infrared sources selected at 250 μm. We have collected data from ultraviolet to far-infrared in order to perform a multiwavelengths analysis. The main goal is to investigate the correlation between star formation rate, stellar mass, and dust mass for a galaxy population with a wide range in dust content and stellar mass, including the low mass regime that most probably dominates the star formation rate density at low redshift. Methods: We define a main sample of ~800 sources with full spectral energy distribution coverage between 0.15 <λ< 500 μm and an extended sample with ~5000 sources in which we remove the constraints on the ultraviolet and near-infrared bands. We analyze both samples with two different spectral energy distribution fitting methods: MAGPHYS and CIGALE, which interpret a galaxy spectral energy distribution as a combination of different simple stellar population libraries and dust emission templates. Results: In the star formation rate versus stellar mass plane our samples occupy a region included between local spirals and higher redshift star forming galaxies. These galaxies represent the population that at z< 0.5 quenches their star formation activity and reduces their contribution to the cosmic star formation rate density. The subsample of galaxies with the higher masses (M∗> 3 × 1010 M⊙) do not lie on the main sequence, but show a small offset as a consequence of the decreased star formation. Low mass galaxies (M∗< 1 × 1010 M⊙) settle in the main sequence with star formation rate and stellar mass consistent with local spirals. Conclusions: Deep Herschel data allow the identification of a mixed galaxy population with galaxies still in an assembly phase or galaxies at the beginning of their passive evolution. We find that the dust luminosity is the parameter that allow us to discriminate between these two galaxy populations. The median spectral energy distribution shows that even at low star formation rate our galaxy sample has a higher mid-infrared emission than previously predicted. Herschel is an ESA space observatory with science instruments provided by a European-led principal investigator consortia and with an important participation from NASA.

Oligocene to Recent tectonic history of the Central Solomon intra-arc basin as determined from marine seismic reflection data and compilation of onland geology

NASA Astrophysics Data System (ADS)

Cowley, Shane; Mann, Paul; Coffin, M. F.; Shipley, Thomas H.

2004-10-01

Systematic analysis of a grid of 3450 km of multichannel seismic reflection lines from the Solomon Islands constrains the late Tertiary sedimentary and tectonic history of the Solomon Island arc and its convergent interaction with the Cretaceous Ontong Java oceanic plateau (OJP). The OJP, the largest oceanic plateau on Earth, subducted beneath the northern edge of the Solomon arc in the late Neogene, but the timing and consequences of this obliquely convergent event and its role in the subduction polarity reversal process remain poorly constrained. The Central Solomon intra-arc basin (CSB), which developed in Oligocene to Recent time above the Solomon arc, provides a valuable record of the tectonic environment prior to and accompanying the OJP convergent event and the subsequent arc polarity reversal. Recognition of regionally extensive stratigraphic sequences—whose ages can be inferred from marine sedimentary sections exposed onland in the Solomon Islands—indicate four distinct tectonic phases affecting the Solomon Island arc. Phase 1: Late Oligocene-Late Miocene rifting of the northeast-facing Solomon Island arc produced basal, normal-fault-controlled, asymmetrical sequences of the CSB; the proto-North Solomon trench was probably much closer to the CSB and is inferred to coincide with the trace of the present-day Kia-Kaipito-Korigole (KKK) fault zone; this protracted period of intra-arc extension shows no evidence for interruption by an early Miocene period of convergent "soft docking" of the Ontong Java Plateau as proposed by previous workers. Phase 2: Late Miocene-Pliocene oblique convergence of the Ontong Java Plateau at the proto-North Solomon trench (KKK fault zone) and folding of the CSB and formation of the Malaita accretionary prism (MAP); the highly oblique and diachronous convergence between the Ontong Java plateau and the Solomon arc terminates intra-arc extension first in the southeast (Russell subbasin of the CSB) during the Late Miocene and later during the Pliocene in the northwest (Shortland subbasin of the CSB); folds in the CSB form by inversion of normal faults formed during Phase 1; Phinney et al. [Sequence stratigraphy, structural style, and age of deformation of the Malaita accretionary prism (Solomon arc-Ontong Java Plateau convergent zone)] show a coeval pattern of southeast to northwest younging in folding and faulting of the MAP. Phase 3: Late Pliocene-early Pleistocene arc polarity reversal and subduction initiation at the San Cristobal trench. Effects of this event in the CSB include the formation of a chain of volcanoes above the subducting Australia plate at the San Cristobal trench, the formation of the broad synclinal structure of the CSB with evidence for truncation at the uplifted flanks, and widespread occurrence of slides and "seismites" (deposits formed by seismic shaking). Phase 4: Pleistocene to Recent continued shortening and synclinal subsidence of the CSB. Continued Australia-Pacific oblique plate convergence has led to deepening of the submarine, elongate basin axis of the synclinal CSB and uplift of the dual chain of the islands on its flanks.

Sequence heuristics to encode phase behaviour in intrinsically disordered protein polymers

PubMed Central

Quiroz, Felipe García; Chilkoti, Ashutosh

2015-01-01

Proteins and synthetic polymers that undergo aqueous phase transitions mediate self-assembly in nature and in man-made material systems. Yet little is known about how the phase behaviour of a protein is encoded in its amino acid sequence. Here, by synthesizing intrinsically disordered, repeat proteins to test motifs that we hypothesized would encode phase behaviour, we show that the proteins can be designed to exhibit tunable lower or upper critical solution temperature (LCST and UCST, respectively) transitions in physiological solutions. We also show that mutation of key residues at the repeat level abolishes phase behaviour or encodes an orthogonal transition. Furthermore, we provide heuristics to identify, at the proteome level, proteins that might exhibit phase behaviour and to design novel protein polymers consisting of biologically active peptide repeats that exhibit LCST or UCST transitions. These findings set the foundation for the prediction and encoding of phase behaviour at the sequence level. PMID:26390327

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

NASA Astrophysics Data System (ADS)

Anan, Tarek; El Shahat, Adam

2014-12-01

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

Concatenated shift registers generating maximally spaced phase shifts of PN-sequences

NASA Technical Reports Server (NTRS)

Hurd, W. J.; Welch, L. R.

1977-01-01

A large class of linearly concatenated shift registers is shown to generate approximately maximally spaced phase shifts of pn-sequences, for use in pseudorandom number generation. A constructive method is presented for finding members of this class, for almost all degrees for which primitive trinomials exist. The sequences which result are not normally characterized by trinomial recursions, which is desirable since trinomial sequences can have some undesirable randomness properties.

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.

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

PubMed Central

Haas, Brian J.; Gevers, Dirk; Earl, Ashlee M.; Feldgarden, Mike; Ward, Doyle V.; Giannoukos, Georgia; Ciulla, Dawn; Tabbaa, Diana; Highlander, Sarah K.; Sodergren, Erica; Methé, Barbara; DeSantis, Todd Z.; Petrosino, Joseph F.; Knight, Rob; Birren, Bruce W.

2011-01-01

Bacterial diversity among environmental samples is commonly assessed with PCR-amplified 16S rRNA gene (16S) sequences. Perceived diversity, however, can be influenced by sample preparation, primer selection, and formation of chimeric 16S amplification products. Chimeras are hybrid products between multiple parent sequences that can be falsely interpreted as novel organisms, thus inflating apparent diversity. We developed a new chimera detection tool called Chimera Slayer (CS). CS detects chimeras with greater sensitivity than previous methods, performs well on short sequences such as those produced by the 454 Life Sciences (Roche) Genome Sequencer, and can scale to large data sets. By benchmarking CS performance against sequences derived from a controlled DNA mixture of known organisms and a simulated chimera set, we provide insights into the factors that affect chimera formation such as sequence abundance, the extent of similarity between 16S genes, and PCR conditions. Chimeras were found to reproducibly form among independent amplifications and contributed to false perceptions of sample diversity and the false identification of novel taxa, with less-abundant species exhibiting chimera rates exceeding 70%. Shotgun metagenomic sequences of our mock community appear to be devoid of 16S chimeras, supporting a role for shotgun metagenomics in validating novel organisms discovered in targeted sequence surveys. PMID:21212162

Sedimentology of paleochannels on foreland coastal plain, Judith River Formation (upper Cretaceous), southeast Alberta

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

Koster, E.H.

1984-04-01

The upper 90 m (295 ft) of the sub-Bearpaw Judith River Formation, continuously exposed in the badlands along the Red Deer River 185 km (115 mi) east of Calgary, is famous for the unrivaled assemblage of dinosaur fossils. Dinosaur Provincial Park presents are a rare opportunity to view the architecture of a foreland coastal-plain sequence as well as to clarify the origin and distribution of subbituminous coal zones and gas reservoirs associated with this formation across southeast Alberta. The distal reaches of paleodrainage from the developing Cordillera to the Western Interior seaway are being examined by north-south traversed across themore » badlands. Sharp-based paleochannel units, enclosed by rooted, olive-gray mudstone sequences that are commonly 4-6 m (13-20 ft) thick, vary between 2 end members. The first contains laterally accreted sand-mud couplets with abundant macrofloral debris, and represents cyclical, low-energy growth of point bars, possible with an estuarine influence. The second, mainly comprising cosets of large trough cross-beds with mudstone intraclasts, was formed by episodic aggradation of high-energy systems. An intermediate composite type displays evidence for an energy increase as channel sinuosity decreased. This variation in paleochannel type is attributed to alternating alluviation/rejuvenation associated with an unstable base level. Coal zones and potential reservoirs appear to be associated with the transgressive and regressive phases, respectively, of the Bearpaw coast. Amalgamation of paleochannels - marked by laterally extensive horizons of bone fragments, lithic and intraclastic gravel - is more common seaward over the axial region of the Sweetgrass arch.« less

Recent Mastcam and MAHLI Visible/Near-Infrared Spectrophotometric Observations: Pahrump Hills to Marias Pass

NASA Astrophysics Data System (ADS)

Johnson, J. R.; Bell, J. F., III; Hayes, A.; Deen, R. G.; Godber, A.; Arvidson, R. E.; Lemmon, M. T.

2015-12-01

The Mastcam imaging system on the Curiosity rover continued acquisition of multispectral images of the same terrain at multiple times of day at three new rover locations between sols 872 and 1003. These data sets will be used to investigate the light scattering properties of rocks and soils along the Curiosity traverse using radiative transfer models. Images were acquired by the Mastcam-34 (M-34) camera on Sols 872-892 at 8 times of day (Mojave drill location), Sols 914-917 (Telegraph Peak drill location) at 9 times of day, and Sols 1000-1003 at 8 times of day (Stimson-Murray Formation contact near Marias Pass). Data sets were acquired using filters centered at 445, 527, 751, and 1012 nm, and the images were jpeg-compressed. Data sets typically were pointed ~east and ~west to provide phase angle coverage from near 0° to 125-140° for a variety of rocks and soils. Also acquired on Sols 917-918 at the Telegraph Peak site was a multiple time-of-day Mastcam sequence pointed southeast using only the broadband Bayer filters that provided losslessly compressed images with phase angles ~55-129°. Navcam stereo images were also acquired with each data set to provide broadband photometry and terrain measurements for computing surface normals and local incidence and emission angles used in photometric modeling. On Sol 1028, the MAHLI camera was used as a goniometer to acquire images at 20 arm positions, all centered at the same location within the work volume from a near-constant distance of 85 cm from the surface. Although this experiment was run at only one time of day (~15:30 LTST), it provided phase angle coverage from ~30° to ~111°. The terrain included the contact between the uppermost portion of the Murray Formation and the Stimson sandstones, and was the first acquisition of both Mastcam and MALHI photometry images at the same rover location. The MAHLI images also allowed construction of a 3D shape model of the Stimson-Murray contact region. The attached figure shows a phase color composite of the western Stimson area, created using phase angles of 8°, 78°, and 130° at 751 nm. The red areas correspond to highly backscattering materials that appear to concentrate along linear fractures throughout this area. The blue areas correspond to more forward scattering materials dispersed through the stratigraphic sequence.

Induction log responses to layered, dipping, and anisotropic formations: Induction log shoulder-bed corrections to anisotropic formations and the effect of shale anisotropy in thinly laminated sand/shale sequences

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

Hagiwara, Teruhiko

1996-12-31

Induction log responses to layered, dipping, and anisotropic formations are examined analytically. The analytical model is especially helpful in understanding induction log responses to thinly laminated binary formations, such as sand/shale sequences, that exhibit macroscopically anisotropic: resistivity. Two applications of the analytical model are discussed. In one application we examine special induction log shoulder-bed corrections for use when thin anisotropic beds are encountered. It is known that thinly laminated sand/shale sequences act as macroscopically anisotropic: formations. Hydrocarbon-bearing formations also act as macroscopically anisotropic formations when they consist of alternating layers of different grain-size distributions. When such formations are thick, inductionmore » logs accurately read the macroscopic conductivity, from which the hydrocarbon saturation in the formations can be computed. When the laminated formations are not thick, proper shoulder-bed corrections (or thin-bed corrections) should be applied to obtain the true macroscopic formation conductivity and to estimate the hydrocarbon saturation more accurately. The analytical model is used to calculate the thin-bed effect and to evaluate the shoulder-bed corrections. We will show that the formation resistivity and hence the hydrocarbon saturation are greatly overestimated when the anisotropy effect is not accounted for and conventional shoulder-bed corrections are applied to the log responses from such laminated formations.« less

Toward a Multi-scale Phase Transition Kinetics Methodology: From Non-Equilibrium Statistical Mechanics to Hydrodynamics

NASA Astrophysics Data System (ADS)

Belof, Jonathan; Orlikowski, Daniel; Wu, Christine; McLaughlin, Keith

2013-06-01

Shock and ramp compression experiments are allowing us to probe condensed matter under extreme conditions where phase transitions and other non-equilibrium aspects can now be directly observed, but first principles simulation of kinetics remains a challenge. A multi-scale approach is presented here, with non-equilibrium statistical mechanical quantities calculated by molecular dynamics (MD) and then leveraged to inform a classical nucleation and growth kinetics model at the hydrodynamic scale. Of central interest is the free energy barrier for the formation of a critical nucleus, with direct NEMD presenting the challenge of relatively long timescales necessary to resolve nucleation. Rather than attempt to resolve the time-dependent nucleation sequence directly, the methodology derived here is built upon the non-equilibrium work theorem in order to bias the formation of a critical nucleus and thus construct the nucleation and growth rates. Having determined these kinetic terms from MD, a hydrodynamics implementation of Kolmogorov-Johnson-Mehl-Avrami (KJMA) kinetics and metastabilty is applied to the dynamic compressive freezing of water and compared with recent ramp compression experiments [Dolan et al., Nature (2007)] Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344.

Sequence Effect on the Formation of DNA Minidumbbells.

PubMed

Liu, Yuan; Lam, Sik Lok

2017-11-16

The DNA minidumbbell (MDB) is a recently identified non-B structure. The reported MDBs contain two TTTA, CCTG, or CTTG type II loops. At present, the knowledge and understanding of the sequence criteria for MDB formation are still limited. In this study, we performed a systematic high-resolution nuclear magnetic resonance (NMR) and native gel study to investigate the effect of sequence variations in tandem repeats on the formation of MDBs. Our NMR results reveal the importance of hydrogen bonds, base-base stacking, and hydrophobic interactions from each of the participating residues. We conclude that in the MDBs formed by tandem repeats, C-G loop-closing base pairs are more stabilizing than T-A loop-closing base pairs, and thymine residues in both the second and third loop positions are more stabilizing than cytosine residues. The results from this study enrich our knowledge on the sequence criteria for the formation of MDBs, paving a path for better exploring their potential roles in biological systems and DNA nanotechnology.

S4(13)-PV cell-penetrating peptide induces physical and morphological changes in membrane-mimetic lipid systems and cell membranes: implications for cell internalization.

PubMed

Cardoso, Ana M S; Trabulo, Sara; Cardoso, Ana L; Lorents, Annely; Morais, Catarina M; Gomes, Paula; Nunes, Cláudia; Lúcio, Marlene; Reis, Salette; Padari, Kärt; Pooga, Margus; Pedroso de Lima, Maria C; Jurado, Amália S

2012-03-01

The present work aims to gain insights into the role of peptide-lipid interactions in the mechanisms of cellular internalization and endosomal escape of the S4(13)-PV cell-penetrating peptide, which has been successfully used in our laboratory as a nucleic acid delivery system. A S4(13)-PV analogue, S4(13)-PVscr, displaying a scrambled amino acid sequence, deficient cell internalization and drug delivery inability, was used in this study for comparative purposes. Differential scanning calorimetry, fluorescence polarization and X-ray diffraction at small and wide angles techniques showed that both peptides interacted with anionic membranes composed of phosphatidylglycerol or a mixture of this lipid with phosphatidylethanolamine, increasing the lipid order, shifting the phase transition to higher temperatures and raising the correlation length between the bilayers. However, S4(13)-PVscr, in contrast to the wild-type peptide, did not promote lipid domain segregation and induced the formation of an inverted hexagonal lipid phase instead of a cubic phase in the lipid systems assayed. Electron microscopy showed that, as opposed to S4(13)-PVscr, the wild-type peptide induced the formation of a non-lamellar organization in membranes of HeLa cells. We concluded that lateral phase separation and destabilization of membrane lamellar structure without compromising membrane integrity are on the basis of the lipid-driven and receptor-independent mechanism of cell entry of S4(13)-PV peptide. Overall, our results can contribute to a better understanding of the role of peptide-lipid interactions in the mechanisms of cell-penetrating peptide membrane translocation, helping in the future design of more efficient cell-penetrating peptide-based drug delivery systems. Copyright © 2011 Elsevier B.V. All rights reserved.

An image processing study of a reentrant discotic cholesteric - biaxial cholesteric phase transition

NASA Astrophysics Data System (ADS)

Luders, D. D.; Zoner, G. A.; Santos, O. R.; Braga, W. S.; Sampaio, A. R.; Kimura, N. M.; Palangana, A. J.; Simões, M.

2018-04-01

In this work, we study and characterize the cholesteric sequence of phases (ChDr - ChB - ChD), where the first ChDr is the reentrant cholesteric discotic phase, ChB is the cholesteric biaxial phase and the second ChD is the cholesteric discotic phase. This sequence of phases is studied through polarized light microscopy and image processing technique, where, for the first time, the domains and borders of these transitions are established and characterized. They are also investigated and optically characterized throughout their textures.

An investigation of Hebbian phase sequences as assembly graphs

PubMed Central

Almeida-Filho, Daniel G.; Lopes-dos-Santos, Vitor; Vasconcelos, Nivaldo A. P.; Miranda, José G. V.; Tort, Adriano B. L.; Ribeiro, Sidarta

2014-01-01

Hebb proposed that synapses between neurons that fire synchronously are strengthened, forming cell assemblies and phase sequences. The former, on a shorter scale, are ensembles of synchronized cells that function transiently as a closed processing system; the latter, on a larger scale, correspond to the sequential activation of cell assemblies able to represent percepts and behaviors. Nowadays, the recording of large neuronal populations allows for the detection of multiple cell assemblies. Within Hebb's theory, the next logical step is the analysis of phase sequences. Here we detected phase sequences as consecutive assembly activation patterns, and then analyzed their graph attributes in relation to behavior. We investigated action potentials recorded from the adult rat hippocampus and neocortex before, during and after novel object exploration (experimental periods). Within assembly graphs, each assembly corresponded to a node, and each edge corresponded to the temporal sequence of consecutive node activations. The sum of all assembly activations was proportional to firing rates, but the activity of individual assemblies was not. Assembly repertoire was stable across experimental periods, suggesting that novel experience does not create new assemblies in the adult rat. Assembly graph attributes, on the other hand, varied significantly across behavioral states and experimental periods, and were separable enough to correctly classify experimental periods (Naïve Bayes classifier; maximum AUROCs ranging from 0.55 to 0.99) and behavioral states (waking, slow wave sleep, and rapid eye movement sleep; maximum AUROCs ranging from 0.64 to 0.98). Our findings agree with Hebb's view that assemblies correspond to primitive building blocks of representation, nearly unchanged in the adult, while phase sequences are labile across behavioral states and change after novel experience. The results are compatible with a role for phase sequences in behavior and cognition. PMID:24782715

High-speed optical phase-shifting apparatus

DOEpatents

Zortman, William A.

2016-11-08

An optical phase shifter includes an optical waveguide, a plurality of partial phase shifting elements arranged sequentially, and control circuitry electrically coupled to the partial phase shifting elements. The control circuitry is adapted to provide an activating signal to each of the N partial phase shifting elements such that the signal is delayed by a clock cycle between adjacent partial phase shifting elements in the sequence. The transit time for a guided optical pulse train between the input edges of consecutive partial phase shifting elements in the sequence is arranged to be equal to a clock cycle, thereby enabling pipelined processing of the optical pulses.

cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on CPU+GPU.

PubMed

Zhang, Jing; Wang, Hao; Feng, Wu-Chun

2017-01-01

BLAST, short for Basic Local Alignment Search Tool, is a ubiquitous tool used in the life sciences for pairwise sequence search. However, with the advent of next-generation sequencing (NGS), whether at the outset or downstream from NGS, the exponential growth of sequence databases is outstripping our ability to analyze the data. While recent studies have utilized the graphics processing unit (GPU) to speedup the BLAST algorithm for searching protein sequences (i.e., BLASTP), these studies use coarse-grained parallelism, where one sequence alignment is mapped to only one thread. Such an approach does not efficiently utilize the capabilities of a GPU, particularly due to the irregularity of BLASTP in both execution paths and memory-access patterns. To address the above shortcomings, we present a fine-grained approach to parallelize BLASTP, where each individual phase of sequence search is mapped to many threads on a GPU. This approach, which we refer to as cuBLASTP, reorders data-access patterns and reduces divergent branches of the most time-consuming phases (i.e., hit detection and ungapped extension). In addition, cuBLASTP optimizes the remaining phases (i.e., gapped extension and alignment with trace back) on a multicore CPU and overlaps their execution with the phases running on the GPU.

Kinetic modeling of secondary organic aerosol formation: effects of particle- and gas-phase reactions of semivolatile products

NASA Astrophysics Data System (ADS)

Chan, A. W. H.; Kroll, J. H.; Ng, N. L.; Seinfeld, J. H.

2007-08-01

The distinguishing mechanism of formation of secondary organic aerosol (SOA) is the partitioning of semivolatile hydrocarbon oxidation products between the gas and aerosol phases. While SOA formation is typically described in terms of partitioning only, the rate of formation and ultimate yield of SOA can also depend on the kinetics of both gas- and aerosol-phase processes. We present a general equilibrium/kinetic model of SOA formation that provides a framework for evaluating the extent to which the controlling mechanisms of SOA formation can be inferred from laboratory chamber data. With this model we examine the effect on SOA formation of gas-phase oxidation of first-generation products to either more or less volatile species, of particle-phase reaction (both first- and second-order kinetics), of the rate of parent hydrocarbon oxidation, and of the extent of reaction of the parent hydrocarbon. The effect of pre-existing organic aerosol mass on SOA yield, an issue of direct relevance to the translation of laboratory data to atmospheric applications, is examined. The importance of direct chemical measurements of gas- and particle-phase species is underscored in identifying SOA formation mechanisms.

Kinetic modeling of Secondary Organic Aerosol formation: effects of particle- and gas-phase reactions of semivolatile products

NASA Astrophysics Data System (ADS)

Chan, A. W. H.; Kroll, J. H.; Ng, N. L.; Seinfeld, J. H.

2007-05-01

The distinguishing mechanism of formation of secondary organic aerosol (SOA) is the partitioning of semivolatile hydrocarbon oxidation products between the gas and aerosol phases. While SOA formation is typically described in terms of partitioning only, the rate of formation and ultimate yield of SOA can also depend on the kinetics of both gas- and aerosol-phase processes. We present a general equilibrium/kinetic model of SOA formation that provides a framework for evaluating the extent to which the controlling mechanisms of SOA formation can be inferred from laboratory chamber data. With this model we examine the effect on SOA formation of gas-phase oxidation of first-generation products to either more or less volatile species, of particle-phase reaction (both first- and second-order kinetics), of the rate of parent hydrocarbon oxidation, and of the extent of reaction of the parent hydrocarbon. The effect of pre-existing organic aerosol mass on SOA yield, an issue of direct relevance to the translation of laboratory data to atmospheric applications, is examined. The importance of direct chemical measurements of gas- and particle-phase species is underscored in identifying SOA formation mechanisms.

Polarized light microscopy study on the reentrant phase transition in a (Ba 1–xK x)Fe 2As 2 single crystal with x = 0.24

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

Liu, Yong; Tanatar, Makariy A.; Timmons, Erik

In this study, a sequence of structural/magnetic transitions on cooling is reported in the literature for hole-doped iron-based superconductor (Ba 1–xK x)Fe 2As 2 with x = 0.24. By using polarized light microscopy, we directly observe the formation of orthorhombic domains in (Ba 1–xK x)Fe 2As 2 (x = 0.24) single crystal below a temperature of simultaneous structural/magnetic transition T N ~ 80 K. The structural domains vanish below ~30 K, but reappear below T = 15 K. Our results are consistent with reentrance transformation sequence from high-temperature tetragonal (HTT) to low temperature orthorhombic (LTO1) structure at T N ~more » 80 K, LTO1 to low temperature tetragonal (LTT) structure at T c ~ 25 K, and LTT to low temperature orthorhombic (LTO2) structure at T ~ 15 K.« less

Polarized light microscopy study on the reentrant phase transition in a (Ba 1–xK x)Fe 2As 2 single crystal with x = 0.24

DOE PAGES

Liu, Yong; Tanatar, Makariy A.; Timmons, Erik; ...

2016-11-09

In this study, a sequence of structural/magnetic transitions on cooling is reported in the literature for hole-doped iron-based superconductor (Ba 1–xK x)Fe 2As 2 with x = 0.24. By using polarized light microscopy, we directly observe the formation of orthorhombic domains in (Ba 1–xK x)Fe 2As 2 (x = 0.24) single crystal below a temperature of simultaneous structural/magnetic transition T N ~ 80 K. The structural domains vanish below ~30 K, but reappear below T = 15 K. Our results are consistent with reentrance transformation sequence from high-temperature tetragonal (HTT) to low temperature orthorhombic (LTO1) structure at T N ~more » 80 K, LTO1 to low temperature tetragonal (LTT) structure at T c ~ 25 K, and LTT to low temperature orthorhombic (LTO2) structure at T ~ 15 K.« less

Super-hard cubic BN layer formation by nitrogen ion implantation

NASA Astrophysics Data System (ADS)

Komarov, F. F.; Pilko, V. V.; Yakushev, V. A.; Tishkov, V. S.

1994-11-01

Microcrystalline and amorphous boron thin films were implanted with nitrogen ions at energies from 25 to 125 keV and with doses from 2 × 10 17 to 1 × 10 18 at.cm 2 at temperatures below 200°C. The structure of boron nitride phases after ion implantation, formation of phases and phase transformations were investigated by TEM and TED methods. The cubic boron nitride phase is revealed. The microhardness of the formed films was satisfactorily explained in terms of chemical compound formation by polyenergetic ion implantation. The influence of the copper impurity on the formation of the cubic boron nitride phase is demonstrated. It has also been shown that low concentrations of copper promote cubic BN boundary formation.

Calorimetric Investigation of Thermal Stability of 304H Cu (Fe-17.7Cr-9.3Ni-2.95Cu-0.91Mn-0.58Nb-0.24Si-0.1C-0.12N-Wt Pct) Austenitic Stainless Steel

NASA Astrophysics Data System (ADS)

Tripathy, Haraprasanna; Subramanian, Raju; Hajra, Raj Narayan; Rai, Arun Kumar; Rengachari, Mythili; Saibaba, Saroja; Jayakumar, Tammana

2016-12-01

The sequence of phase instabilities that take place in a Fe-17.7Cr-9.3Ni-0.58Nb-2.95Cu-0.12N (wt pct) austenitic stainless steel (304H Cu grade) as a function of temperature has been investigated using dynamic calorimetry. The results obtained from this investigation are supplemented by Thermocalc-based equilibrium and Scheil-Gulliver nonequilibrium solidification simulation. The following phase transformation sequence is found upon slow cooling from liquid: L → L + γ → L + γ + MX → γ + MX + δ → γ +MX + M23C6 → γ + MX + M23C6 + Cu. Under slow cooling, the solidification follows austenite + ferrite (AF) mode, which is in accordance with Thermocalc prediction and Scheil-Gulliver simulation. However, higher cooling rates result in skeletal δ-ferrite formation, due to increased segregation tendency of Nb and Cr to segregate to interdendritic liquid. The solidification mode is found to depend on combined Nb + Cu content. Experimental estimates of enthalpy change associated with melting and secondary phase precipitation are also obtained. In addition a semi-quantitative study on the dissolution kinetics of M23C6 type carbides has also been investigated. The standard solution treatment at 1413 K (1140 °C) is found to be adequate to dissolve both Cu and M23C6 into γ-austenite; but the complete dissolution of MX type carbonitrides occurs near the melting region.

Depositional History and Sequence Stratigraphy of the Middle Ordovician Yeongheung Formation (Yeongweol Group), Taebaeksan Basin, mid-east Korea

NASA Astrophysics Data System (ADS)

Kwon, Yoo Jin; Kwon, Yi Kyun

2017-04-01

The Middle Ordovician Yeongheung Formation consists of numerous meter-scale, shallowing-upward cycles which were deposited on a shallow-marine carbonate platform. Many diagnostic sedimentary textures and structures such as supratidal laminite, tepee structure, and solution-collapsed breccia are observed, which enable to infer the dry climate and high salinity conditions during deposition of the formation. In order to understand its depositional history, this study focuses on vertical and spatial stacking patterns of the second- to third-order sequences through the detailed outcrop description and geologic mapping. A total 19 lithofacies have been recognized, which can be grouped into 5 facies associations (FAs): FA1 (Supratidal flat), FA2 (Supratidal or dolomitization of peritidal facies), FA3 (Intertidal flat), FA4 (Shallow subtidal to peritidal platform), FA5 (Shallow subtidal shoal). Global mega-sequence boundary (Sauk-Tippecanoe) occurs in solution-collapsed breccia zone in the lower part of the formation. Correlation of the shallowing-upward cycle stacking pattern across the study area defines 6 transgressive-regressive depositional sequences. Each depositional sequences comprises a package of vertical and spatial staking of shallow subtidal cycles in the lower part and peritidal cycles in the upper part of the formation. According to sequence stratigraphic interpretation, the reconstructed relative sea-level curve of the Yeongweol platform is very similar to that of the Taebaek platform. Based on the absence of siliciclastic sequence such as the Jigunsan Formation and the lithologic & stratigraphic differences, however, the Yeongweol and Taebaek groups might not belong to a single depositional system within the North China platform. The Yeongweol Group can be divided by the four subunits into their unique lithologic successions and geographic distributions. The Eastern subunit of the Yeongweol Group is composed dominantly of carbonate rocks with a high composition ratio of siliciclastic materials dominated facies in the upper part of the Yeongheung Formation. The Middle1 subunit is pervasively recognized by subaerial exposures facies (carbonate breccia, paleosol), whereas the Middle2 subunit is similar to the Middle1 subunit except for the absence of subaerial exposure features. The Western subunit lost some of its primary sedimentary structure and texture in comparison to other subunits, because of the active recrystallization, metamorphism, structural deformation and carbonate diagenesis. This study reveals depositional history and refines sequence stratigraphy of the Yeongheung Formation, promoting understanding of the basin evolution of the Yeongweol Group.

Logo2PWM: a tool to convert sequence logo to position weight matrix.

PubMed

Gao, Zhen; Liu, Lu; Ruan, Jianhua

2017-10-03

position weight matrix (PWM) and sequence logo are the most widely used representations of transcription factor binding site (TFBS) in biological sequences. Sequence logo - a graphical representation of PWM, has been widely used in scientific publications and reports, due to its easiness of human perception, rich information, and simple format. Different from sequence logo, PWM works great as a precise and compact digitalized form, which can be easily used by a variety of motif analysis software. There are a few available tools to generate sequence logos from PWM; however, no tool does the reverse. Such tool to convert sequence logo back to PWM is needed to scan a TFBS represented in logo format in a publication where the PWM is not provided or hard to be acquired. A major difficulty in developing such tool to convert sequence logo to PWM is to deal with the diversity of sequence logo images. We propose logo2PWM for reconstructing PWM from a large variety of sequence logo images. Evaluation results on over one thousand logos from three sources of different logo format show that the correlation between the reconstructed PWMs and the original PWMs are constantly high, where median correlation is greater than 0.97. Because of the high recognition accuracy, the easiness of usage, and, the availability of both web-based service and stand-alone application, we believe that logo2PWM can readily benefit the study of transcription by filling the gap between sequence logo and PWM.

Stratigraphy and depositional environments of Fox Hills Formation in Williston basin

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

Daly, D.J.

The Fox Hills Formation (Maestrichtian), representing part of a regressive wedge deposited during the withdrawal of the sea from the Western Interior at the close of the Cretaceous, consists of marginal marine strata transitional between the offshore deposits of the underlying Pierre Shale and the terrestrial deltaic and coastal deposits of the overlying Hell Creek Formation. An investigation of outcrops of the Fox Hills Formation along the western and southern flanks of the Williston basin and study of over 300 oil and gas well logs from the central part of the basin indicate that the formation can be divided bothmore » stratigraphically and areally. Stratigraphically, the Fox Hills can be divided into lower and upper sequences; the lower includes the Trail City and Timber Lake Members, and the upper sequence includes the Colgate Member in the west and the Iron Lightning and Linton Members in the east. Areally, the formation can be divided into a northeastern and western part, where the strata are 30-45 m thick and are dominated by the lower sequence, and into a southeastern area where both the lower and upper sequences are well developed in a section 80-130 m thick. Typically, the lower Fox Hills consists of upward-coarsening shoreface or delta-front sequences containing hummocky bedding and a limited suite of trace fossils, most notably Ophiomorpha. In the southeast, however, these strata are dominated by bar complexes, oriented northeast-southwest, composed of cross-bedded medium to very fine-grained sand with abundant trace and body fossils. The upper Fox Hills represents a variety of shoreface, deltaic, and channel environments. The strata of the Fox Hills Formation exhibit facies similar to those reported for Upper Cretaceous gas reservoirs in the northern Great Plains.« less

ITS all right mama: investigating the formation of chimeric sequences in the ITS2 region by DNA metabarcoding analyses of fungal mock communities of different complexities.

PubMed

Bjørnsgaard Aas, Anders; Davey, Marie Louise; Kauserud, Håvard

2017-07-01

The formation of chimeric sequences can create significant methodological bias in PCR-based DNA metabarcoding analyses. During mixed-template amplification of barcoding regions, chimera formation is frequent and well documented. However, profiling of fungal communities typically uses the more variable rDNA region ITS. Due to a larger research community, tools for chimera detection have been developed mainly for the 16S/18S markers. However, these tools are widely applied to the ITS region without verification of their performance. We examined the rate of chimera formation during amplification and 454 sequencing of the ITS2 region from fungal mock communities of different complexities. We evaluated the chimera detecting ability of two common chimera-checking algorithms: perseus and uchime. Large proportions of the chimeras reported were false positives. No false negatives were found in the data set. Verified chimeras accounted for only 0.2% of the total ITS2 reads, which is considerably less than what is typically reported in 16S and 18S metabarcoding analyses. Verified chimeric 'parent sequences' had significantly higher per cent identity to one another than to random members of the mock communities. Community complexity increased the rate of chimera formation. GC content was higher around the verified chimeric break points, potentially facilitating chimera formation through base pair mismatching in the neighbouring regions of high similarity in the chimeric region. We conclude that the hypervariable nature of the ITS region seems to buffer the rate of chimera formation in comparison with other, less variable barcoding regions, due to shorter regions of high sequence similarity. © 2016 John Wiley & Sons Ltd.

Decreased Load on General Motor Preparation and Visual-Working Memory while Preparing Familiar as Compared to Unfamiliar Movement Sequences

ERIC Educational Resources Information Center

De Kleine, Elian; Van der Lubbe, Rob H. J.

2011-01-01

Learning movement sequences is thought to develop from an initial controlled attentive phase to a more automatic inattentive phase. Furthermore, execution of sequences becomes faster with practice, which may result from changes at a general motor processing level rather than at an effector specific motor processing level. In the current study, we…

Preferential amino acid sequences in alumina-catalyzed peptide bond formation.

PubMed

Bujdák, J; Rode, B M

2002-05-21

The catalytic effect of activated alumina on amino acid condensation was investigated. The readiness of amino acids to form peptide sequences was estimated on the basis of the yield of dipeptides and was found to decrease in the order glycine (Gly), alanine (Ala), leucine (Leu), valine (Val), proline (Pro). For example, approximately 15% Gly was converted to the dipeptide (Gly(2)), 5% to cyclic anhydride (cyc(Gly(2))) and small amounts of tri- (Gly(3)) and tetrapeptide (Gly(4)) were formed after 28 days. On the other hand, only trace amounts of Pro(2) were formed from proline under the same conditions. Preferential formation of certain sequences was observed in the mixed reaction systems containing two amino acids. For example, almost ten times more Gly-Val than Val-Gly was formed in the Gly+Val reaction system. The preferred sequences can be explained on the basis of an inductive effect that side groups have on the nucleophilicity and electrophilicity, respectively, of the amino and carboxyl groups. A comparison with published data of amino acid reactions in other reaction systems revealed that the main trends of preferential sequence formation were the same as those described for the salt-induced peptide formation (SIPF) reaction. The results of this work and other previously published papers show that alumina and related mineral surfaces might have played a crucial role in the prebiotic formation of the first peptides on the primitive earth.

Exploration of the region near the sun-earth collinear libration points for the control of large formations

NASA Astrophysics Data System (ADS)

Heritier, Aurelie

Spacecraft formations possess many applications in the future of space exploration. During the last decade, due to the detection of a large number of extrasolar planets, new studies on formation flying in multi-body regimes have emerged to support searches for Earth-like planets in other solar systems. The L2 Sun-Earth libration point region has been a popular destination in creating an architecture for astronomical missions. It is a relatively cold environment, far from the disturbances of the Sun and, therefore, ideal for astronomical instruments. However, controlling multiple spacecraft in a multi-body environment is challenging and a good understanding of the natural dynamics in this regime is essential. The current investigation explores the dynamical environment near the L2 Sun-Earth libration point to aid in the control of formations of spacecraft. By exploiting the natural dynamics in the circular restricted three-body model (CR3BP), natural regions are determined that are particularly suitable for maintaining formations of spacecraft. The natural dynamics at small distances from a given reference trajectory are initially investigated for the placement of small formations of spacecraft. Some regions with low relative drift represent suitable locations to maintain small formations and are derived analytically using variational equations. Spacecraft located in such regions avoid large variations in their mutual distances while maintaining the orientation of the formation. These regions represent quadric surfaces, and the type of quadric surfaces, either ellipsoids or elliptic cylinders, depends on the eigenstructure reflecting the phase space along the given reference trajectory. The natural flow at large distances from a given reference trajectory is explored next to characterize regions that are suitable to maintain large formations, i.e., when the mutual distances between the spacecraft reaches tens of thousands of kilometers. Spheres of points at various locations along the reference orbit are constructed to classify the space, and regions of low natural drift on the spheres are numerically identified when the distance between two vehicles is large. These low drift regions are examined in detail, and a correspondance with the quadric surfaces that are derived for small formations is established. In particular, the orientation of these low drift zones along a given reference orbit are investigated as some parameters vary, such as the size of the formation as well as the reference orbit. Using the low natural drift regions, control strategies are then developed for large formations. Traditional controllers, such as impulsive maneuvers and linear quadratic regulators (LQR), are employed to quantify the level of control that is required to maintain large formations along specific directions in the CR3BP. Designs of new controllers are also investigated to produce some set of desired relative motions between two spacecraft placed at large mutual distances. In a potential formation option investigated in this analysis, a deputy vehicle maintains a fixed circular motion in a plane relative to a chief spacecraft moving along its reference trajectory. Finally, the effectiveness of using the low natural drift regions as derived for large formations is tested for the New Worlds Observer mission concept. This scenario involves a large telescope-occulter formation for star observations, to detect and characterize habitable terrestrial exoplanets. The low drift zones are employed to reduce the control effort to maintain a large telescope-occulter formation during the observation of inertially-fixed target stars. In particular, the occulter is maintained via a linear quadratic regulator during star observations. Given a set of inertially-fixed target stars, an automatic star sequence design process is proposed with observation and reconfiguration phases using the low drift regions. This design creates star sequences that lead to relatively small overall maneuver costs for this particular mission concept.

Induced and catalysed mineral precipitation in the deep biosphere

NASA Astrophysics Data System (ADS)

Meister, Patrick

2017-04-01

Authigenic and early diagenetic minerals provide archives of past (bio)geochemical processes. In particular, isotopic signatures preserved in the diagenetic phases have been shown to document drastic changes of subsurface microbial activity (the deep biosphere) over geological time periods (Contreras et al., 2013; Meister, 2015). Geochemical and isotopic signatures in authigenic minerals may also document surface conditions and past climate. Nevertheless, such use of authigenic mineral phases as (bio)geochemical archives is often hampered by the insufficient understanding of mineral precipitation mechanisms. Accordingly the time, place and rate of mineral precipitation are often not well constrained. Also, element partitioning and isotopic fractionation may be modified as a result of the precipitation mechanism. Early diagenetic dolomite and quartz from drilled sequences in the Pacific were compared with adjacent porewater compositions and isotope signatures to gain fundamental insight into the factors controlling mineral precipitation. The formation of dolomite in carbonate-free organic carbon-rich ocean margin sediments (e.g. Peru Margin; Ocean Drilling Program, ODP, Site 1229; Meister et al., 2007) relies on the alkalinity-increase driven by anaerobic oxidation of methane and, perhaps, by alteration of clay minerals. In contrast, quartz is often significantly oversaturated in marine porewaters as the dissolved silica concentration is buffered by more soluble opal-A. For example, quartz does not form throughout a 400 metre thick sedimentary sequence in the Eastern Equatorial Pacific (ODP Site 1226; Meister et al., 2014) because it is kinetically inhibited. This behaviour can be explained by Ostwald's step rule, which suggests that the metastable phase forms faster. However, hard-lithified quartz readily forms where silica concentration drops sharply below opal-saturation. This violation of Ostwald's step rule must be driven by an auxiliary process, such as the adsorption of silica to freshly precipitated iron oxides along a deep iron oxidation front. In conclusion, two different modes of precipitation can be observed in modern sub-seafloor porewater systems. Dolomite precipitation is thermodynamically controlled through microbially induced supersaturation. Quartz formation is controlled through an auxiliary process that helps it to overcome a kinetic barrier. These observations exemplify the importance to distinguish between kinetic and thermodynamic effects on mineral formation under Earth surface conditions. To evaluate geochemical signatures, these modes of precipitation need to be taken into account. Contreras et al. (2013) Proc. Natl. Acad. Sci., doi/10.1073/pnas.1305981110 Meister, et al. (2007) Sedimentology 54, 1007-1032. Meister, et al. (2014) Geochim. Cosmochim. Acta 137, 188-207. Meister, P. (2015) Terra Nova, Focus Article, 00, 1-9.

The barium iron ruthenium oxide system

NASA Technical Reports Server (NTRS)

Kemmler-Sack, S.; Ehmann, A.

1986-01-01

In the system BaFe(1-x)Ru(x)O(3-y), three phases, separated by immiscibility gaps, are present: an Fe-rich phase (x = 0 to 0.75) with hexagonal BaTiO3 structure (6H; sequence (hcc)2), a Ru-rich phase (x = 0.9) of hexagonal 4H-type (sequence (hc)2), and the pure Ru compounds BaRuO3 with rhombohedral 9R structure (sequence (hhc)3). By vibrational spectroscopic investigations in the 6H phase a transition from n-type semiconduction (Fe-rich compounds with complete O lattice) can be detected. The 4H and 9R stacking polytypes are good, metal-like conductors. The lattice parameters are given.

Sequence-Dependent Diastereospecific and Diastereodivergent Crosslinking of DNA by Decarbamoylmitomycin C.

PubMed

Aguilar, William; Paz, Manuel M; Vargas, Anayatzinc; Clement, Cristina C; Cheng, Shu-Yuan; Champeil, Elise

2018-04-20

Mitomycin C (MC), a potent antitumor drug, and decarbamoylmitomycin C (DMC), a derivative lacking the carbamoyl group, form highly cytotoxic DNA interstrand crosslinks. The major interstrand crosslink formed by DMC is the C1'' epimer of the major crosslink formed by MC. The molecular basis for the stereochemical configuration exhibited by DMC was investigated using biomimetic synthesis. The formation of DNA-DNA crosslinks by DMC is diastereospecific and diastereodivergent: Only the 1''S-diastereomer of the initially formed monoadduct can form crosslinks at GpC sequences, and only the 1''R-diastereomer of the monoadduct can form crosslinks at CpG sequences. We also show that CpG and GpC sequences react with divergent diastereoselectivity in the first alkylation step: 1"S stereochemistry is favored at GpC sequences and 1''R stereochemistry is favored at CpG sequences. Therefore, the first alkylation step results, at each sequence, in the selective formation of the diastereomer able to generate an interstrand DNA-DNA crosslink after the "second arm" alkylation. Examination of the known DNA adduct pattern obtained after treatment of cancer cell cultures with DMC indicates that the GpC sequence is the major target for the formation of DNA-DNA crosslinks in vivo by this drug. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Program for Editing Spacecraft Command Sequences

NASA Technical Reports Server (NTRS)

Gladden, Roy; Waggoner, Bruce; Kordon, Mark; Hashemi, Mahnaz; Hanks, David; Salcedo, Jose

2006-01-01

Sequence Translator, Editor, and Expander Resource (STEER) is a computer program that facilitates construction of sequences and blocks of sequences (hereafter denoted generally as sequence products) for commanding a spacecraft. STEER also provides mechanisms for translating among various sequence product types and quickly expanding activities of a given sequence in chronological order for review and analysis of the sequence. To date, construction of sequence products has generally been done by use of such clumsy mechanisms as text-editor programs, translating among sequence product types has been challenging, and expanding sequences to time-ordered lists has involved arduous processes of converting sequence products to "real" sequences and running them through Class-A software (defined, loosely, as flight and ground software critical to a spacecraft mission). Also, heretofore, generating sequence products in standard formats has been troublesome because precise formatting and syntax are required. STEER alleviates these issues by providing a graphical user interface containing intuitive fields in which the user can enter the necessary information. The STEER expansion function provides a "quick and dirty" means of seeing how a sequence and sequence block would expand into a chronological list, without need to use of Class-A software.

Scaling up the 454 Titanium Library Construction and Pooling of Barcoded Libraries

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

Phung, Wilson; Hack, Christopher; Shapiro, Harris

2009-03-23

We have been developing a high throughput 454 library construction process at the Joint Genome Institute to meet the needs of de novo sequencing a large number of microbial and eukaryote genomes, EST, and metagenome projects. We have been focusing efforts in three areas: (1) modifying the current process to allow the construction of 454 standard libraries on a 96-well format; (2) developing a robotic platform to perform the 454 library construction; and (3) designing molecular barcodes to allow pooling and sorting of many different samples. In the development of a high throughput process to scale up the number ofmore » libraries by adapting the process to a 96-well plate format, the key process change involves the replacement of gel electrophoresis for size selection with Solid Phase Reversible Immobilization (SPRI) beads. Although the standard deviation of the insert sizes increases, the overall quality sequence and distribution of the reads in the genome has not changed. The manual process of constructing 454 shotgun libraries on 96-well plates is a time-consuming, labor-intensive, and ergonomically hazardous process; we have been experimenting to program a BioMek robot to perform the library construction. This will not only enable library construction to be completed in a single day, but will also minimize any ergonomic risk. In addition, we have implemented a set of molecular barcodes (AKA Multiple Identifiers or MID) and a pooling process that allows us to sequence many targets simultaneously. Here we will present the testing of pooling a set of selected fosmids derived from the endomycorrhizal fungus Glomus intraradices. By combining the robotic library construction process and the use of molecular barcodes, it is now possible to sequence hundreds of fosmids that represent a minimal tiling path of this genome. Here we present the progress and the challenges of developing these scaled-up processes.« less

Rapid Conversion of Traditional Introductory Physics Sequences to an Activity-Based Format

ERIC Educational Resources Information Center

Yoder, Garett; Cook, Jerry

2014-01-01

The Department of Physics at EKU [Eastern Kentucky University] with support from the National Science Foundations Course Curriculum and Laboratory Improvement Program has successfully converted our entire introductory physics sequence, both algebra-based and calculus-based courses, to an activity-based format where laboratory activities,…

CDSbank: taxonomy-aware extraction, selection, renaming and formatting of protein-coding DNA or amino acid sequences.

PubMed

Hazes, Bart

2014-02-28

Protein-coding DNA sequences and their corresponding amino acid sequences are routinely used to study relationships between sequence, structure, function, and evolution. The rapidly growing size of sequence databases increases the power of such comparative analyses but it makes it more challenging to prepare high quality sequence data sets with control over redundancy, quality, completeness, formatting, and labeling. Software tools for some individual steps in this process exist but manual intervention remains a common and time consuming necessity. CDSbank is a database that stores both the protein-coding DNA sequence (CDS) and amino acid sequence for each protein annotated in Genbank. CDSbank also stores Genbank feature annotation, a flag to indicate incomplete 5' and 3' ends, full taxonomic data, and a heuristic to rank the scientific interest of each species. This rich information allows fully automated data set preparation with a level of sophistication that aims to meet or exceed manual processing. Defaults ensure ease of use for typical scenarios while allowing great flexibility when needed. Access is via a free web server at http://hazeslab.med.ualberta.ca/CDSbank/. CDSbank presents a user-friendly web server to download, filter, format, and name large sequence data sets. Common usage scenarios can be accessed via pre-programmed default choices, while optional sections give full control over the processing pipeline. Particular strengths are: extract protein-coding DNA sequences just as easily as amino acid sequences, full access to taxonomy for labeling and filtering, awareness of incomplete sequences, and the ability to take one protein sequence and extract all synonymous CDS or identical protein sequences in other species. Finally, CDSbank can also create labeled property files to, for instance, annotate or re-label phylogenetic trees.

KMOS{sup 3D} Reveals Low-level Star Formation Activity in Massive Quiescent Galaxies at 0.7 < z < 2.7

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

Belli, Sirio; Genzel, Reinhard; Förster Schreiber, Natascha M.

2017-05-20

We explore the H α emission in the massive quiescent galaxies observed by the KMOS{sup 3D} survey at 0.7 < z < 2.7. The H α line is robustly detected in 20 out of 120 UVJ -selected quiescent galaxies, and we classify the emission mechanism using the H α line width and the [N ii]/H α line ratio. We find that AGNs are likely to be responsible for the line emission in more than half of the cases. We also find robust evidence for star formation activity in nine quiescent galaxies, which we explore in detail. The H α kinematicsmore » reveal rotating disks in five of the nine galaxies. The dust-corrected H α star formation rates are low (0.2–7 M {sub ⊙} yr{sup −1}), and place these systems significantly below the main sequence. The 24 μ m-based, infrared luminosities, instead, overestimate the star formation rates. These galaxies present a lower gas-phase metallicity compared to star-forming objects with similar stellar mass, and many of them have close companions. We therefore conclude that the low-level star formation activity in these nine quiescent galaxies is likely to be fueled by inflowing gas or minor mergers, and could be a sign of rejuvenation events.« less

Accuracy of magnetic resonance imaging in differentiating between benign and malignant vertebral lesions: role of diffusion-weighted imaging, in-phase/opposed-phase imaging and apparent diffusion coefficient.

PubMed

Martel Villagrán, J; Bueno Horcajadas, Á; Pérez Fernández, E; Martín Martín, S

2015-01-01

To determine the ability of MRI to distinguish between benign and malignant vertebral lesions. We included 85 patients and studied a total of 213 vertebrae (both pathologic and normal). For each vertebra, we determined whether the lesion was hypointense in T1-weighted sequences and whether it was hyperintense in STIR and in diffusion-weighted sequences. We calculated the in-phase/out-of-phase quotient and the apparent diffusion coefficient for each vertebra. We combined parameters from T1-weighted, diffusion-weighted, and STIR sequences to devise a formula to distinguish benign from malignant lesions. The group comprised 60 (70.6%) women and 25 (29.4%) men with a mean age of 67±13.5 years (range, 33-90 y). Of the 85 patients, 26 (30.6%) had a known primary tumor. When the lesion was hypointense on T1-weighted sequences, hyperintense on STIR and diffusion-weighted sequences, and had a signal intensity quotient greater than 0.8, the sensitivity was 97.2%, the specificity was 90%, and the diagnostic accuracy was 91.2%. If the patient had a known primary tumor, these values increased to 97.2%, 99.4%, and 99%, respectively. Benign lesions can be distinguished from malignant lesions if we combine the information from T1-weighted, STIR, and diffusion-weighted sequences together with the in-phase/out-of-phase quotient of the lesion detected in the vertebral body on MRI. Copyright © 2013 SERAM. Published by Elsevier España, S.L.U. All rights reserved.

TRAP: automated classification, quantification and annotation of tandemly repeated sequences.

PubMed

Sobreira, Tiago José P; Durham, Alan M; Gruber, Arthur

2006-02-01

TRAP, the Tandem Repeats Analysis Program, is a Perl program that provides a unified set of analyses for the selection, classification, quantification and automated annotation of tandemly repeated sequences. TRAP uses the results of the Tandem Repeats Finder program to perform a global analysis of the satellite content of DNA sequences, permitting researchers to easily assess the tandem repeat content for both individual sequences and whole genomes. The results can be generated in convenient formats such as HTML and comma-separated values. TRAP can also be used to automatically generate annotation data in the format of feature table and GFF files.

Identification of genes differentially expressed during adventitious shoot induction in Pinus pinea cotyledons by subtractive hybridization and quantitative PCR.

PubMed

Alonso, Pablo; Cortizo, Millán; Cantón, Francisco R; Fernández, Belén; Rodríguez, Ana; Centeno, Maria L; Cánovas, Francisco M; Ordás, Ricardo J

2007-12-01

As part of a study aimed at understanding the physiological and molecular mechanisms involved in adventitious shoot bud formation in pine cotyledons, we conducted a transcriptome analysis to identify early-induced genes during the first phases of adventitious caulogenesis in Pinus pinea L. cotyledons cultured in the presence of benzyladenine. A subtractive cDNA library with more than 700 clones was constructed. Of these clones, 393 were sequenced, analyzed and grouped according to their putative function. Quantitative real-time PCR analysis was performed to confirm the differential expression of 30 candidate genes. Results are contrasted with available data for other species.

10.7 Gb/s uncompensated transmission over a 470 km hybrid fiber link with in-line SOAs using MLSE and duobinary signals.

PubMed

Downie, John D; Hurley, Jason; Mauro, Yihong

2008-09-29

We experimentally demonstrate uncompensated 8-channel wavelength division multiplexing (WDM) and single channel transmission at 10.7 Gb/s over a 470 km hybrid fiber link with in-line semiconductor optical amplifiers (SOAs). Two different forms of the duobinary modulation format are investigated and compared. Maximum Likelihood Sequence Estimation (MLSE) receiver technology is found to significantly mitigate nonlinear effects from the SOAs and to enable the long transmission, especially for optical duobinary signals derived from differential phase shift keying (DPSK) signals directly detected after narrowband optical filter demodulation. The MLSE also helps to compensate for a non-optimal Fabry-Perot optical filter demodulator.

The Vaguries of Pyroxene Nucleation and the Resulting Chondrule Textures

NASA Technical Reports Server (NTRS)

Lofgren, G. E.; Le, L.

2004-01-01

Pyroxene is a major phase in chondrules, but often follows olivine in the crystallization sequence and depending on the melting temperature and time may not nucleate readily upon cooling. Dynamic crystallization experiments based on total or near total melting were used to study PO (porphyritic olivine) and PP (Porphyritic pyroxene) compositions as defined by. The experiments showed that pyroxene nucleated only at subliquidus temperatures in the PP melts and rarely in the PO melts. Porphyritic chondrules with phenocrysts of both olivine and pyroxene (POP chondrules) were not easily produced in the experiments. POP chondrules are common and it is important for deciphering their formation that we understand pyroxene nucleation properties of chondrule melts.

White dwarfs in the Gaia era

NASA Astrophysics Data System (ADS)

Tremblay, P.-E.; Gentile-Fusillo, N.; Cummings, J.; Jordan, S.; Gänsicke, B. T.; Kalirai, J. S.

2018-04-01

The vast majority of stars will become white dwarfs at the end of the stellar life cycle. These remnants are precise cosmic clocks owing to their well constrained cooling rates. Gaia Data Release 2 is expected to discover hundreds of thousands of white dwarfs, which can then be observed spectroscopically with WEAVE and 4MOST. By employing spectroscopically derived atmospheric parameters combined with Gaia parallaxes, white dwarfs can constrain the stellar formation history in the early developing phases of the Milky Way, the initial mass function in the 1.5 to 8 M ⊙ range, and the stellar mass loss as well as the state of planetary systems during the post main-sequence evolution.

IAA RAS Radio Telescope Monitoring System

NASA Astrophysics Data System (ADS)

Mikhailov, A.; Lavrov, A.

2007-07-01

Institute of Applied Astronomy of the Russian Academy of Sciences (IAA RAS) has three identical radio telescopes, the receiving complex of which consists of five two-channel receivers of different bands, six cryogen systems, and additional devices: four local oscillators, phase calibration generators and IF commutator. The design, hardware and data communication protocol are described. The most convenient way to join the devices of the receiving complex into the common monitoring system is to use the interface which allows to connect numerous devices to the data bus. For the purpose of data communication regulation and to exclude conflicts, a data communication protocol has been designed, which operates with complex formatted data sequences. Formation of such sequences requires considerable data processing capability. That is provided by a microcontroller chip in each slave device. The test version of the software for the central computer has been developed in IAA RAS. We are developing the Mark IV FS software extension modules, which will allow us to control the receiving complex of the radio telescope by special SNAP commands from both operator input and schedule files. We are also developing procedures of automatic measurements of SEFD, system noise temperature and other parameters, available both in VLBI and single-dish modes of operation. The system described has been installed on all IAA RAS radio telescopes at "Svetloe", "Zelenchukskaya" and "Badary" observatories. It has proved to be working quite reliably and to show the perfonmance expected.

Comparison of phasing strategies for whole human genomes

PubMed Central

Kirkness, Ewen; Schork, Nicholas J.

2018-01-01

Humans are a diploid species that inherit one set of chromosomes paternally and one homologous set of chromosomes maternally. Unfortunately, most human sequencing initiatives ignore this fact in that they do not directly delineate the nucleotide content of the maternal and paternal copies of the 23 chromosomes individuals possess (i.e., they do not ‘phase’ the genome) often because of the costs and complexities of doing so. We compared 11 different widely-used approaches to phasing human genomes using the publicly available ‘Genome-In-A-Bottle’ (GIAB) phased version of the NA12878 genome as a gold standard. The phasing strategies we compared included laboratory-based assays that prepare DNA in unique ways to facilitate phasing as well as purely computational approaches that seek to reconstruct phase information from general sequencing reads and constructs or population-level haplotype frequency information obtained through a reference panel of haplotypes. To assess the performance of the 11 approaches, we used metrics that included, among others, switch error rates, haplotype block lengths, the proportion of fully phase-resolved genes, phasing accuracy and yield between pairs of SNVs. Our comparisons suggest that a hybrid or combined approach that leverages: 1. population-based phasing using the SHAPEIT software suite, 2. either genome-wide sequencing read data or parental genotypes, and 3. a large reference panel of variant and haplotype frequencies, provides a fast and efficient way to produce highly accurate phase-resolved individual human genomes. We found that for population-based approaches, phasing performance is enhanced with the addition of genome-wide read data; e.g., whole genome shotgun and/or RNA sequencing reads. Further, we found that the inclusion of parental genotype data within a population-based phasing strategy can provide as much as a ten-fold reduction in phasing errors. We also considered a majority voting scheme for the construction of a consensus haplotype combining multiple predictions for enhanced performance and site coverage. Finally, we also identified DNA sequence signatures associated with the genomic regions harboring phasing switch errors, which included regions of low polymorphism or SNV density. PMID:29621242

Insights into the diagenetic environment of fossil marine vertebrates of the Pisco Formation (late Miocene, Peru) from mineralogical and Sr-isotope data

NASA Astrophysics Data System (ADS)

Gioncada, A.; Petrini, R.; Bosio, G.; Gariboldi, K.; Collareta, A.; Malinverno, E.; Bonaccorsi, E.; Di Celma, C.; Pasero, M.; Urbina, M.; Bianucci, G.

2018-01-01

The late Miocene Pisco Formation of Peru is an outstanding example of richness and high-quality preservation of fossil marine vertebrates. In order to reconstruct the fossilization path, we present new textural, mineralogical and Sr-isotope data of diagenetic minerals formed in correspondence of fossil specimens such as marine vertebrates and mollusks. These fossil specimens were found at Cerro los Quesos, in the Ica Desert, within the diatomaceous strata of the Pisco Formation. Dolomite, gypsum, anhydrite and Mn minerals are the main phases found, while the calcium carbonate originally forming the mollusk valves is replaced by gypsum. An early formation of dolomite and of Mn minerals, triggered by the modifications of the geochemical environment due to organic matter degradation, is suggested by the textural relationships and is confirmed by the Sr isotopic ratio of dolomite, which agrees with that of seawater at the time of sedimentation. Instead, gypsum Sr isotopic ratios indicate a pre-Miocene seawater-derived brine circulating within the sedimentary sequence as a source for Sr. Oxidation of diagenetic sulfide causing a lowering of the pH of porewater is proposed as an explanation for Ca-carbonate dissolution. The diagenetic chemical environment was, nevertheless, favorable to bone preservation.

Pangea break-up: from passive to active margin in the Colombian Caribbean Realm

NASA Astrophysics Data System (ADS)

Gómez, Cristhian; Kammer, Andreas

2017-04-01

The break-up of Western Pangea has lead to a back-arc type tectonic setting along the periphery of Gondwana, with the generation of syn-rift basins filled with sedimentary and volcanic sequences during the Middle to Late Triassic. The Indios and Corual formations in the Santa Marta massif of Northern Andes were deposited in this setting. In this contribution we elaborate a stratigraphic model for both the Indios and Corual formations, based on the description and classification of sedimentary facies and their architecture and a provenance analysis. Furthermore, geotectonic environments for volcanic and volcanoclastic rock of both units are postulated. The Indios Formation is a shallow-marine syn-rift basin fill and contains gravity flows deposits. This unit is divided into three segments; the lower and upper segments are related to fan-deltas, while the middle segment is associated to offshore deposits with lobe incursions of submarine fans. Volcanoclastic and volcanic rocks of the Indios and Corual formations are bimodal in composition and are associated to alkaline basalts. Volcanogenic deposits comprise debris, pyroclastic and lava flows of both effusive and explosive eruptions. These units record multiple phases of rifting and reveal together a first stage in the break-up of Pangea during Middle and Late Triassic in North Colombia.

THE RED SEQUENCE AT BIRTH IN THE GALAXY CLUSTER Cl J1449+0856 AT z = 2

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

Strazzullo, V.; Pannella, M.; Daddi, E.

We use Hubble Space Telescope /WFC3 imaging to study the red population in the IR-selected, X-ray detected, low-mass cluster Cl J1449+0856 at z = 2, one of the few bona fide established clusters discovered at this redshift, and likely a typical progenitor of an average massive cluster today. This study explores the presence and significance of an early red sequence in the core of this structure, investigating the nature of red-sequence galaxies, highlighting environmental effects on cluster galaxy populations at high redshift, and at the same time underlining similarities and differences with other distant dense environments. Our results suggest thatmore » the red population in the core of Cl J1449+0856 is made of a mixture of quiescent and dusty star-forming galaxies, with a seedling of the future red sequence already growing in the very central cluster region, and already characterizing the inner cluster core with respect to lower-density environments. On the other hand, the color–magnitude diagram of this cluster is definitely different from that of lower-redshift z ≲ 1 clusters, as well as of some rare particularly evolved massive clusters at similar redshift, and it is suggestive of a transition phase between active star formation and passive evolution occurring in the protocluster and established lower-redshift cluster regimes.« less

The Blue Straggler Star Population in NGC 1261: Evidence for a Post-core-collapse Bounce State

NASA Astrophysics Data System (ADS)

Simunovic, Mirko; Puzia, Thomas H.; Sills, Alison

2014-11-01

We present a multi-passband photometric study of the Blue Straggler Star (BSS) population in the Galactic globular cluster (GC) NGC 1261, using available space- and ground-based survey data. The inner BSS population is found to have two distinct sequences in the color-magnitude diagram (CMD), similar to double BSS sequences detected in other GCs. These well defined sequences are presumably linked to single short-lived events such as core collapse, which are expected to boost the formation of BSSs. In agreement with this, we find a BSS sequence in NGC 1261 which can be well reproduced individually by a theoretical model prediction of a 2 Gyr old population of stellar collision products, which are expected to form in the denser inner regions during short-lived core contraction phases. Additionally, we report the occurrence of a group of BSSs with unusually blue colors in the CMD, which are consistent with a corresponding model of a 200 Myr old population of stellar collision products. The properties of the NGC 1261 BSS populations, including their spatial distributions, suggest an advanced dynamical evolutionary state of the cluster, but the core of this GC does not show the classical signatures of core collapse. We argue that these apparent contradictions provide evidence for a post-core-collapse bounce state seen in dynamical simulations of old GCs.

Extracting flat-field images from scene-based image sequences using phase correlation

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

Caron, James N., E-mail: Caron@RSImd.com; Montes, Marcos J.; Obermark, Jerome L.

Flat-field image processing is an essential step in producing high-quality and radiometrically calibrated images. Flat-fielding corrects for variations in the gain of focal plane array electronics and unequal illumination from the system optics. Typically, a flat-field image is captured by imaging a radiometrically uniform surface. The flat-field image is normalized and removed from the images. There are circumstances, such as with remote sensing, where a flat-field image cannot be acquired in this manner. For these cases, we developed a phase-correlation method that allows the extraction of an effective flat-field image from a sequence of scene-based displaced images. The method usesmore » sub-pixel phase correlation image registration to align the sequence to estimate the static scene. The scene is removed from sequence producing a sequence of misaligned flat-field images. An average flat-field image is derived from the realigned flat-field sequence.« less

Mapping and phasing of structural variation in patient genomes using nanopore sequencing.

PubMed

Cretu Stancu, Mircea; van Roosmalen, Markus J; Renkens, Ivo; Nieboer, Marleen M; Middelkamp, Sjors; de Ligt, Joep; Pregno, Giulia; Giachino, Daniela; Mandrile, Giorgia; Espejo Valle-Inclan, Jose; Korzelius, Jerome; de Bruijn, Ewart; Cuppen, Edwin; Talkowski, Michael E; Marschall, Tobias; de Ridder, Jeroen; Kloosterman, Wigard P

2017-11-06

Despite improvements in genomics technology, the detection of structural variants (SVs) from short-read sequencing still poses challenges, particularly for complex variation. Here we analyse the genomes of two patients with congenital abnormalities using the MinION nanopore sequencer and a novel computational pipeline-NanoSV. We demonstrate that nanopore long reads are superior to short reads with regard to detection of de novo chromothripsis rearrangements. The long reads also enable efficient phasing of genetic variations, which we leveraged to determine the parental origin of all de novo chromothripsis breakpoints and to resolve the structure of these complex rearrangements. Additionally, genome-wide surveillance of inherited SVs reveals novel variants, missed in short-read data sets, a large proportion of which are retrotransposon insertions. We provide a first exploration of patient genome sequencing with a nanopore sequencer and demonstrate the value of long-read sequencing in mapping and phasing of SVs for both clinical and research applications.

Frequency-locked pulse sequencer for high-frame-rate monochromatic tissue motion imaging.

PubMed

Azar, Reza Zahiri; Baghani, Ali; Salcudean, Septimiu E; Rohling, Robert

2011-04-01

To overcome the inherent low frame rate of conventional ultrasound, we have previously presented a system that can be implemented on conventional ultrasound scanners for high-frame-rate imaging of monochromatic tissue motion. The system employs a sector subdivision technique in the sequencer to increase the acquisition rate. To eliminate the delays introduced during data acquisition, a motion phase correction algorithm has also been introduced to create in-phase displacement images. Previous experimental results from tissue- mimicking phantoms showed that the system can achieve effective frame rates of up to a few kilohertz on conventional ultrasound systems. In this short communication, we present a new pulse sequencing strategy that facilitates high-frame-rate imaging of monochromatic motion such that the acquired echo signals are inherently in-phase. The sequencer uses the knowledge of the excitation frequency to synchronize the acquisition of the entire imaging plane to that of an external exciter. This sequencing approach eliminates any need for synchronization or phase correction and has applications in tissue elastography, which we demonstrate with tissue-mimicking phantoms. © 2011 IEEE

Technical Note: MR-visualization of interventional devices using transient field alterations and balanced steady-state free precession imaging.

PubMed

Eibofner, Frank; Martirosian, Petros; Würslin, Christian; Graf, Hansjörg; Syha, Roland; Clasen, Stephan

2015-11-01

In interventional magnetic resonance imaging, instruments can be equipped with conducting wires for visualization by current application. The potential of sequence triggered application of transient direct currents in balanced steady-state free precession (bSSFP) imaging is demonstrated. A conductor and a modified catheter were examined in water phantoms and in an ex vivo porcine liver. The current was switched by a trigger pulse in the bSSFP sequence in an interval between radiofrequency pulse and signal acquisition. Magnitude and phase images were recorded. Regions with transient field alterations were evaluated by a postprocessing algorithm. A phase mask was computed and overlaid with the magnitude image. Transient field alterations caused continuous phase shifts, which were separated by the postprocessing algorithm from phase jumps due to persistent field alterations. The overlaid images revealed the position of the conductor. The modified catheter generated visible phase offset in all orientations toward the static magnetic field and could be unambiguously localized in the ex vivo porcine liver. The application of a sequence triggered, direct current in combination with phase imaging allows conspicuous localization of interventional devices with a bSSFP sequence.

Paleomagnetism of the Puente Piedra Formation, Central Peru

NASA Astrophysics Data System (ADS)

May, Steven R.; Butler, Robert F.

1985-02-01

Paleomagnetic samples were collected from 15 sites in the early Cretaceous Puente Piedra Formation near Lima, Peru. This formation consists of interbedded volcanic flows and marine sediments and represents the oldest known rocks of the Andean coastal province in this region. The Puente Piedra Formation is interpreted as a submarine volcanic arc assemblage which along with an overlying sequence of early Cretaceous clastic and carbonate rocks represents a terrane whose paleogeographic relationship with respect to the Peruvian miogeocline in pre-Albian time is unknown. Moderate to high coercivities, blocking temperatures below 320°C, and diagnostic strong-field thermomagnetic behavior indicate that pyrrhotite is the dominant magnetic phase in the Puente Piedra Formation. This pyrrhotite carries a stable CRM acquired during an event of copper mineralization associated with the intrusion of the Santa Rosa super-unit of the Coastal Batholith at about 90 ± 5 m.y. B.P. The tectonically uncorrected formation mean direction of: D = 343.2°, I = -28.6°, α 95 = 3.4° is statistically concordant in inclination but discordant in declination with respect to the expected direction calculated from the 90-m.y. reference pole for cratonic South America. The observed declination indicates approximately 20° of counterclockwise rotation of the Puente Piedra rocks since about 90 m.y. This is consistent with other paleomagnetic data from a larger crustal block which may indicate modest counterclockwise rotation during the Cenozoic associated with crustal shortening and thickening in the region of the Peru-Chile deflection.

THE FORMATION AND EVOLUTION OF YOUNG LOW-MASS STARS WITHIN HALOS WITH HIGH CONCENTRATION OF DARK MATTER PARTICLES

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

Casanellas, Jordi; Lopes, IlIDio, E-mail: jordicasanellas@ist.utl.p, E-mail: ilidio.lopes@ist.utl.p

2009-11-01

The formation and evolution of low-mass stars within dense halos of dark matter (DM) leads to evolution scenarios quite different from the classical stellar evolution. As a result of our detailed numerical work, we describe these new scenarios for a range of DM densities on the host halo, for a range of scattering cross sections of the DM particles considered, and for stellar masses from 0.7 to 3 M {sub sun}. For the first time, we also computed the evolution of young low-mass stars in their Hayashi track in the pre-main-sequence phase and found that, for high DM densities, thesemore » stars stop their gravitational collapse before reaching the main sequence, in agreement with similar studies on first stars. Such stars remain indefinitely in an equilibrium state with lower effective temperatures (|DELTAT{sub eff}|>10{sup 3} K for a star of one solar mass), the annihilation of captured DM particles in their core being the only source of energy. In the case of lower DM densities, these protostars continue their collapse and progress through the main-sequence burning hydrogen at a lower rate. A star of 1 M{sub sun} will spend a time period greater than the current age of the universe consuming all the hydrogen in its core if it evolves in a halo with DM density rho{sub c}hi = 10{sup 9} GeV cm{sup -3}. We also show the strong dependence of the effective temperature and luminosity of these stars on the characteristics of the DM particles and how this can be used as an alternative method for DM research.« less

The Evolutionary Status of Be Stars: Results from a Photometric Study of Southern Open Clusters

NASA Astrophysics Data System (ADS)

McSwain, M. Virginia; Gies, Douglas R.

2005-11-01

Be stars are a class of rapidly rotating B stars with circumstellar disks that cause Balmer and other line emission. There are three possible reasons for the rapid rotation of Be stars: they may have been born as rapid rotators, spun up by binary mass transfer, or spun up during the main-sequence (MS) evolution of B stars. To test the various formation scenarios, we have conducted a photometric survey of 55 open clusters in the southern sky. Of these, five clusters are probably not physically associated groups and our results for two other clusters are not reliable, but we identify 52 definite Be stars and an additional 129 Be candidates in the remaining clusters. We use our results to examine the age and evolutionary dependence of the Be phenomenon. We find an overall increase in the fraction of Be stars with age until 100 Myr, and Be stars are most common among the brightest, most massive B-type stars above the zero-age main sequence (ZAMS). We show that a spin-up phase at the terminal-age main sequence (TAMS) cannot produce the observed distribution of Be stars, but up to 73% of the Be stars detected may have been spun-up by binary mass transfer. Most of the remaining Be stars were likely rapid rotators at birth. Previous studies have suggested that low metallicity and high cluster density may also favor Be star formation. Our results indicate a possible increase in the fraction of Be stars with increasing cluster distance from the Galactic center (in environments of decreasing metallicity). However, the trend is not significant and could be ruled out due to the intrinsic scatter in our data. We also find no relationship between the fraction of Be stars and cluster density.

Sequence analysis of the phs operon in Salmonella typhimurium and the contribution of thiosulfate reduction to anaerobic energy metabolism.

PubMed Central

Heinzinger, N K; Fujimoto, S Y; Clark, M A; Moreno, M S; Barrett, E L

1995-01-01

The phs chromosomal locus of Salmonella typhimurium is essential for the dissimilatory anaerobic reduction of thiosulfate to hydrogen sulfide. Sequence analysis of the phs region revealed a functional operon with three open reading frames, designated phsA, phsB, and phsC, which encode peptides of 82.7, 21.3, and 28.5 kDa, respectively. The predicted products of phsA and phsB exhibited significant homology with the catalytic and electron transfer subunits of several other anaerobic molybdoprotein oxidoreductases, including Escherichia coli dimethyl sulfoxide reductase, nitrate reductase, and formate dehydrogenase. Simultaneous comparison of PhsA to seven homologous molybdoproteins revealed numerous similarities among all eight throughout the entire frame, hence, significant amino acid conservation among molybdoprotein oxidoreductases. Comparison of PhsB to six other homologous sequences revealed four highly conserved iron-sulfur clusters. The predicted phsC product was highly hydrophobic and similar in size to the hydrophobic subunits of the molybdoprotein oxidoreductases containing subunits homologous to phsA and phsB. Thus, phsABC appears to encode thiosulfate reductase. Single-copy phs-lac translational fusions required both anaerobiosis and thiosulfate for full expression, whereas multicopy phs-lac translational fusions responded to either thiosulfate or anaerobiosis, suggesting that oxygen and thiosulfate control of phs involves negative regulation. A possible role for thiosulfate reduction in anaerobic respiration was examined. Thiosulfate did not significantly augment the final densities of anaerobic cultures grown on any of the 18 carbon sources tested. on the other hand, washed stationary-phase cells depleted of ATP were shown to synthesize small amounts of ATP on the addition of the formate and thiosulfate, suggesting that the thiosulfate reduction plays a unique role in anaerobic energy conservation by S typhimurium. PMID:7751291

Stellar Evolution with Rotation: Mixing Processes in AGB Stars

NASA Astrophysics Data System (ADS)

Driebe, T.; Blöcker, T.

We included diffusive angular momentum transport and rotationally induced mixing processes in our stellar evolution code and studied the influence of rotation on the evolution of intermediate mass stars (M*=2dots6 Msolar) towards and along the asymptotic giant branch (AGB). The calculations start in the fully convective pre-main sequence phase and the initial angular momentu m was adjusted such that on the zero-age main sequence vrot=200 km/ s is achieved. The diffusion coefficients for the five rotational instabilities considered (dynamical shear, secular shear, Eddington-Sweet (ES) circulation, Solberg-Høiland-instability and Goldreich-Schubert-Fricke (GSF) instability) were adopted from Heger et al. (2000, ApJ 528, 368). Mixing efficiency and sensitivity of these processes against molecular weight gradients have been determined by calibration of the main sequence width. In this study we focus on the abundance evolution of carbon. On the one hand, the surface abundance ratios of 12C/13C a nd 12C/16O at the base of the AGB were found to be ≈ 7dots 10 and ≈ 0.1, resp., being a factor of two lower than in non-rotating models. This results from the slow but continuously operating rotationally induced mixing due to the ES-circulation and the GSF-instability during the long main sequence phase. On the other hand, 13C serves as neutron source for interior s-process nucleosynthesis in AGB stars vi a 13C(α,n)16O. Herwig et al. (1997, A&A 324, L81) found that a 13C pocket is forme d in the intershell region of 3 Msolar AGB star if diffusive overshoot is considered. Our calculations show, that mixing processes due to rotation open an alternative channel for the formation of a 13C pocket as found by Langer et al. (1999, A&A 346, L37). Again, ES-circulation and GSF-instability are the predominant rotational mixing processes.

Prediction of Phase Formation in Nanoscale Sn-Ag-Cu Solder Alloy

NASA Astrophysics Data System (ADS)

Wu, Min; Lv, Bailin

2016-01-01

In a dynamic nonequilibrium process, the effective heat of formation allows the heat of formation to be calculated as a function of concentrations of the reacting atoms. In this work, we used the effective heat of formation rule to predict the formation and size of compound phases in a nanoscale Sn-Ag-Cu lead-free solder. We calculated the formation enthalpy and effective formation enthalpy of compounds in the Sn-Ag, Sn-Cu, and Ag-Cu systems by using the Miedema model and effective heat of formation. Our results show that, considering the surface effect of the nanoparticle, the effective heat of formation rule successfully predicts the phase formation and sizes of Ag3Sn and Cu6Sn5 compounds, which agrees well with experimental data.

The effects of DNA supercoiling on G-quadruplex formation.

PubMed

Sekibo, Doreen A T; Fox, Keith R

2017-12-01

Guanine-rich DNAs can fold into four-stranded structures that contain stacks of G-quartets. Bioinformatics studies have revealed that G-rich sequences with the potential to adopt these structures are unevenly distributed throughout genomes, and are especially found in gene promoter regions. With the exception of the single-stranded telomeric DNA, all genomic G-rich sequences will always be present along with their C-rich complements, and quadruplex formation will be in competition with the corresponding Watson-Crick duplex. Quadruplex formation must therefore first require local dissociation (melting) of the duplex strands. Since negative supercoiling is known to facilitate the formation of alternative DNA structures, we have investigated G-quadruplex formation within negatively supercoiled DNA plasmids. Plasmids containing multiple copies of (G3T)n and (G3T4)n repeats, were probed with dimethylsulphate, potassium permanganate and S1 nuclease. While dimethylsulphate footprinting revealed some evidence for G-quadruplex formation in (G3T)n sequences, this was not affected by supercoiling, and permanganate failed to detect exposed thymines in the loop regions. (G3T4)n sequences were not protected from DMS and showed no reaction with permanganate. Similarly, both S1 nuclease and 2D gel electrophoresis of DNA topoisomers did not detect any supercoil-dependent structural transitions. These results suggest that negative supercoiling alone is not sufficient to drive G-quadruplex formation. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Lateral diffusion study of the Pt-Al system using the NAC nuclear microprobe.

NASA Astrophysics Data System (ADS)

de Waal, H.; Pretorius, R.

1999-10-01

In this study a nuclear microprobe (NMP) was used to analyse phase formation during reaction in Pt-Al lateral diffusion couples. Phase identification was done by Rutherford backscattering spectroscopy. These results were compared with phase formation during conventional thin film Pt-Al interactions. The co-existence of multiple phases in lateral diffusion couples is discussed with reference to the effective heat of formation (EHF) model.

Growth dynamics and cytoskeleton organization during stem maturation and gravity-induced stem bending in Zea mays L

NASA Technical Reports Server (NTRS)

Collings, D. A.; Winter, H.; Wyatt, S. E.; Allen, N. S.; Davies, E. (Principal Investigator)

1998-01-01

Characterization of gravitropic bending in the maize stem pulvinus, a tissue that functions specifically in gravity responses, demonstrates that the pulvinus is an ideal system for studying gravitropism. Gravistimulation during the second of three developmental phases of the pulvinus induces a gradient of cell elongation across the non-growing cells of the pulvinus, with the most elongation occurring on the lower side. This cell elongation is spatially and temporally separated from normal internodal cell elongation. The three characterized growth phases in the pulvinus correspond closely to a specialized developmental sequence in which structural features typical of cells not fully matured are retained while cell maturation occurs in surrounding internodal and nodal tissue. For example, the lignification of supporting tissue and rearrangement of transverse microtubules to oblique that occur in the internode when cell elongation ceases are delayed for up to 10 d in the adjacent cells of the pulvinus, and only occurs as a pulvinus loses its capacity to respond to gravistimulation. Gravistimulation does not modify this developmental sequence. Neither wall lignification nor rearrangement of transverse microtubules occurs in the rapidly elongating lower side or non-responsive upper side of the pulvinus until the pulvinus loses the capacity to bend further. Gravistimulation does, however, lead to the formation of putative pit fields within the expanding cells of the pulvinus.

Developmental transcriptome profiling of bovine muscle tissue reveals an abundant GosB that regulates myoblast proliferation and apoptosis

PubMed Central

Yang, Jiameng; Dong, Dong; Huang, Yongzhen; Lan, Xianyong; Plath, Martin; Lei, Chuzhao; Qi, Xinglei; Bai, Yueyu; Chen, Hong

2017-01-01

The formation of bovine skeletal muscle involves complex developmental and physiological processes that play a vital role in determining the quality of beef; however, the regulatory mechanisms underlying differences in meat quality are largely unknown. We conducted transcriptome analysis of bovine muscle tissues to compare gene expression profiles between embryonic and adult stages. Total RNAs from skeletal muscle of Qinchuan cattle at fetal and adult stages were used to construct libraries for Illumina next-generation sequencing using the Ribo-Zero RNA sequencing (RNA-Seq) method. We found a total of 19,695 genes to be expressed in fetal and adult stages, whereby 3,299 were expressed only in fetal, and 433 only in adult tissues. We characterized the role of a candidate gene (GosB), which was highly (but differentially) expressed in embryonic and adult skeletal muscle tissue. GosB increased the number of myoblasts in the S-phase of the cell cycle, and decreased the proportion of cells in the G0/G1 phase. GosB promoted the proliferation of myoblasts and protected them from apoptosis via regulating Bcl-2 expression and controlling the intracellular calcium concentration. Modulation of GosB expression in muscle tissue may emerge as a potential target in breeding strategies attempting to alter myoblast numbers in cattle. PMID:28404879

Anaerosporomusa subterranea gen. nov., sp. nov., a spore-forming anaerobe belonging to the class Negativicutes isolated from saprolite.

PubMed

Choi, Jessica K; Shah, Madhavi; Yee, Nathan

2016-10-01

A Gram-stain-negative, spore-forming, anaerobic bacterium designated strain RU4T was isolated from a saprolite core collected from Oak Ridge, Tennessee, USA. Cells were slightly curved rods and exhibited an outer membrane exterior to a thin cell wall. Strain RU4T formed heat-resistant endospores in late-log phase and stationary phase cultures. Under anaerobic conditions, strain RU4T grew by fermenting fumarate and maleate, but did not grow on glucose, glycerol, pyruvate, lactate, succinate, citrate, formate, acetate, propionate, butyrate or valerate. Strain RU4T did not reduce sulfate or ferric iron. The main cellular fatty acids were C17 : 0 cyclo, C16 : 0 and C15 : 0. The DNA G+C content was 52 mol%. Analysis of the 16S rRNA, rpoB, recA, infB, gyrB and atpD gene sequences indicated that the isolate is related to members of the family Sporomusaceae. Based on 92 % sequence similarity of the 16S rRNA gene to its closest relatives in the family Sporomusaceae and divergent physiological traits, the newly-cultivated isolate was assigned to a novel species of a new genus, Anaerosporomusa subterranea gen. nov., sp. nov. The type strain of Anaerosporomusa subterranea is RU4T (=DSM 29728T=ATCC BAA-2723T).

Monte Carlo studies on the interfacial properties and interfacial structures of ternary symmetric blends with gradient copolymers.

PubMed

Sun, Dachuan; Guo, Hongxia

2012-08-09

Using Monte Carlo simulation methods, the effects of the comonomer sequence distribution on the interfacial properties (including interfacial tension, interfacial thickness, saturated interfacial area per copolymer, and bending modulus) and interfacial structures (including chain conformations and comonomer distributions of the simulated copolymers at the interfaces) of a ternary symmetric blend containing two immiscible homopolymers and one gradient copolymer are investigated. We find that copolymers with a larger composition gradient width have a broader comonomer distribution along the interface normal, and hence more pronouncedly enlarge the interfacial thickness and reduce the interfacial tension. Furthermore, the counteraction effect, which arises from the tendency of heterogeneous segments in gradient copolymers to phase separate and enter their miscible phases to reduce the local enthalpy, decreases the stretching of copolymers along the interface normal direction. As a result, copolymers with a larger width of gradient composition can occupy a larger interfacial area and form softer monolayers at saturation and are more efficient in facilitating the formation of bicontinuous microemulsions. Additionally, chain length ratio, segregation strength, and interactions between homopolymers and copolymers can alter the interfacial character of gradient copolymers. There exists a strong coupling between the comonomer sequence distribution, chain conformation, and interfacial properties. Especially, bending modulus is mainly determined by the complicated interplay of interfacial copolymer density and interfacial chain conformation.

MinION Analysis and Reference Consortium: Phase 1 data release and analysis

PubMed Central

Eccles, David A.; Zalunin, Vadim; Urban, John M.; Piazza, Paolo; Bowden, Rory J.; Paten, Benedict; Mwaigwisya, Solomon; Batty, Elizabeth M.; Simpson, Jared T.; Snutch, Terrance P.

2015-01-01

The advent of a miniaturized DNA sequencing device with a high-throughput contextual sequencing capability embodies the next generation of large scale sequencing tools. The MinION™ Access Programme (MAP) was initiated by Oxford Nanopore Technologies™ in April 2014, giving public access to their USB-attached miniature sequencing device. The MinION Analysis and Reference Consortium (MARC) was formed by a subset of MAP participants, with the aim of evaluating and providing standard protocols and reference data to the community. Envisaged as a multi-phased project, this study provides the global community with the Phase 1 data from MARC, where the reproducibility of the performance of the MinION was evaluated at multiple sites. Five laboratories on two continents generated data using a control strain of Escherichia coli K-12, preparing and sequencing samples according to a revised ONT protocol. Here, we provide the details of the protocol used, along with a preliminary analysis of the characteristics of typical runs including the consistency, rate, volume and quality of data produced. Further analysis of the Phase 1 data presented here, and additional experiments in Phase 2 of E. coli from MARC are already underway to identify ways to improve and enhance MinION performance. PMID:26834992

Phase selection during crystallization of undercooled liquid eutectic lead-tin alloys

NASA Technical Reports Server (NTRS)

Fecht, H. J.

1991-01-01

During rapid solidification substantial amounts of undercooling are in general required for formation of metastable phases. Crystallization at varying levels of undercooling and melting of metastable phases were studied during slow cooling and heating of emulsified PB-Sn alloys. Besides the experimental demonstration of the reversibility of metastable phase equilibra, two different principal solidification paths have been identified and compared with the established metastable phase diagram and predictions from classical nucleation theory. The results suggest that the most probable solidification path is described by the 'step rule' resulting in the formation of metastable phases at low undercooling, whereas the stable eutectic phase mixture crystallizes without metastable phase formation at high undercooling.

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

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

Microbial community structure in three deep-sea carbonate crusts.

PubMed

Heijs, S K; Aloisi, G; Bouloubassi, I; Pancost, R D; Pierre, C; Sinninghe Damsté, J S; Gottschal, J C; van Elsas, J D; Forney, L J

2006-10-01

Carbonate crusts in marine environments can act as sinks for carbon dioxide. Therefore, understanding carbonate crust formation could be important for understanding global warming. In the present study, the microbial communities of three carbonate crust samples from deep-sea mud volcanoes in the eastern Mediterranean were characterized by sequencing 16S ribosomal RNA (rRNA) genes amplified from DNA directly retrieved from the samples. In combination with the mineralogical composition of the crusts and lipid analyses, sequence data were used to assess the possible role of prokaryotes in crust formation. Collectively, the obtained data showed the presence of highly diverse communities, which were distinct in each of the carbonate crusts studied. Bacterial 16S rRNA gene sequences were found in all crusts and the majority was classified as alpha-, gamma-, and delta- Proteobacteria. Interestingly, sequences of Proteobacteria related to Halomonas and Halovibrio sp., which can play an active role in carbonate mineral formation, were present in all crusts. Archaeal 16S rRNA gene sequences were retrieved from two of the crusts studied. Several of those were closely related to archaeal sequences of organisms that have previously been linked to the anaerobic oxidation of methane (AOM). However, the majority of archaeal sequences were not related to sequences of organisms known to be involved in AOM. In combination with the strongly negative delta 13C values of archaeal lipids, these results open the possibility that organisms with a role in AOM may be more diverse within the Archaea than previously suggested. Different communities found in the crusts could carry out similar processes that might play a role in carbonate crust formation.

Effect of boron additions on phase formation and magnetic properties of TbCu7-type melt spun SmFe ribbons

NASA Astrophysics Data System (ADS)

Zheng, Chuanjiang; Yu, Dunbo; Li, Kuoshe; Luo, Yang; Jin, Jinling; Lu, Shuo; Li, Hongwei; Mao, Yongjun; Quan, Ningtao

2016-08-01

Melt spun ribbons of a series of SmFe12Bx (x=0.0, 0.5, 0.75, 1.0, 1.25, and 1.5) have been prepared by the melt spinning technique. Sm-Fe-B melt spun ribbons with single phase TbCu7-type structure were prepared from the SmFe12Bx (x=0.5, 0.75, and 1.0) alloys at the surface velocity around 40 m/s. The addition of boron not only inhibits the appearance of soft magnetic phase α-Fe, but also enhances the ability of amorphous formation for melt spun Sm-Fe ribbons. The concentration of boron atoms, however, exceeds the limit of the solubility (x>1.0) of Sm-Fe alloys, which does not impede the appearance of α-Fe but accelerates the formation of metastable phase Sm2Fe23B3 that is unfavorable to their magnetic properties. Moreover, it is found that the addition of boron whose concentration is 0.0≤x≤0.75 can stabilize the metastable TbCu7-type structure because of the increase of the lattice parameter ratio c/a. The magnetic properties of as-annealed SmFe12B1.0 melt spun ribbons with an energy product of 2.19MGOe, a coercivity of 2.36 kOe and a remanence of 4.8 kGs have been achieved. The microstructural characteristics of as-annealed melt spun SmFe12 and SmFe12B1.0 ribbons have been discussed as well. The following sequence of the hyperfine field H(6l)

A TALE OF DWARFS AND GIANTS: USING A z = 1.62 CLUSTER TO UNDERSTAND HOW THE RED SEQUENCE GREW OVER THE LAST 9.5 BILLION YEARS

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

Rudnick, Gregory H.; Tran, Kim-Vy; Papovich, Casey

2012-08-10

We study the red sequence in a cluster of galaxies at z = 1.62 and follow its evolution over the intervening 9.5 Gyr to the present day. Using deep YJK{sub s} imaging with the HAWK-I instrument on the Very Large Telescope, we identify a tight red sequence and construct its rest-frame i-band luminosity function (LF). There is a marked deficit of faint red galaxies in the cluster that causes a turnover in the LF. We compare the red-sequence LF to that for clusters at z < 0.8, correcting the luminosities for passive evolution. The shape of the cluster red-sequence LFmore » does not evolve between z = 1.62 and z = 0.6 but at z < 0.6 the faint population builds up significantly. Meanwhile, between z = 1.62 and 0.6 the inferred total light on the red sequence grows by a factor of {approx}2 and the bright end of the LF becomes more populated. We construct a simple model for red-sequence evolution that grows the red sequence in total luminosity and matches the constant LF shape at z > 0.6. In this model the cluster accretes blue galaxies from the field whose star formation is quenched and who are subsequently allowed to merge. We find that three to four mergers among cluster galaxies during the 4 Gyr between z = 1.62 and z = 0.6 match the observed LF evolution between the two redshifts. The inferred merger rate is consistent with other studies of this cluster. Our result supports the picture that galaxy merging during the major growth phase of massive clusters is an important process in shaping the red-sequence population at all luminosities.« less

The MLH1 ATPase domain is needed for suppressing aberrant formation of interstitial telomeric sequences.

PubMed

Jia, Pingping; Chai, Weihang

2018-05-01

Genome instability gives rise to cancer. MLH1, commonly known for its important role in mismatch repair (MMR), DNA damage signaling and double-strand break (DSB) repair, safeguards genome stability. Recently we have reported a novel role of MLH1 in preventing aberrant formation of interstitial telomeric sequences (ITSs) at intra-chromosomal regions. Deficiency in MLH1, in particular its N-terminus, leads to an increase of ITSs. Here, we identify that the ATPase activity in the MLH1 N-terminal domain is important for suppressing the formation of ITSs. The ATPase activity is also needed for recruiting MLH1 to DSBs. Moreover, defective ATPase activity of MLH1 causes an increase in micronuclei formation. Our results highlight the crucial role of MLH1's ATPase domain in preventing the aberrant formation of telomeric sequences at the intra-chromosomal regions and preserving genome stability. Copyright © 2018 Elsevier B.V. All rights reserved.

Geology and biostratigraphy of the Potomac River cliffs at Stratford Hall, Westmoreland County, Virginia

USGS Publications Warehouse

Weems, Robert E.; Edwards, Lucy E.; Landacre, Bryan D.

2017-01-01

The cliffs along the Potomac River at Stratford Hall display extensive exposures of Miocene marine strata that belong successively to the Calvert, Choptank, St. Marys, and Eastover Formations. Within the lower part of this sequence, in the Calvert and Choptank Formations, there is well-developed cyclic stratigraphy. Above the Miocene units lies the marginal marine to deltaic Pleistocene Bacons Castle Formation, which is the highest and youngest formation exposed in the cliffs. The goals of this field trip guide are to (1) show the Miocene formations exposed in the cliffs and discuss the paleoenvironments within which they formed, (2) demonstrate the cyclicity in the Miocene marine formations and discuss its origin, (3) compare and contrast the section exposed at the Stratford and Nomini Cliffs with the classic Miocene Calvert Cliffs sequence exposed to the northeast in Calvert County, Maryland, and the Miocene sequence recovered in the Haynesville cores to the southeast in Richmond County, Virginia, (4) discuss and explain why a detailed correlation among these three places has been so difficult to attain, and (5) show typical lithologies of the Bacons Castle Formation and discuss the paleoenvironments in which they formed.

Using DNA mechanics to predict in vitro nucleosome positions and formation energies

PubMed Central

Morozov, Alexandre V.; Fortney, Karissa; Gaykalova, Daria A.; Studitsky, Vasily M.; Widom, Jonathan; Siggia, Eric D.

2009-01-01

In eukaryotic genomes, nucleosomes function to compact DNA and to regulate access to it both by simple physical occlusion and by providing the substrate for numerous covalent epigenetic tags. While competition with other DNA-binding factors and action of chromatin remodeling enzymes significantly affect nucleosome formation in vivo, nucleosome positions in vitro are determined by steric exclusion and sequence alone. We have developed a biophysical model, DNABEND, for the sequence dependence of DNA bending energies, and validated it against a collection of in vitro free energies of nucleosome formation and a set of in vitro nucleosome positions mapped at high resolution. We have also made a first ab initio prediction of nucleosomal DNA geometries, and checked its accuracy against the nucleosome crystal structure. We have used DNABEND to design both strong and weak histone- binding sequences, and measured the corresponding free energies of nucleosome formation. We find that DNABEND can successfully predict in vitro nucleosome positions and free energies, providing a physical explanation for the intrinsic sequence dependence of histone–DNA interactions. PMID:19509309

High-resolution biophysical analysis of the dynamics of nucleosome formation

PubMed Central

Hatakeyama, Akiko; Hartmann, Brigitte; Travers, Andrew; Nogues, Claude; Buckle, Malcolm

2016-01-01

We describe a biophysical approach that enables changes in the structure of DNA to be followed during nucleosome formation in in vitro reconstitution with either the canonical “Widom” sequence or a judiciously mutated sequence. The rapid non-perturbing photochemical analysis presented here provides ‘snapshots’ of the DNA configuration at any given moment in time during nucleosome formation under a very broad range of reaction conditions. Changes in DNA photochemical reactivity upon protein binding are interpreted as being mainly induced by alterations in individual base pair roll angles. The results strengthen the importance of the role of an initial (H3/H4)2 histone tetramer-DNA interaction and highlight the modulation of this early event by the DNA sequence. (H3/H4)2 binding precedes and dictates subsequent H2A/H2B-DNA interactions, which are less affected by the DNA sequence, leading to the final octameric nucleosome. Overall, our results provide a novel, exciting way to investigate those biophysical properties of DNA that constitute a crucial component in nucleosome formation and stabilization. PMID:27263658

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

A comprehensively molecular haplotype-resolved genome of a European individual

PubMed Central

Suk, Eun-Kyung; McEwen, Gayle K.; Duitama, Jorge; Nowick, Katja; Schulz, Sabrina; Palczewski, Stefanie; Schreiber, Stefan; Holloway, Dustin T.; McLaughlin, Stephen; Peckham, Heather; Lee, Clarence; Huebsch, Thomas; Hoehe, Margret R.

2011-01-01

Independent determination of both haplotype sequences of an individual genome is essential to relate genetic variation to genome function, phenotype, and disease. To address the importance of phase, we have generated the most complete haplotype-resolved genome to date, “Max Planck One” (MP1), by fosmid pool-based next generation sequencing. Virtually all SNPs (>99%) and 80,000 indels were phased into haploid sequences of up to 6.3 Mb (N50 ∼1 Mb). The completeness of phasing allowed determination of the concrete molecular haplotype pairs for the vast majority of genes (81%) including potential regulatory sequences, of which >90% were found to be constituted by two different molecular forms. A subset of 159 genes with potentially severe mutations in either cis or trans configurations exemplified in particular the role of phase for gene function, disease, and clinical interpretation of personal genomes (e.g., BRCA1). Extended genomic regions harboring manifold combinations of physically and/or functionally related genes and regulatory elements were resolved into their underlying “haploid landscapes,” which may define the functional genome. Moreover, the majority of genes and functional sequences were found to contain individual or rare SNPs, which cannot be phased from population data alone, emphasizing the importance of molecular phasing for characterizing a genome in its molecular individuality. Our work provides the foundation to understand that the distinction of molecular haplotypes is essential to resolve the (inherently individual) biology of genes, genomes, and disease, establishing a reference point for “phase-sensitive” personal genomics. MP1's annotated haploid genomes are available as a public resource. PMID:21813624

Evolution dynamics of a model for gene duplication under adaptive conflict

NASA Astrophysics Data System (ADS)

Ancliff, Mark; Park, Jeong-Man

2014-06-01

We present and solve the dynamics of a model for gene duplication showing escape from adaptive conflict. We use a Crow-Kimura quasispecies model of evolution where the fitness landscape is a function of Hamming distances from two reference sequences, which are assumed to optimize two different gene functions, to describe the dynamics of a mixed population of individuals with single and double copies of a pleiotropic gene. The evolution equations are solved through a spin coherent state path integral, and we find two phases: one is an escape from an adaptive conflict phase, where each copy of a duplicated gene evolves toward subfunctionalization, and the other is a duplication loss of function phase, where one copy maintains its pleiotropic form and the other copy undergoes neutral mutation. The phase is determined by a competition between the fitness benefits of subfunctionalization and the greater mutational load associated with maintaining two gene copies. In the escape phase, we find a dynamics of an initial population of single gene sequences only which escape adaptive conflict through gene duplication and find that there are two time regimes: until a time t* single gene sequences dominate, and after t* double gene sequences outgrow single gene sequences. The time t* is identified as the time necessary for subfunctionalization to evolve and spread throughout the double gene sequences, and we show that there is an optimum mutation rate which minimizes this time scale.

Carbonization of α-Fe upon mechanical alloying

NASA Astrophysics Data System (ADS)

Barinov, V. A.; Tsurin, V. A.; Kazantsev, V. A.; Surikov, V. T.

2014-01-01

Methods of thermomagnetic analysis (TMA) and Mössbauer spectrometry (57Fe) have been used to study the processes of the carburizing of α-Fe under the conditions of mechanical milling in a medium of liquid hydrocarbons. It has been established that, under the chosen conditions of the mechanical synthesis of carbides, the process of carbonization at T < 375 K occurs through the decomposition of the deformation-induced martensite, i.e., the supersaturated bct solid solution α″-Fe(C) with the formation of transitional hcp ɛ and ɛ' phases that precede the formation of cementite. The milling of the metallic iron in the toluene medium substantially enhances the catalytic capability of disperse powders of α-Fe in the process of conversion of cyclic structures of hydrocarbons into other chemical forms. The increase in the dispersity of the iron powder to a nanocrystalline state leads to an increase in the chemical activity of carbon and an increase in the rate of diffusion sufficient for the formation in the Fe-C mixture of both primary cementite (θ') with an anomalously low Curie temperature T C(θ')(first stage) and secondary cementite (θ″) at the second stage of mechanosynthesis. The parameters of hyperfine interactions have been calculated for a number of synthesized carbides. It has been shown that the change in the carbon concentration in iron carbides is determined by the following inequality: c C(θ') > c C(ɛ) > c C(ɛ'). The boundary of the temperature stability of cementite has been established. The effect of the decomposition of the θ phase (Fe3C) upon thermal cycling θ ⇔ γ in the temperature range of 300 < T < 1075 K has been revealed. Based on the results obtained, a scheme of the sequence of phase transformations that occur in the Fe-C system under the conditions of low-temperature mechanosynthesis has been derived.

Quantification of turbulence and velocity in stenotic flow using spiral three-dimensional phase-contrast MRI.

PubMed

Petersson, Sven; Dyverfeldt, Petter; Sigfridsson, Andreas; Lantz, Jonas; Carlhäll, Carl-Johan; Ebbers, Tino

2016-03-01

Evaluate spiral three-dimensional (3D) phase contrast MRI for the assessment of turbulence and velocity in stenotic flow. A-stack-of-spirals 3D phase contrast MRI sequence was evaluated in vitro against a conventional Cartesian sequence. Measurements were made in a flow phantom with a 75% stenosis. Both spiral and Cartesian imaging were performed using different scan orientations and flow rates. Volume flow rate, maximum velocity and turbulent kinetic energy (TKE) were computed for both methods. Moreover, the estimated TKE was compared with computational fluid dynamics (CFD) data. There was good agreement between the turbulent kinetic energy from the spiral, Cartesian and CFD data. Flow rate and maximum velocity from the spiral data agreed well with Cartesian data. As expected, the short echo time of the spiral sequence resulted in less prominent displacement artifacts compared with the Cartesian sequence. However, both spiral and Cartesian flow rate estimates were sensitive to displacement when the flow was oblique to the encoding directions. Spiral 3D phase contrast MRI appears favorable for the assessment of stenotic flow. The spiral sequence was more than three times faster and less sensitive to displacement artifacts when compared with a conventional Cartesian sequence. © 2015 Wiley Periodicals, Inc.

Phase transitions in biogenic amorphous calcium carbonate

NASA Astrophysics Data System (ADS)

Gong, Yutao

Geological calcium carbonate exists in both crystalline phases and amorphous phases. Compared with crystalline calcium carbonate, such as calcite, aragonite and vaterite, the amorphous calcium carbonate (ACC) is unstable. Unlike geological calcium carbonate crystals, crystalline sea urchin spicules (99.9 wt % calcium carbonate and 0.1 wt % proteins) do not present facets. To explain this property, crystal formation via amorphous precursors was proposed in theory. And previous research reported experimental evidence of ACC on the surface of forming sea urchin spicules. By using X-ray absorption near-edge structure (XANES) spectroscopy and photoelectron emission microscopy (PEEM), we studied cross-sections of fresh sea urchin spicules at different stages (36h, 48h and 72h after fertilization) and observed the transition sequence of three mineral phases: hydrated ACC → dehydrated ACC → biogenic calcite. In addition, we unexpectedly found hydrated ACC nanoparticles that are surrounded by biogenic calcite. This observation indicates the dehydration from hydrated ACC to dehydrated ACC is inhibited, resulting in stabilization of hydrated ACC nanoparticles. We thought that the dehydration was inhibited by protein matrix components occluded within the biomineral, and we designed an in vitro assay to test the hypothesis. By utilizing XANES-PEEM, we found that SM50, the most abundant occluded matrix protein in sea urchin spicules, has the function to stabilize hydrated ACC in vitro.

Diversity in Requirement of Genetic and Epigenetic Factors for Centromere Function in Fungi ▿

PubMed Central

Roy, Babhrubahan; Sanyal, Kaustuv

2011-01-01

A centromere is a chromosomal region on which several proteins assemble to form the kinetochore. The centromere-kinetochore complex helps in the attachment of chromosomes to spindle microtubules to mediate segregation of chromosomes to daughter cells during mitosis and meiosis. In several budding yeast species, the centromere forms in a DNA sequence-dependent manner, whereas in most other fungi, factors other than the DNA sequence also determine the centromere location, as centromeres were able to form on nonnative sequences (neocentromeres) when native centromeres were deleted in engineered strains. Thus, in the absence of a common DNA sequence, the cues that have facilitated centromere formation on a specific DNA sequence for millions of years remain a mystery. Kinetochore formation is facilitated by binding of a centromere-specific histone protein member of the centromeric protein A (CENP-A) family that replaces a canonical histone H3 to form a specialized centromeric chromatin structure. However, the process of kinetochore formation on the rapidly evolving and seemingly diverse centromere DNAs in different fungal species is largely unknown. More interestingly, studies in various yeasts suggest that the factors required for de novo centromere formation (establishment) may be different from those required for maintenance (propagation) of an already established centromere. Apart from the DNA sequence and CENP-A, many other factors, such as posttranslational modification (PTM) of histones at centric and pericentric chromatin, RNA interference, and DNA methylation, are also involved in centromere formation, albeit in a species-specific manner. In this review, we discuss how several genetic and epigenetic factors influence the evolution of structure and function of centromeres in fungal species. PMID:21908596

Behaviour of Ni-PGE-Au-Cu in mafic-ultramafic volcanic suites of the 2.7 Ga Kambalda Sequence, Kalgoorlie Terrane, Yilgarn Craton

NASA Astrophysics Data System (ADS)

Said, Nuru; Kerrich, Robert; Maier, W. D.; McCuaig, Campbell

2011-05-01

The 2.7 Ga Kambalda Sequence comprises a mafic to ultramafic dominated volcanic rock sequence of the Kalgoorlie Terrane, Yilgarn Craton, Western Australia. The Sequence is divided into Lower and Upper Units separated by the Kambalda Komatiite Formation. Five basalt suites of the Lower Unit are tholeiitic where MgO spans 5-10 wt.% MgO, with minor assimilation-fractional crystallization (AFC), whereas six volcanic suites identified in the Upper Unit are tholeiitic to komatiitic-basalts with MgO 24-5 wt.% having generally greater degrees of AFC. Upper suites plot at Al 2O 3/TiO 2 (17-26) close to the primitive mantle ratio of 21, and Pt + Pd (19-31 ppb), whereas the PGE-depleted Lower basalts plot at generally lower Al 2O 3/TiO 2 (<16) and Pt + Pd (<10 ppb). Most suites have an average Pt/Pd ratio of 1.11, despite large variations in MgO contents, broadly consistent with the Pt/Pd ratio in the primitive mantle. On primitive mantle-normalised PGE plots, Upper suites generally display less fractionated patterns of the IPGE (Os, Ir, Ru and Rh) from the PPGE (Pt and Pd) relative to the Lower basalts. Most suites exhibit patterns with positive slopes reflecting relative enrichment of Pd, Pt, Au and Cu relative to Ni and IPGE. In suites of both Units, the concentrations of Ir and Ru fall with decreasing MgO contents, indicating their broadly compatible behaviour during magmatic evolution that involved AFC. Platinum and Pd behave as incompatible elements in the high-MgO suites, whereas Pt and Pd behave compatibly during crystallisation of the Lower basalt magmas, an interpretation consistent with progressively higher Cu/Pt and Cu/Pd ratios at decreasing MgO contents, and with falling Pt/Ti, collectively due to sulphur saturation induced by AFC as recorded in an antivariance of Pd/Ir with Nb/Th, a monitor of AFC. Collectively, the data suggest that several of the Lower Basalt suites crystallised under sulphide-saturated conditions, whereas most of the Upper Basalt Sequences remained sulphur undersaturated during magmatic evolution. Alteration, and fractional crystallisation of silicate and oxide phases, can be ruled out as factors governing PGE distribution in these mafic-ultramafic suites. Instead, the data suggest that discrete PGE-bearing phase (s) fractionated from the magmas. Such phases could be platinum group minerals (PGM; e.g., laurite) and/or alloys, or discrete PGE-rich nuggets or sulphides.

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.

Massive dominance of Epsilonproteobacteria in formation waters from a Canadian oil sands reservoir containing severely biodegraded oil

PubMed Central

Hubert, Casey R J; Oldenburg, Thomas B P; Fustic, Milovan; Gray, Neil D; Larter, Stephen R; Penn, Kevin; Rowan, Arlene K; Seshadri, Rekha; Sherry, Angela; Swainsbury, Richard; Voordouw, Gerrit; Voordouw, Johanna K; Head, Ian M

2012-01-01

Summary The subsurface microbiology of an Athabasca oil sands reservoir in western Canada containing severely biodegraded oil was investigated by combining 16S rRNA gene- and polar lipid-based analyses of reservoir formation water with geochemical analyses of the crude oil and formation water. Biomass was filtered from formation water, DNA was extracted using two different methods, and 16S rRNA gene fragments were amplified with several different primer pairs prior to cloning and sequencing or community fingerprinting by denaturing gradient gel electrophoresis (DGGE). Similar results were obtained irrespective of the DNA extraction method or primers used. Archaeal libraries were dominated by Methanomicrobiales (410 of 414 total sequences formed a dominant phylotype affiliated with a Methanoregula sp.), consistent with the proposed dominant role of CO2-reducing methanogens in crude oil biodegradation. In two bacterial 16S rRNA clone libraries generated with different primer pairs, > 99% and 100% of the sequences were affiliated with Epsilonproteobacteria (n = 382 and 72 total clones respectively). This massive dominance of Epsilonproteobacteria sequences was again obtained in a third library (99% of sequences; n = 96 clones) using a third universal bacterial primer pair (inosine-341f and 1492r). Sequencing of bands from DGGE profiles and intact polar lipid analyses were in accordance with the bacterial clone library results. Epsilonproteobacterial OTUs were affiliated with Sulfuricurvum, Arcobacter and Sulfurospirillum spp. detected in other oil field habitats. The dominant organism revealed by the bacterial libraries (87% of all sequences) is a close relative of Sulfuricurvum kujiense – an organism capable of oxidizing reduced sulfur compounds in crude oil. Geochemical analysis of organic extracts from bitumen at different reservoir depths down to the oil water transition zone of these oil sands indicated active biodegradation of dibenzothiophenes, and stable sulfur isotope ratios for elemental sulfur and sulfate in formation waters were indicative of anaerobic oxidation of sulfur compounds. Microbial desulfurization of crude oil may be an important metabolism for Epsilonproteobacteria indigenous to oil reservoirs with elevated sulfur content and may explain their prevalence in formation waters from highly biodegraded petroleum systems. PMID:21824242

Principles of quantitation of viral loads using nucleic acid sequence-based amplification in combination with homogeneous detection using molecular beacons.

PubMed

Weusten, Jos J A M; Carpay, Wim M; Oosterlaken, Tom A M; van Zuijlen, Martien C A; van de Wiel, Paul A

2002-03-15

For quantitative NASBA-based viral load assays using homogeneous detection with molecular beacons, such as the NucliSens EasyQ HIV-1 assay, a quantitation algorithm is required. During the amplification process there is a constant growth in the concentration of amplicons to which the beacon can bind while generating a fluorescence signal. The overall fluorescence curve contains kinetic information on both amplicon formation and beacon binding, but only the former is relevant for quantitation. In the current paper, mathematical modeling of the relevant processes is used to develop an equation describing the fluorescence curve as a function of the amplification time and the relevant kinetic parameters. This equation allows reconstruction of RNA formation, which is characterized by an exponential increase in concentrations as long as the primer concentrations are not rate limiting and by linear growth over time after the primer pool is depleted. During the linear growth phase, the actual quantitation is based on assessing the amplicon formation rate from the viral RNA relative to that from a fixed amount of calibrator RNA. The quantitation procedure has been successfully applied in the NucliSens EasyQ HIV-1 assay.

FAM83D activates the MEK/ERK signaling pathway and promotes cell proliferation in hepatocellular carcinoma

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

Wang, Dong; Han, Sheng; Peng, Rui

2015-03-06

Publicly available microarray data suggests that the expression of FAM83D (Family with sequence similarity 83, member D) is elevated in a wide variety of tumor types, including hepatocellular carcinoma (HCC). However, its role in the pathogenesis of HCC has not been elucidated. Here, we showed that FAM83D was frequently up-regulated in HCC samples. Forced FAM83D expression in HCC cell lines significantly promoted their proliferation and colony formation while FAM83D knockdown resulted in the opposite effects. Mechanistic analyses indicated that FAM83D was able to activate the MEK/ERK signaling pathway and promote the entry into S phase of cell cycle progression. Takenmore » together, these results demonstrate that FAM83D is a novel oncogene in HCC development and may constitute a potential therapeutic target in HCC. - Highlights: • FAM83D is up-regulated in HCC tissues and cell lines. • Ectopic expression of FAM83D promotes HCC cell proliferation and colony formation. • Depletion of FAM83D inhibits HCC cell proliferation and colony formation. • FAM83D activates the MEK/ERK signaling pathway in HCC.« less

Cellulose- and xylan-degrading thermophilic anaerobic bacteria from biocompost.

PubMed

Sizova, M V; Izquierdo, J A; Panikov, N S; Lynd, L R

2011-04-01

Nine thermophilic cellulolytic clostridial isolates and four other noncellulolytic bacterial isolates were isolated from self-heated biocompost via preliminary enrichment culture on microcrystalline cellulose. All cellulolytic isolates grew vigorously on cellulose, with the formation of either ethanol and acetate or acetate and formate as principal fermentation products as well as lactate and glycerol as minor products. In addition, two out of nine cellulolytic strains were able to utilize xylan and pretreated wood with roughly the same efficiency as for cellulose. The major products of xylan fermentation were acetate and formate, with minor contributions of lactate and ethanol. Phylogenetic analyses of 16S rRNA and glycosyl hydrolase family 48 (GH48) gene sequences revealed that two xylan-utilizing isolates were related to a Clostridium clariflavum strain and represent a distinct novel branch within the GH48 family. Both isolates possessed high cellulase and xylanase activity induced independently by either cellulose or xylan. Enzymatic activity decayed after growth cessation, with more-rapid disappearance of cellulase activity than of xylanase activity. A mixture of xylan and cellulose was utilized simultaneously, with a significant synergistic effect observed as a reduction of lag phase in cellulose degradation.

Coniacian-Turonian Carbonates of the Miskar Field, offshore Tunisia

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

Knott, I.; Moody, R.; Sandman, R.

1995-08-01

The R1 and R1 Superior Carbonates of the Miskar Field, offshore Tunisia are of Coniacian-Turonian age. These ages are constrained by several biostratigraphic events including a rapid increase in ostracod diversity at the base of the overlying Aleg Formation and the occurrence of several diagnostic benthonic foraminifera including Rotalia algeriana. The indication is that the R1 and R1 Superior Carbonates are the lateral equivalents, in part, of the Douleb Formation which is a known reservoir, onshore Tunisia. During the Coniacian-Turonian the area of the Miskar Field was subject to regional extension with the opening of several major North-South trending fractures.more » These culminate in the contemporaneous outpouring of submarine serpentinized volcanics during deposition of the R1 Superior/Aleg Formation. The R1 lithologies are deposited in a shallow water regime and consist of rudist buildup and debraic carbonates overlain by lagoonal facies in the North with an increase in beach/sabkha facies to the South. The indication is for a shallowing upward sequence and a general progradation of lithofacies northwards across a tilted block. In contrast the R1 Superior is indicative of a flooding event with relative sea-level changes reflected in variations of both lithofacies and biofacies. Overall the lithofacies are dominated by calcispheric/bioclastic wackestone-packstones probably deposited in a mid-platform setting. The diagenetic history of the R1 is the more complex of the two carbonate sequences reflecting several phases of fluid movement through the constituent lithologies. Original depositional characteristics and subsequent diagenetic meditation result in the development of highly variable reservoir properties.« less

ATLASGAL - towards a complete sample of massive star forming clumps

NASA Astrophysics Data System (ADS)

Urquhart, J. S.; Moore, T. J. T.; Csengeri, T.; Wyrowski, F.; Schuller, F.; Hoare, M. G.; Lumsden, S. L.; Mottram, J. C.; Thompson, M. A.; Menten, K. M.; Walmsley, C. M.; Bronfman, L.; Pfalzner, S.; König, C.; Wienen, M.

2014-09-01

By matching infrared-selected, massive young stellar objects (MYSOs) and compact H II regions in the Red MSX Source survey to massive clumps found in the submillimetre ATLASGAL (APEX Telescope Large Area Survey of the Galaxy) survey, we have identified ˜1000 embedded young massive stars between 280° < ℓ < 350° and 10° < ℓ < 60° with | b | < 1.5°. Combined with an existing sample of radio-selected methanol masers and compact H II regions, the result is a catalogue of ˜1700 massive stars embedded within ˜1300 clumps located across the inner Galaxy, containing three observationally distinct subsamples, methanol-maser, MYSO and H II-region associations, covering the most important tracers of massive star formation, thought to represent key stages of evolution. We find that massive star formation is strongly correlated with the regions of highest column density in spherical, centrally condensed clumps. We find no significant differences between the three samples in clump structure or the relative location of the embedded stars, which suggests that the structure of a clump is set before the onset of star formation, and changes little as the embedded object evolves towards the main sequence. There is a strong linear correlation between clump mass and bolometric luminosity, with the most massive stars forming in the most massive clumps. We find that the MYSO and H II-region subsamples are likely to cover a similar range of evolutionary stages and that the majority are near the end of their main accretion phase. We find few infrared-bright MYSOs associated with the most massive clumps, probably due to very short pre-main-sequence lifetimes in the most luminous sources.

Paleo-ocean environments before and after the Ordovician glaciation and the correlation with heterogeneous marine black shale: a stratigraphic case study of Wufeng-Longmaxi formation in Fuling, Sichuan basin, SW China

NASA Astrophysics Data System (ADS)

Lu, Yangbo; Hao, Fang; Lu, Yongchao

2017-04-01

The discovery of Fuling gas field in the Sichuan basin led China shale gas exploration to an unprecedented boom. The most important shale gas plays are the upper Ordovician Wufeng formation and Lower Silurian Longmaxi formation which demonstrate intriguing characteristics which are comprising of stable regional distribution, high abundance of organic matter, high thermal maturity and high brittle mineral content etc. As the Ordovician-Silurian transition was a critical interval in Earth's history marked by dramatic climatic, oceanic, and biological turnovers; these two advantageous organic rich shale deposited before and after Hirnantian glaciation are showing differences in many aspects. In this study, the stratigraphy and lithofacies within the stratigraphy framework of the upper Ordovician Wufeng formation and Lower Silurian Longmaxi formation in Fuling were quantitatively analyzed based on outcrops, cores, well logs data, and geochemical proxies. A total of three third-order sequences were divided based on the recognition of four third-order boundaries. The Wufeng Formation is equivalent to a third-order sequence and is subdivided into a transgressive system tract (TST) (black shale of lower Wufeng Formation) and a highstand system tract (HST) (Guanyinqiao Member of upper Wufeng Formation). Long-1 Member is equivalent to a third-order sequence and is subdivided into a TST, an early highstand system tract (EHST) and a late highstand system tract (LHST); Long-2 and Long-3 Member are combined to be one third-order sequence and is subdivided into a lowstand system tract (LST), a TST and a HST. Sequence development and sedimentary environment characteristics were analyzed within each system tract unit. TOC% was correlated to V/Cr and EF-Ni respectively within each system tract unit, suggesting paleoproductivity and water redox condition are the main controlling factors of organic enrichment and its preservation. The heterogeneity in shale lithofacies throughout the stratigraphic frame work reflects the vertical evolution of the paleo-climate and paleo-ocean environment across the Ordovician-Silurian transition. We suggest that the high primary productivity of Wufeng formation was due to the boom of diatom triggered by large scale coverage of volcanic ash before Hirnantian glaciation. Marine anoxia may have been a kill mechanism that cause the mass extinction of marine macro-organism during the glacial period. And the up sequence TOC deterioration of Longmaxi formation is likely subjected to influence of ocean bottom flow and slow recovery of marine organism after the glaciation.

Integrated digital flight-control system for the space shuttle orbiter

NASA Technical Reports Server (NTRS)

1973-01-01

The integrated digital flight control system is presented which provides rotational and translational control of the space shuttle orbiter in all phases of flight: from launch ascent through orbit to entry and touchdown, and during powered horizontal flights. The program provides a versatile control system structure while maintaining uniform communications with other programs, sensors, and control effectors by using an executive routine/functional subroutine format. The program reads all external variables at a single point, copies them into its dedicated storage, and then calls the required subroutines in the proper sequence. As a result, the flight control program is largely independent of other programs in the GN&C computer complex and is equally insensitive to the characteristics of the processor configuration. The integrated structure of the control system and the DFCS executive routine which embodies that structure are described along with the input and output. The specific estimation and control algorithms used in the various mission phases are given.

Gold-Catalyzed Solid-Phase Synthesis of 3,4-Dihydropyrazin-2(1H)-ones: Relevant Pharmacophores and Peptide Backbone Constraints.

PubMed

Přibylka, Adam; Krchňák, Viktor

2017-11-13

Here, we report the efficient solid-phase synthesis of N-propargyl peptides using Fmoc-amino acids and propargyl alcohol as key building blocks. Gold-catalyzed nucleophilic addition to the triple bond induced C-N bond formation, which triggered intramolecular cyclization, yielding 1,3,4-trisubstituted-5-methyl-3,4-dihydropyrazin-2(1H)-ones. Conformations of acyclic and constrained peptides were compared using a two-step conformer distribution analysis at the molecular mechanics level and density functional theory. The results indicated that the incorporation of heterocyclic molecular scaffold into a short peptide sequence adopted extended conformation of peptide chain. The amide bond adjacent to the constraint did not show significant preference for either cis or trans isomerism. Prepared model compounds demonstrate a proof of concept for gold-catalyzed polymer-supported synthesis of variously substituted 3,4-dihydropyrazin-2(1H)-ones for applications in drug discovery and peptide backbone constraints.

Electronic and structural ground state of heavy alkali metals at high pressure

NASA Astrophysics Data System (ADS)

Fabbris, G.; Lim, J.; Veiga, L. S. I.; Haskel, D.; Schilling, J. S.

2015-02-01

Alkali metals display unexpected properties at high pressure, including emergence of low-symmetry crystal structures, which appear to occur due to enhanced electronic correlations among the otherwise nearly free conduction electrons. We investigate the high-pressure electronic and structural ground state of K, Rb, and Cs using x-ray absorption spectroscopy and x-ray diffraction measurements together with a b i n i t i o theoretical calculations. The sequence of phase transitions under pressure observed at low temperature is similar in all three heavy alkalis except for the absence of the o C 84 phase in Cs. Both the experimental and theoretical results point to pressure-enhanced localization of the valence electrons characterized by pseudogap formation near the Fermi level and strong s p d hybridization. Although the crystal structures predicted to host magnetic order in K are not observed, the localization process appears to drive these alkalis closer to a strongly correlated electron state.

A Unified Dynamic Model for Learning, Replay, and Sharp-Wave/Ripples.

PubMed

Jahnke, Sven; Timme, Marc; Memmesheimer, Raoul-Martin

2015-12-09

Hippocampal activity is fundamental for episodic memory formation and consolidation. During phases of rest and sleep, it exhibits sharp-wave/ripple (SPW/R) complexes, which are short episodes of increased activity with superimposed high-frequency oscillations. Simultaneously, spike sequences reflecting previous behavior, such as traversed trajectories in space, are replayed. Whereas these phenomena are thought to be crucial for the formation and consolidation of episodic memory, their neurophysiological mechanisms are not well understood. Here we present a unified model showing how experience may be stored and thereafter replayed in association with SPW/Rs. We propose that replay and SPW/Rs are tightly interconnected as they mutually generate and support each other. The underlying mechanism is based on the nonlinear dendritic computation attributable to dendritic sodium spikes that have been prominently found in the hippocampal regions CA1 and CA3, where SPW/Rs and replay are also generated. Besides assigning SPW/Rs a crucial role for replay and thus memory processing, the proposed mechanism also explains their characteristic features, such as the oscillation frequency and the overall wave form. The results shed a new light on the dynamical aspects of hippocampal circuit learning. During phases of rest and sleep, the hippocampus, the "memory center" of the brain, generates intermittent patterns of strongly increased overall activity with high-frequency oscillations, the so-called sharp-wave/ripples. We investigate their role in learning and memory processing. They occur together with replay of activity sequences reflecting previous behavior. Developing a unifying computational model, we propose that both phenomena are tightly linked, by mutually generating and supporting each other. The underlying mechanism depends on nonlinear amplification of synchronous inputs that has been prominently found in the hippocampus. Besides assigning sharp-wave/ripples a crucial role for replay generation and thus memory processing, the proposed mechanism also explains their characteristic features, such as the oscillation frequency and the overall wave form. Copyright © 2015 the authors 0270-6474/15/3516236-23$15.00/0.

Aerobic granules formation and nutrients removal characteristics in sequencing batch airlift reactor (SBAR) at low temperature.

PubMed

Bao, Ruiling; Yu, Shuili; Shi, Wenxin; Zhang, Xuedong; Wang, Yulan

2009-09-15

To understand the effect of low temperature on the formation of aerobic granules and their nutrient removal characteristics, an aerobic granular sequencing batch airlift reactor (SBAR) has been operated at 10 degrees C using a mixed carbon source of glucose and sodium acetate. The results showed that aerobic granules were obtained and that the reactor performed in stable manner under the applied conditions. The granules had a compact structure and a clear out-surface. The average parameters of the granules were: diameter 3.4mm, wet density 1.036 g mL(-1), sludge volume index 37 mL g(-1), and settling velocity 18.6-65.1 cm min(-1). Nitrite accumulation was observed, with a nitrite accumulation rate (NO(2)(-)-N/NO(x)(-)-N) between 35% and 43% at the beginning of the start-up stage. During the stable stage, NO(x) was present at a level below the detection limit. However, when the influent COD concentration was halved (resulting in COD/N a reduction of the COD/N from 20:1 to 10:1) nitrite accumulation was observed once more with an effluent nitrite accumulation rate of 94.8%. Phosphorus release was observed in the static feeding phase and also during the initial 20-30 min of the aerobic phase. Neither the low temperature nor adjustment of the COD/P ratio from 100:1 to 25:1 had any influence on the phosphorus removal efficiency under the operating conditions. In the granular reactor with the influent load rates for COD, NH(4)(+)-N, and PO(4)(3-)-P of 1.2-2.4, 0.112 and 0.012-0.024 kg m(-3)d(-1), the respective removal efficiencies at low temperature were 90.6-95.4%, 72.8-82.1% and 95.8-97.9%.

Different Effect of Co on the Formation of Topologically Close-Packed Phases in Ni-Cr-Mo and Ni-Cr-Re Alloys

NASA Astrophysics Data System (ADS)

Shi, Qianying; An, Ning; Huo, Jiajie; Ding, Xianfei; Zheng, Yunrong; Feng, Qiang

2017-11-01

In current study, two sets of Ni-based alloys (Ni-Cr-Mo and Ni-Cr-Re series) containing 0 to 15 at. pct of Co addition were investigated to understand the formation behavior of TCP phases. Significant difference on the formation behavior of TCP phases and corresponding Co effect was found in two series alloys. TCP precipitates ( P and µ phase) were observed in both grain interiors and boundaries in Ni-Cr-Mo series alloys. Higher levels of Co addition increased the supersaturation of Mo in the γ matrix, which explained that Co addition promoted µ phase formation. In contrast, the TCP precipitates ( σ phase) formed by the manner of discontinuous precipitation transformation in the grain boundaries in Ni-Cr-Re series alloys. More Co additions suppressed the formation of σ phase, which was mainly attributed to the decreased supersaturation of Re in thermodynamically metastable γ matrix. The information obtained from simplified alloy systems in this study is helpful for the design of multicomponent Ni-based superalloys.

An intuitive graphical webserver for multiple-choice protein sequence search.

PubMed

Banky, Daniel; Szalkai, Balazs; Grolmusz, Vince

2014-04-10

Every day tens of thousands of sequence searches and sequence alignment queries are submitted to webservers. The capitalized word "BLAST" becomes a verb, describing the act of performing sequence search and alignment. However, if one needs to search for sequences that contain, for example, two hydrophobic and three polar residues at five given positions, the query formation on the most frequently used webservers will be difficult. Some servers support the formation of queries with regular expressions, but most of the users are unfamiliar with their syntax. Here we present an intuitive, easily applicable webserver, the Protein Sequence Analysis server, that allows the formation of multiple choice queries by simply drawing the residues to their positions; if more than one residue are drawn to the same position, then they will be nicely stacked on the user interface, indicating the multiple choice at the given position. This computer-game-like interface is natural and intuitive, and the coloring of the residues makes possible to form queries requiring not just certain amino acids in the given positions, but also small nonpolar, negatively charged, hydrophobic, positively charged, or polar ones. The webserver is available at http://psa.pitgroup.org. Copyright © 2014 Elsevier B.V. All rights reserved.

The rate and efficiency of high-mass star formation along the Hubble sequence

NASA Technical Reports Server (NTRS)

Devereux, Nicholas A.; Young, Judith S.

1991-01-01

Data obtained with IRAS are used to compare and contrast the global star formation rates for a galactic sample which represents essentially all known noninteracting spiral and lenticular galaxies within 40 Mpc. The distribution of 60 micron luminosity is similar for spirals of types Sa-Scd inclusively, although the luminosities of the very early and very late types are, on average, one order of magnitude lower. High-mass star formation rates are similar for early, intermediate, and late type spirals, and the average high-mass star formation rate per unit molecular gas mass is independent of type for spiral galaxies. A remarkable homogeneity exists in the high-mass star-forming capabilities of spiral galaxies, particularly among the Sa-Scd types. The Hubble sequence is therefore not a sequence in the present-day rate or production efficiency of high-mass stars.

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

USGS Publications Warehouse

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

1998-01-01

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

Microbial diversity and methanogenic activity of Antrim Shale formation waters from recently fractured wells

PubMed Central

Wuchter, Cornelia; Banning, Erin; Mincer, Tracy J.; Drenzek, Nicholas J.; Coolen, Marco J. L.

2013-01-01

The Antrim Shale in the Michigan Basin is one of the most productive shale gas formations in the U.S., but optimal resource recovery strategies must rely on a thorough understanding of the complex biogeochemical, microbial, and physical interdependencies in this and similar systems. We used Illumina MiSeq 16S rDNA sequencing to analyze the diversity and relative abundance of prokaryotic communities present in Antrim shale formation water of three closely spaced recently fractured gas-producing wells. In addition, the well waters were incubated with a suite of fermentative and methanogenic substrates in an effort to stimulate microbial methane generation. The three wells exhibited substantial differences in their community structure that may arise from their different drilling and fracturing histories. Bacterial sequences greatly outnumbered those of archaea and shared highest similarity to previously described cultures of mesophiles and moderate halophiles within the Firmicutes, Bacteroidetes, and δ- and ε-Proteobacteria. The majority of archaeal sequences shared highest sequence similarity to uncultured euryarchaeotal environmental clones. Some sequences closely related to cultured methylotrophic and hydrogenotrophic methanogens were also present in the initial well water. Incubation with methanol and trimethylamine stimulated methylotrophic methanogens and resulted in the largest increase in methane production in the formation waters, while fermentation triggered by the addition of yeast extract and formate indirectly stimulated hydrogenotrophic methanogens. The addition of sterile powdered shale as a complex natural substrate stimulated the rate of methane production without affecting total methane yields. Depletion of methane indicative of anaerobic methane oxidation (AMO) was observed over the course of incubation with some substrates. This process could constitute a substantial loss of methane in the shale formation. PMID:24367357

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.

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.

Stratigraphic evolution of the Late Jurassic Hanifa Formation along the Tuwaiq Escarpment, Saudi Arabia: Evidence for a carbonate ramp system

NASA Astrophysics Data System (ADS)

Fallatah, Mohammed I.; Kerans, Charles

2018-01-01

A sequence stratigraphic framework of the Late Jurassic (Oxfordian) Hanifa Formation at its exposure in Central Arabia is presented for the first time. This study offers the first high-resolution stratigraphic framework of the Hanifa along the Tuwaiq Escarpment by measuring 15 sections ( 770 m total thickness) over an oblique-to-dip distance of 260 km and collecting 295 samples for petrographic analysis. On the basis of these data, the Hanifa Formation can be subdivided into eight facies; 1) tabular cross-bedded quartz-peloidal-skeletal grainstone, 2) cross-bedded skeletal-peloidal grainstone, 3) bioturbated foraminiferal wackestone/mud-dominated packstone, 4) oncolitic rudstone, 5) stromatoporoid-coral biostrome/bioherm, 6) peloidal/composite-grain grain-dominated packstone/grainstone, 7) bioturbated spiculitic wackestone/mud-dominated packstone, and 8) thinly-bedded argillaceous mudstone/wackestone. The vertical and lateral distributions of these facies along the exposure define their sequence setting using the principals of sequence stratigraphy. By recognizing erosional surfaces, facies offset, and changes in facies proportions, five third-order sequences, with an average duration of 1.1 Myr, are interpreted for the Hanifa Formation. The correlation of the sequences across the study area shows that only four sequences are preserved in the north where shallow-water deposits are well-developed. Facies trends within these sequences are further illustrated in depositional models representing the highstand systems tracts (HST) and the transgressive systems tracts (TST) of the Hanifa Formation. These proposed models represent depositional settings of a carbonate ramp with normal open-marine conditions. The HST depositional model is characterized by a high-energy shoreline and depicts the presence of an offshore, structurally controlled skeletal-peloidal shoal body described here for the first time at the Hanifa exposure in the Hozwa area. This work provides a predictive framework and outcrop analog for applications in hydrocarbon exploration and development. Furthermore, a basinal setting predicted to the south of the study area is a potential site for unconventional plays.

Insights into fungal communities in composts revealed by 454-pyrosequencing: implications for human health and safety.

PubMed

De Gannes, Vidya; Eudoxie, Gaius; Hickey, William J

2013-01-01

Fungal community composition in composts of lignocellulosic wastes was assessed via 454-pyrosequencing of ITS1 libraries derived from the three major composting phases. Ascomycota represented most (93%) of the 27,987 fungal sequences. A total of 102 genera, 120 species, and 222 operational taxonomic units (OTUs; >97% similarity) were identified. Thirty genera predominated (ca. 94% of the sequences), and at the species level, sequences matching Chaetomium funicola and Fusarium oxysporum were the most abundant (26 and 12%, respectively). In all composts, fungal diversity in the mature phase exceeded that of the mesophilic phase, but there was no consistent pattern in diversity changes occurring in the thermophilic phase. Fifteen species of human pathogens were identified, eight of which have not been previously identified in composts. This study demonstrated that deep sequencing can elucidate fungal community diversity in composts, and that this information can have important implications for compost use and human health.

Insights into fungal communities in composts revealed by 454-pyrosequencing: implications for human health and safety

PubMed Central

De Gannes, Vidya; Eudoxie, Gaius; Hickey, William J.

2013-01-01

Fungal community composition in composts of lignocellulosic wastes was assessed via 454-pyrosequencing of ITS1 libraries derived from the three major composting phases. Ascomycota represented most (93%) of the 27,987 fungal sequences. A total of 102 genera, 120 species, and 222 operational taxonomic units (OTUs; >97% similarity) were identified. Thirty genera predominated (ca. 94% of the sequences), and at the species level, sequences matching Chaetomium funicola and Fusarium oxysporum were the most abundant (26 and 12%, respectively). In all composts, fungal diversity in the mature phase exceeded that of the mesophilic phase, but there was no consistent pattern in diversity changes occurring in the thermophilic phase. Fifteen species of human pathogens were identified, eight of which have not been previously identified in composts. This study demonstrated that deep sequencing can elucidate fungal community diversity in composts, and that this information can have important implications for compost use and human health. PMID:23785368

Stratigraphy, geochronology, and accretionary terrane settings of two Bronson Hill arc sequences, northern New England

USGS Publications Warehouse

Moench, R.H.; Aleinikoff, J.N.

2002-01-01

The Ammonoosuc Volcanics, Partridge Formation, and the Oliverian and Highlandcroft Plutonic Suites of the Bronson Hill anticlinorium (BHA) in axial New England are widely accepted as a single Middle to Late Ordovician magmatic arc that was active during closure of Iapetus. Mapping and U-Pb dating indicate, however, that the BHA contains two volcano-sedimentary-intrusive sequences of probable opposite subduction polarity, here termed the Ammonoosuc and Quimby sequences. The Ammonoosuc sequence is defined by the Middle Ordovician Ammonoosuc Volcanics near Littleton, N.H., the type area, northeast to Milan, N.H., and Oquossoc, Me.; it also includes black slate of the Partidge Formation (C. bicornis zone graptolites, ???457 Ma). Related metamorphosed intrusive are the tonalitic Joslin Turn pluton (469 ?? 2 Ma), the Cambridge Black granitic pluton (468 ?? 3 Ma), and gabbro, tonalite (467 ?? 4 Ma), and sheeted diabase of the Chickwolnepy instructions. These intrusives cut lowermost Ammonoosuc (therefore>469 Ma). Probable uppermost Ammonoosuc is dated at 465 ?? 6 and 461 ?? 8 Ma. Successively below the Ammonoosuc are the Dead River and Hurricane Mountain Formations (flysch and melange), and the Jim Pond Formation (484 ?? 5 Ma) and Boil Mountain Complex (both ophiolite), which are structurally underlain by the Neoproterozoic(?) Chain Lakes massif. The Quimby sequence is defined by the Lower Silurian(?) to Upper Ordovician Quimby Formation, composed of bimodal volcanics (443 ?? 4 Ma) and sulfidic shale and graywacke that lie conformably to unconformably above the Ammonoosuc Volcanics and Partridge Formation. Also in the Quimby sequence are several granitic to sparsely gabbroic plutons of the Highlandcroft (441-452 Ma) and Oliverian (435-456 Ma) Plutonic Suites, which intrude the Dead River, Ammonoosuc and Partridge, but not the Quimby Formation. Based on faunal, paleolatitude, and isotropic data, the Ammonoosuc sequence and its correlative and underlying sequences formed off the southern Laurentian margin, but northwest of the principal Iapetan suture, or Red Indian line (RIL). The Boil Mountain-Jim Pond-Hurricane Mountain sequence was ramped northwestward over the Chain Lakes massif at ???475 Ma, on the basal Boil Mountain surface. This obduction probably occurred slightly before obduction on the Baie Verte-Brompton surface (BBL), farther NW, over the Laurentian margin, and was followed by Dead River flysch sedimentation, which ended with the abrupt onset of Ammonoosuc-sequence arc magmatism at ???470 Ma. Ammonoosuc eruptions probably ended at ???460 Ma, when Iapetus closed along the Red Indian line. During a following magmatic hiatus of ???3-5 m.y., now represented by portions of the Partridge Formation that overlie the Ammonoosuc Volcanics, subduction polarity reversed, and subduction resumed below the northwest-dipping Brunswick subduction complex (BSC) of New Brunswick, Canada. Quimby-sequence magmatism (???456-435 Ma) on the the newly accreted Laurentian margin occurred above the BSC, whose footwall is now buried to the southeast by mainly Silurian clastic sediments of the Merrimack-Fredericton trough, deposited in the "Fredericton Sea". In Silurian to Early Devonian time, the NW-dipping BSC footwall was paired with a SE-dipping subduction zone that produced arc magmas of the Coastal Volcanic belt, built on the composite Avalon and adjacent peri-Avalonian terranes. Orogen-normal extension produced by rapid rollback of both subduction zones narrowed the Fredericton Sea, produced the Central Maine and Connecticut Valley-Gaspe?? basins, and culminated in the Acadian orogeny when the sea completely closed in Early Devonian time. Published by Elsevier Science Ltd.

Stratigraphy, geochronology, and accretionary terrane settings of two Bronson Hill arc sequences, northern New England

USGS Publications Warehouse

Moench, R.H.; Aleinikoff, J.N.

2003-01-01

The Ammonoosuc Volcanics, Partridge Formation, and the Oliverian and Highlandcroft Plutonic Suites of the Bronson Hill anticlinorium (BHA) in axial New England are widely accepted as a single Middle to Late Ordovician magmatic arc that was active during closure of Iapetus. Mapping and U-Pb dating indicate, however, that the BHA contains two volcano-sedimentary-intrusive sequences of probable opposite subduction polarity, here termed the Ammonoosuc and Quimby sequences. The Ammonoosuc sequence is defined by the Middle Ordovician Ammonoosuc Volcanics near Littleton, NH, the type area, northeast to Milan, NH, and Oquossoc, ME; it also includes black slate of the Partridge Formation ( C. bicornis--zone graptolites, ???457 Ma). Related metamorphosed intrusives are the tonalitic Joslin Turn pluton (469 ?? 2 Ma), the Cambridge Black granitic pluton (468 ?? 3 Ma), and gabbro, tonalite (467 ?? 4 Ma), and sheeted diabase of the Chickwolnepy intrusions. These intrusives cut lowermost Ammonoosuc (therefore >469 Ma). Probable uppermost Ammonoosuc is dated at 465 ?? 6 and 461 ?? 8 Ma. Successively below the Ammonoosuc are the Dead River and Hurricane Mountain Formations (flysch and melange), and the Jim Pond Formation (484 ?? 5 Ma) and Boil Mountain Complex (both ophiolite), which are structurally underlain by the Neoproterozoic(?) Chain Lakes massif. The Quimby sequence is defined by the Lower Silurian(?) to Upper Ordovician Quimby Formation, composed of bimodal volcanics (443 ?? 4 Ma) and sulfidic shale and graywacke that lie conformably to unconformably above the Ammmonoosuc Volcanics and Partridge Formation. Also in the Quimby sequence are several granitic to sparsely gabbroic plutons of the Highlandcroft (441-452 Ma) and Oliverian (435-456 Ma) Plutonic Suites, which intrude the Dead River, Ammonoouc and Partridge, but not the Quimby Formation. Based on faunal, paleolatitude, and isotopic data, the Ammonoosuc sequence and its correlatives and underlying sequences formed off the southern Laurentian margin, but northwest of the principal Iapetan suture, or Red Indian line. The Boil Mountain-Jim Pond-Hurricane Mountain sequence was ramped northwestward over the Chain Lakes massif at ???475 Ma, on the basal Boil Mountain surface. This obduction probably occurred slightly before obduction on the Baie Vert-Brompton surface (BBL), farther NW, over the Laurentian margin, and was followed by Dead River flysch sedimentation, which ended with the abrupt onset of Ammonoosuc-sequence arc magmatism at ???470 Ma. Ammonoosuc eruptions probably ended at ???460 Ma, when Iapetus closed along the Red Indian line. During a following magmatic hiatus of ???3-5 m.y., now represented by portions of the Partridge Formation that overlie the Ammonoosuc Volcanics, subduction polarity reversed, and subduction resumed below the northwest-dipping Brunswick subduction complex (BSC) of New Brunswick, Canada. Quimby-sequence magmatism (???456-435 Ma) on the newly accreted Laurentian margin occurred above the BSC, whose footwall is now buried to the southeast by mainly Silurian clastic sediments of the Merrimack-Fredericton trough, deposited in the "Fredericton Sea". In Silurian to Early Devonian time, the NW-dipping BSC footwall was paired with a SE-dipping subduction zone that produced arc magmas of the Coastal Volcanic belt, built on the composite Avalon and adjacent peri-Avalonian terranes. Orogen-normal extension produced by rapid rollback of both subduction zones narrowed the Fredericton Sea, produced the Central Maine and Connecticut Valley-Gaspe?? basins, and culminated in the Acadian orogeny when the sea completely closed in Early Devonian time. Published by Elsevier Science Ltd.

Stratigraphy, geochronology, and accretionary terrane settings of two Bronson Hill arc sequences, northern New England

NASA Astrophysics Data System (ADS)

Moench, Robert H.; Aleinikoff, John N.

The Ammonoosuc Volcanics, Partridge Formation, and the Oliverian and Highlandcroft Plutonic Suites of the Bronson Hill anticlinorium (BHA) in axial New England are widely accepted as a single Middle to Late Ordovician magmatic arc that was active during closure of Iapetus. Mapping and U-Pb dating indicate, however, that the BHA contains two volcano-sedimentary-intrusive sequences of probable opposite subduction polarity, here termed the Ammonoosuc and Quimby sequences. The Ammonoosuc sequence is defined by the Middle Ordovician Ammonoosuc Volcanics near Littleton, NH, the type area, northeast to Milan, NH, and Oquossoc, ME; it also includes black slate of the Partridge Formation ( C. bicornis--zone graptolites, ∼457 Ma). Related metamorphosed intrusives are the tonalitic Joslin Turn pluton (469 ± 2 Ma), the Cambridge Black granitic pluton (468 ± 3 Ma), and gabbro, tonalite (467 ± 4 Ma), and sheeted diabase of the Chickwolnepy intrusions. These intrusives cut lowermost Ammonoosuc (therefore >469 Ma). Probable uppermost Ammonoosuc is dated at 465 ± 6 and 461 ± 8 Ma. Successively below the Ammonoosuc are the Dead River and Hurricane Mountain Formations (flysch and melange), and the Jim Pond Formation (484 ± 5 Ma) and Boil Mountain Complex (both ophiolite), which are structurally underlain by the Neoproterozoic(?) Chain Lakes massif. The Quimby sequence is defined by the Lower Silurian(?) to Upper Ordovician Quimby Formation, composed of bimodal volcanics (443 ± 4 Ma) and sulfidic shale and graywacke that lie conformably to unconformably above the Ammmonoosuc Volcanics and Partridge Formation. Also in the Quimby sequence are several granitic to sparsely gabbroic plutons of the Highlandcroft (441-452 Ma) and Oliverian (435-456 Ma) Plutonic Suites, which intrude the Dead River, Ammonoouc and Partridge, but not the Quimby Formation. Based on faunal, paleolatitude, and isotopic data, the Ammonoosuc sequence and its correlatives and underlying sequences formed off the southern Laurentian margin, but northwest of the principal Iapetan suture, or Red Indian line. The Boil Mountain-Jim Pond-Hurricane Mountain sequence was ramped northwestward over the Chain Lakes massif at ∼475 Ma, on the basal Boil Mountain surface. This obduction probably occurred slightly before obduction on the Baie Vert-Brompton surface (BBL), farther NW, over the Laurentian margin, and was followed by Dead River flysch sedimentation, which ended with the abrupt onset of Ammonoosuc-sequence arc magmatism at ∼470 Ma. Ammonoosuc eruptions probably ended at ∼460 Ma, when Iapetus closed along the Red Indian line. During a following magmatic hiatus of ∼3-5 m.y., now represented by portions of the Partridge Formation that overlie the Ammonoosuc Volcanics, subduction polarity reversed, and subduction resumed below the northwest-dipping Brunswick subduction complex (BSC) of New Brunswick, Canada. Quimby-sequence magmatism (∼456-435 Ma) on the newly accreted Laurentian margin occurred above the BSC, whose footwall is now buried to the southeast by mainly Silurian clastic sediments of the Merrimack-Fredericton trough, deposited in the “Fredericton Sea”. In Silurian to Early Devonian time, the NW-dipping BSC footwall was paired with a SE-dipping subduction zone that produced arc magmas of the Coastal Volcanic belt, built on the composite Avalon and adjacent peri-Avalonian terranes. Orogen-normal extension produced by rapid rollback of both subduction zones narrowed the Fredericton Sea, produced the Central Maine and Connecticut Valley-Gaspé basins, and culminated in the Acadian orogeny when the sea completely closed in Early Devonian time.

Stratigraphy, geochronology, and accretionary terrane settings of two Bronson Hill arc sequences, northern New England

NASA Astrophysics Data System (ADS)

Moench, Robert H.; Aleinikoff, John N.

2002-01-01

The Ammonoosuc Volcanics, Partridge Formation, and the Oliverian and Highlandcroft Plutonic Suites of the Bronson Hill anticlinorium (BHA) in axial New England are widely accepted as a single Middle to Late Ordovician magmatic arc that was active during closure of Iapetus. Mapping and U-Pb dating indicate, however, that the BHA contains two volcano-sedimentary-intrusive sequences of probable opposite subduction polarity, here termed the Ammonoosuc and Quimby sequences. The Ammonoosuc sequence is defined by the Middle Ordovician Ammonoosuc Volcanics near Littleton, N.H., the type area, northeast to Milan, N.H., and Oquossoc, Me.; it also includes black slate of the Partidge Formation ( C. bicornis zone graptolites, ∼457 Ma). Related metamorphosed intrusive are the tonalitic Joslin Turn pluton (469±2 Ma), the Cambridge Black granitic pluton (468±3 Ma), and gabbro, tonalite (467±4 Ma), and sheeted diabase of the Chickwolnepy instructions. These intrusives cut lowermost Ammonoosuc (therefore >469 Ma). Probable uppermost Ammonoosuc is dated at 465±6 and 461±8 Ma. Successively below the Ammonoosuc are the Dead River and Hurricane Mountain Formations (flysch and melange), and the Jim Pond Formation (484±5 Ma) and Boil Mountain Complex (both ophiolite), which are structurally underlain by the Neoproterozoic(?) Chain Lakes massif. The Quimby sequence is defined by the Lower Silurian(?) to Upper Ordovician Quimby Formation, composed of bimodal volcanics (443±4 Ma) and sulfidic shale and graywacke that lie conformably to unconformably above the Ammonoosuc Volcanics and Partridge Formation. Also in the Quimby sequence are several granitic to sparsely gabbroic plutons of the Highlandcroft (441-452 Ma) and Oliverian (435-456 Ma) Plutonic Suites, which intrude the Dead River, Ammonoosuc and Partridge, but not the Quimby Formation. Based on faunal, paleolatitude, and isotropic data, the Ammonoosuc sequence and its correlative and underlying sequences formed off the southern Laurentian margin, but northwest of the principal Iapetan suture, or Red Indian line (RIL). The Boil Mountain-Jim Pond-Hurricane Mountain sequence was ramped northwestward over the Chain Lakes massif at ∼475 Ma, on the basal Boil Mountain surface. This obduction probably occurred slightly before obduction on the Baie Verte-Brompton surface (BBL), farther NW, over the Laurentian margin, and was followed by Dead River flysch sedimentation, which ended with the abrupt onset of Ammonoosuc-sequence arc magmatism at ∼470 Ma. Ammonoosuc eruptions probably ended at ∼460 Ma, when Iapetus closed along the Red Indian line. During a following magmatic hiatus of ∼3-5 m.y., now represented by portions of the Partridge Formation that overlie the Ammonoosuc Volcanics, subduction polarity reversed, and subduction resumed below the northwest-dipping Brunswick subduction complex (BSC) of New Brunswick, Canada. Quimby-sequence magmatism (∼456-435 Ma) on the the newly accreted Laurentian margin occurred above the BSC, whose footwall is now buried to the southeast by mainly Silurian clastic sediments of the Merrimack-Fredericton trough, deposited in the “Fredericton Sea”. In Silurian to Early Devonian time, the NW-dipping BSC footwall was paired with a SE-dipping subduction zone that produced arc magmas of the Coastal Volcanic belt, built on the composite Avalon and adjacent peri-Avalonian terranes. Orogen-normal extension produced by rapid rollback of both subduction zones narrowed the Fredericton Sea, produced the Central Maine and Connecticut Valley-Gaspé basins, and culminated in the Acadian orogeny when the sea completely closed in Early Devonian time.

On the phase evolution of AlCoCrCuFeMnSix high entropy alloys prepared by mechanical alloying and arc melting route

NASA Astrophysics Data System (ADS)

Kumar, Anil; Chopkar, Manoj

2018-05-01

Effect of Si addition on phase formation of AlCoCrCuFeMnSix (x=0, 0.3, 0.6 and 0.9) high entropy alloy have been investigated in this work. The alloys are prepared by mechanical alloying and vacuum arc melting technique. The X-ray diffraction results reveals the formation of mixture of face centered and body centered cubic solid solution phases in milled powders. The addition of Si favours body centered cubic structure formation during milling process. Whereas, after melting the milled powders, body centered phases formed during milling is partial transformed into sigma phases. XRD results were also correlated with the SEM elemental mapping of as casted samples. Addition of Si favours σ phase formation in the as cast samples.

Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments

USDA-ARS?s Scientific Manuscript database

Copy number variants (CNV) are large scale duplications or deletions of genomic sequence that are caused by a diverse set of molecular phenomena that are distinct from single nucleotide polymorphism (SNP) formation. Due to their different mechanisms of formation, CNVs are often difficult to track us...

Atrx promotes heterochromatin formation at retrotransposons

PubMed Central

Sadic, Dennis; Schmidt, Katharina; Groh, Sophia; Kondofersky, Ivan; Ellwart, Joachim; Fuchs, Christiane; Theis, Fabian J; Schotta, Gunnar

2015-01-01

More than 50% of mammalian genomes consist of retrotransposon sequences. Silencing of retrotransposons by heterochromatin is essential to ensure genomic stability and transcriptional integrity. Here, we identified a short sequence element in intracisternal A particle (IAP) retrotransposons that is sufficient to trigger heterochromatin formation. We used this sequence in a genome-wide shRNA screen and identified the chromatin remodeler Atrx as a novel regulator of IAP silencing. Atrx binds to IAP elements and is necessary for efficient heterochromatin formation. In addition, Atrx facilitates a robust and largely inaccessible heterochromatin structure as Atrx knockout cells display increased chromatin accessibility at retrotransposons and non-repetitive heterochromatic loci. In summary, we demonstrate a direct role of Atrx in the establishment and robust maintenance of heterochromatin. PMID:26012739

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

NASA Astrophysics Data System (ADS)

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

2007-04-01

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

Whole Genome Sequence of Two Wild-Derived Mus musculus domesticus Inbred Strains, LEWES/EiJ and ZALENDE/EiJ, with Different Diploid Numbers

PubMed Central

Morgan, Andrew P.; Didion, John P.; Doran, Anthony G.; Holt, James M.; McMillan, Leonard; Keane, Thomas M.; de Villena, Fernando Pardo-Manuel

2016-01-01

Wild-derived mouse inbred strains are becoming increasingly popular for complex traits analysis, evolutionary studies, and systems genetics. Here, we report the whole-genome sequencing of two wild-derived mouse inbred strains, LEWES/EiJ and ZALENDE/EiJ, of Mus musculus domesticus origin. These two inbred strains were selected based on their geographic origin, karyotype, and use in ongoing research. We generated 14× and 18× coverage sequence, respectively, and discovered over 1.1 million novel variants, most of which are private to one of these strains. This report expands the number of wild-derived inbred genomes in the Mus genus from six to eight. The sequence variation can be accessed via an online query tool; variant calls (VCF format) and alignments (BAM format) are available for download from a dedicated ftp site. Finally, the sequencing data have also been stored in a lossless, compressed, and indexed format using the multi-string Burrows-Wheeler transform. All data can be used without restriction. PMID:27765810

Sequence stratigraphy and a revised sea-level curve for the Middle Devonian of eastern North America

USGS Publications Warehouse

Brett, Carlton E.; Baird, G.C.; Bartholomew, A.J.; DeSantis, M.K.; Ver Straeten, C.A.

2011-01-01

The well-exposed Middle Devonian rocks of the Appalachian foreland basin (Onondaga Formation; Hamilton Group, Tully Formation, and the Genesee Group of New York State) preserve one of the most detailed records of high-order sea-level oscillation cycles for this time period in the world. Detailed examination of coeval units in distal areas of the Appalachian Basin, as well as portions of the Michigan and Illinois basins, has revealed that the pattern of high-order sea-level oscillations documented in the New York-Pennsylvania section can be positively identified in all areas of eastern North America where coeval units are preserved. The persistence of the pattern of high-order sea-level cycles across such a wide geographic area suggests that these cycles are allocyclic in nature with primary control on deposition being eustatic sea-level oscillation, as opposed to autocylic controls, such as sediment supply, which would be more local in their manifestation. There is strong evidence from studies of cyclicity and spectral analysis that these cycles are also related to Milankovitch orbital variations, with the short and long-term eccentricity cycles (100. kyr and 405. kyr) being the dominant oscillations in many settings. Relative sea-level oscillations of tens of meters are likely and raise considerable issues about the driving mechanism, given that the Middle Devonian appears to record a greenhouse phase of Phanerozoic history. These new correlations lend strong support to a revised high-resolution sea-level oscillation curve for the Middle Devonian for the eastern portion of North America. Recognized third-order sequences are: Eif-1 lower Onondaga Formation, Eif-2: upper Onondaga and Union Springs formations; Eif-Giv: Oatka Creek Formation; Giv-1: Skaneateles, Giv-2: Ludlowville, Giv-3: lower Moscow, Giv-4: upper Moscow-lower Tully, and Giv-5: middle Tully-Geneseo formations. Thus, in contrast with the widely cited eustatic curve of Johnson et al. (1985), which recognizes just one major transgressive-regressive (T-R) cycle in the early-mid Givetian (If) prior to the major late Givetian Taghanic unconformity (IIa, upper Tully-Geneseo Shale), we recognize four T-R cycles: If (restricted), Ig, Ih, and Ii. We surmise that third-order sequences record eustatic sea-level fluctuations of tens of meters with periodicities of 0.8-2. myr, while their medial-scale (fourth-order) subdivisions record lesser variations primarily of 405. kyr duration (long-term eccentricity). This high-resolution record of sea-level change provides strong evidence for high-order eustatic cycles with probable Milankovitch periodicities, despite the fact that no direct evidence for Middle Devonian glacial sediments has been found to date. ?? 2010.

Gas-Phase Infrared; JCAMP Format

National Institute of Standards and Technology Data Gateway

SRD 35 NIST/EPA Gas-Phase Infrared; JCAMP Format (PC database for purchase)   This data collection contains 5,228 infrared spectra in the JCAMP-DX (Joint Committee for Atomic and Molecular Physical Data "Data Exchange") format.

SEQ-REVIEW: A tool for reviewing and checking spacecraft sequences

NASA Astrophysics Data System (ADS)

Maldague, Pierre F.; El-Boushi, Mekki; Starbird, Thomas J.; Zawacki, Steven J.

1994-11-01

A key component of JPL's strategy to make space missions faster, better and cheaper is the Advanced Multi-Mission Operations System (AMMOS), a ground software intensive system currently in use and in further development. AMMOS intends to eliminate the cost of re-engineering a ground system for each new JPL mission. This paper discusses SEQ-REVIEW, a component of AMMOS that was designed to facilitate and automate the task of reviewing and checking spacecraft sequences. SEQ-REVIEW is a smart browser for inspecting files created by other sequence generation tools in the AMMOS system. It can parse sequence-related files according to a computer-readable version of a 'Software Interface Specification' (SIS), which is a standard document for defining file formats. It lets users display one or several linked files and check simple constraints using a Basic-like 'Little Language'. SEQ-REVIEW represents the first application of the Quality Function Development (QFD) method to sequence software development at JPL. The paper will show how the requirements for SEQ-REVIEW were defined and converted into a design based on object-oriented principles. The process starts with interviews of potential users, a small but diverse group that spans multiple disciplines and 'cultures'. It continues with the development of QFD matrices that related product functions and characteristics to user-demanded qualities. These matrices are then turned into a formal Software Requirements Document (SRD). The process concludes with the design phase, in which the CRC (Class, Responsibility, Collaboration) approach was used to convert requirements into a blueprint for the final product.

SEQ-REVIEW: A tool for reviewing and checking spacecraft sequences

NASA Technical Reports Server (NTRS)

Maldague, Pierre F.; El-Boushi, Mekki; Starbird, Thomas J.; Zawacki, Steven J.

1994-01-01

A key component of JPL's strategy to make space missions faster, better and cheaper is the Advanced Multi-Mission Operations System (AMMOS), a ground software intensive system currently in use and in further development. AMMOS intends to eliminate the cost of re-engineering a ground system for each new JPL mission. This paper discusses SEQ-REVIEW, a component of AMMOS that was designed to facilitate and automate the task of reviewing and checking spacecraft sequences. SEQ-REVIEW is a smart browser for inspecting files created by other sequence generation tools in the AMMOS system. It can parse sequence-related files according to a computer-readable version of a 'Software Interface Specification' (SIS), which is a standard document for defining file formats. It lets users display one or several linked files and check simple constraints using a Basic-like 'Little Language'. SEQ-REVIEW represents the first application of the Quality Function Development (QFD) method to sequence software development at JPL. The paper will show how the requirements for SEQ-REVIEW were defined and converted into a design based on object-oriented principles. The process starts with interviews of potential users, a small but diverse group that spans multiple disciplines and 'cultures'. It continues with the development of QFD matrices that related product functions and characteristics to user-demanded qualities. These matrices are then turned into a formal Software Requirements Document (SRD). The process concludes with the design phase, in which the CRC (Class, Responsibility, Collaboration) approach was used to convert requirements into a blueprint for the final product.

A spectroscopic and photometric study of the unique pre- main sequence system KH 15D

NASA Astrophysics Data System (ADS)

Hamilton, Catrina Marie

2004-09-01

As a class, T Tauri stars are YSOs, some which are surrounded by circumstellar disks, and are recognized as the final stage of low-mass star formation. They also represent the earliest stage of stellar evolution that is optically visible, and, therefore, can be easily studied in detail. Understanding the processes through which these young stars interact with and eventually disperse their circumstellar disks is critical for understanding how they evolve from the T Tauri phase to the zero age main sequence (ZAMS), and how this affects the formation of planets, as well as their rotational evolution. KH 15D is a unique eclipsing system that could provide invaluable insight into the evolution of circumstellar disk material, as well as clues to the close stellar environment. Discovered in 1997, this star system has been observed to undergo an eclipse every 48 days in which the star's light is diminished by 3.5 magnitudes. What is so unusual about the eclipse is that the length of the eclipse has evolved over time, growing in length from 16 days initially, to ˜25 days in 2002/2003. Evolution of disk material on these timescales has never been observed before, and therefore provides us with a unique opportunity to refine our theories about remnant disks around young stars, how they transition, possibly into planets, and what role they play as the star matures and arrives on the zero age main sequence. Additionally, high resolution spectra obtained at specific phases during the December 2001 eclipse showed that as the obscuring matter cut across the star, dramatic spectral changes in the Hα and Hβ lines were seen. Its unique eclipse produces a “natural coronographic” effect in which the stellar photosphere is occulted, revealing details of its magnetosphere and surroundings during eclipse. There is evidence that the weak-lined T Tauri star (WTTS) central to the system is actively accreting gas, although probably not at the rate of a typical classical T Tauri star, calling into question the common practice of associating WTTS characteristics with the absence of an accretion disk. Here I present an investigation of the photometric and spectroscopic properties of the KH 15D eclipsing system, and discuss the implications that this system holds for the future research of T Tauri stars.

The Star Formation Histories of Disk Galaxies: The Live, the Dead, and the Undead

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

Oemler, Augustus Jr; Dressler, Alan; Abramson, Louis E.

We reexamine the properties of local galaxy populations using published surveys of star formation, structure, and gas content. After recalibrating star formation measures, we are able to reliably measure specific star formation rates well below that of the so-called “main sequence” of star formation versus mass. We find an unexpectedly large population of quiescent galaxies with star formation rates intermediate between the main sequence and passive populations and with disproportionately high star formation rates. We demonstrate that a tight main sequence is a natural outcome of most histories of star formation and has little astrophysical significance but that the quiescentmore » population requires additional astrophysics to explain its properties. Using a simple model for disk evolution based on the observed dependence of star formation on gas content in local galaxies, and assuming simple histories of cold gas inflow, we show that the evolution of galaxies away from the main sequence can be attributed to the depletion of gas due to star formation after a cutoff of gas inflow. The quiescent population is composed of galaxies in which the density of disk gas has fallen below a threshold for star formation probably set by disk stability. The evolution of galaxies beyond the quiescent state to gas exhaustion and the end of star formation requires another process, probably wind-driven mass loss. The environmental dependence of the three galaxy populations is consistent with recent numerical modeling, which indicates that cold gas inflows into galaxies are truncated at earlier epochs in denser environments.« less

The star forming universe after z=1

NASA Astrophysics Data System (ADS)

Harker, Justin J.

This dissertation explores three projects in the field of galaxy formation and evolution: the formation of the red sequence via quenching, the detection, characterization, and frequency of starbursts in the DEEP2 sample, and the behavior of a main sequence of star forming galaxies whose behavior is determined by baryonic mass, referred to as staged star formation. The first section, in Chapter 2, presents a breakdown of several population synthesis models designed to probe the history of the red sequence. Known from measurements at low redshift to be composed of objects with a large range of ages, the red sequence is not well-modeled as being the result of a single monolithic event in the distant past. By combining information on restframe color, Balmer absorption line strengths, and the number density of L* galaxies as a function of redshift, we find evidence that the red sequence is built up over time. The second section, in Chapter 3 and 4, presents a novel method for determining simultaneously the absorption line and emission line contributions to the total measured equivalent width of Balmer lines. Relying on the predictable behavior of both absorption lines, which are to first order equivalent to one another, and emission lines, which follow a predictable decrement toward shorter wavelengths, a single measurement of total line strength for Hb and Hd yield uncoupled emission and absorption line components. Using the measurement of Hd in absorption against D n 4000 and Hb in emission, we isolate a population of potential starbursts in the DEEP2 sample. The final section, in Chapter 5, explores the regularity of star formation as a function of redshift, using the staged star formation prescription of Noeske et al. (2007a). We compute a set of t-models using the prescription, and compare them to the data in a number of parameters in addition to mass and star formation. While the staged star formation model is a good match in a number of parameters, we find several irregularities.

Genomic Sequence Variation Markup Language (GSVML).

PubMed

Nakaya, Jun; Kimura, Michio; Hiroi, Kaei; Ido, Keisuke; Yang, Woosung; Tanaka, Hiroshi

2010-02-01

With the aim of making good use of internationally accumulated genomic sequence variation data, which is increasing rapidly due to the explosive amount of genomic research at present, the development of an interoperable data exchange format and its international standardization are necessary. Genomic Sequence Variation Markup Language (GSVML) will focus on genomic sequence variation data and human health applications, such as gene based medicine or pharmacogenomics. We developed GSVML through eight steps, based on case analysis and domain investigations. By focusing on the design scope to human health applications and genomic sequence variation, we attempted to eliminate ambiguity and to ensure practicability. We intended to satisfy the requirements derived from the use case analysis of human-based clinical genomic applications. Based on database investigations, we attempted to minimize the redundancy of the data format, while maximizing the data covering range. We also attempted to ensure communication and interface ability with other Markup Languages, for exchange of omics data among various omics researchers or facilities. The interface ability with developing clinical standards, such as the Health Level Seven Genotype Information model, was analyzed. We developed the human health-oriented GSVML comprising variation data, direct annotation, and indirect annotation categories; the variation data category is required, while the direct and indirect annotation categories are optional. The annotation categories contain omics and clinical information, and have internal relationships. For designing, we examined 6 cases for three criteria as human health application and 15 data elements for three criteria as data formats for genomic sequence variation data exchange. The data format of five international SNP databases and six Markup Languages and the interface ability to the Health Level Seven Genotype Model in terms of 317 items were investigated. GSVML was developed as a potential data exchanging format for genomic sequence variation data exchange focusing on human health applications. The international standardization of GSVML is necessary, and is currently underway. GSVML can be applied to enhance the utilization of genomic sequence variation data worldwide by providing a communicable platform between clinical and research applications. Copyright 2009 Elsevier Ireland Ltd. All rights reserved.

Determination of initiation of DNA replication before and after nuclear formation in Xenopus egg cell free extracts

PubMed Central

1993-01-01

Xenopus egg extracts prepared before and after egg activation retain M- and S-phase specific activity, respectively. Staurosporine, a potent inhibitor of protein kinase, converted M-phase extracts into interphase- like extracts that were capable of forming nuclei upon the addition of sperm DNA. The nuclei formed in the staurosporine treated M-phase extract were incapable of replicating DNA, and they were unable to initiate replication upon the addition of S-phase extracts. Furthermore, replication was inhibited when the staurosporine-treated M- phase extract was added in excess to the staurosporine-treated S-phase extract before the addition of DNA. The membrane-depleted S-phase extract supported neither nuclear formation nor replication; however, preincubation of sperm DNA with these extracts allowed them to form replication-competent nuclei upon the addition of excess staurosporine- treated M-phase extract. These results demonstrate that positive factors in the S-phase extracts determined the initiation of DNA replication before nuclear formation, although these factors were unable to initiate replication after nuclear formation. PMID:8253833

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

USGS Publications Warehouse

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

2004-01-01

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

Expanding the RpoS/σS-Network by RNA Sequencing and Identification of σS-Controlled Small RNAs in Salmonella

PubMed Central

Lévi-Meyrueis, Corinne; Monteil, Véronique; Sismeiro, Odile; Dillies, Marie-Agnès; Monot, Marc; Jagla, Bernd; Coppée, Jean-Yves; Dupuy, Bruno; Norel, Françoise

2014-01-01

The RpoS/σS sigma subunit of RNA polymerase (RNAP) controls a global adaptive response that allows many Gram-negative bacteria to survive starvation and various stresses. σS also contributes to biofilm formation and virulence of the food-borne pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium). In this study, we used directional RNA-sequencing and complementary assays to explore the σS-dependent transcriptome of S. Typhimurium during late stationary phase in rich medium. This study confirms the large regulatory scope of σS and provides insights into the physiological functions of σS in Salmonella. Extensive regulation by σS of genes involved in metabolism and membrane composition, and down-regulation of the respiratory chain functions, were important features of the σS effects on gene transcription that might confer fitness advantages to bacterial cells and/or populations under starving conditions. As an example, we show that arginine catabolism confers a competitive fitness advantage in stationary phase. This study also provides a firm basis for future studies to address molecular mechanisms of indirect regulation of gene expression by σS. Importantly, the σS-controlled downstream network includes small RNAs that might endow σS with post-transcriptional regulatory functions. Of these, four (RyhB-1/RyhB-2, SdsR, SraL) were known to be controlled by σS and deletion of the sdsR locus had a competitive fitness cost in stationary phase. The σS-dependent control of seven additional sRNAs was confirmed in Northern experiments. These findings will inspire future studies to investigate molecular mechanisms and the physiological impact of post-transcriptional regulation by σS. PMID:24810289

ALMA observations of TiO2 around VY Canis Majoris

NASA Astrophysics Data System (ADS)

De Beck, E.; Vlemmings, W.; Muller, S.; Black, J. H.; O'Gorman, E.; Richards, A. M. S.; Baudry, A.; Maercker, M.; Decin, L.; Humphreys, E. M.

2015-08-01

Context. Titanium dioxide, TiO2, is a refractory species that could play a crucial role in the dust-condensation sequence around oxygen-rich evolved stars. To date, gas phase TiO2 has been detected only in the complex environment of the red supergiant VY CMa. Aims: We aim to constrain the distribution and excitation of TiO2 around VY CMa in order to clarify its role in dust formation. Methods: We analyse spectra and channel maps for TiO2 extracted from ALMA science verification data. Results: We detect 15 transitions of TiO2, and spatially resolve the emission for the first time. The maps demonstrate a highly clumpy, anisotropic outflow in which the TiO2 emission likely traces gas exposed to the stellar radiation field. An accelerating bipolar-like structure is found, oriented roughly east-west, of which the blue component runs into and breaks up around a solid continuum component. A distinct tail to the south-west is seen for some transitions, consistent with features seen in the optical and near-infrared. Conclusions: We find that a significant fraction of TiO2 remains in the gas phase outside the dust-formation zone and suggest that this species might play only a minor role in the dust-condensation process around extreme oxygen-rich evolved stars like VY CMa. Appendix A is available in electronic form at http://www.aanda.org

Shallow Methane Hydrates: Rates, Mechanisms of Formation and Environmental Significance.

NASA Astrophysics Data System (ADS)

Torres, M. E.; Trehu, A. M.

2005-05-01

Shallow gas hydrates have been identified at more than 20 locations worldwide, and are commonly associated with observations of bubble discharge at the seafloor. These deposits are host to active chemosynthetic communities and are likely to play a predominant role in energy, climate and carbon cycle issues associated with hydrate processes. Because seafloor gas hydrates are not in equilibrium with seawater, these deposits require a constant supply of methane to replace loss by continuous diffusion to bottom water. We will summarize evidence documenting that at the shallow deposits on Hydrate Ridge (OR) methane must be delivered in the free gas phase and present simple models used to infer formation rates, which are orders of magnitude higher than those for hydrates formed deeper in the sediment column (Torres et al., 2004). At Hydrate Ridge, methane gas is channeled from deep accretionary margin sequences to the gas hydrate stability zone (GHSZ) through a permeable layer that has been mapped seismically (Horizon A). High gas pressure in this horizon can drive gas through the GHSZ to the seafloor (Trehu et al., 2004). We will review current ideas that address mechanisms whereby gas migrates from Horizon A to the seafloor, including inhibition by capillary effects and the development of a high salinity front that can shift the hydrate stability field enough to allow for methane transport as a gas phase.

Lower permian reef-bank bodies’ characterization in the pre-caspian basin

NASA Astrophysics Data System (ADS)

Wang, Zhen; Wang, Yankun; Yin, Jiquan; Luo, Man; Liang, Shuang

2018-02-01

Reef-bank reservoir is one of the targets for exploration of marine carbonate rocks in the Pre-Caspian Basin. Within this basin, the reef-bank bodies were primarily developed in the subsalt Devonian-Lower Permian formations, and are dominated by carbonate platform interior and margin reef-banks. The Lower Permian reef-bank present in the eastern part of the basin is considered prospective. This article provides a sequence and sedimentary facies study utilizing drilling and other data, as well as an analysis and identification of the Lower Permian reef-bank features along the eastern margin of the Pre-Caspian Basin using sub-volume coherence and seismic inversion techniques. The results indicate that the sub-volume coherence technique gives a better reflection of lateral distribution of reefs, and the seismic inversion impedance enables the identification of reef bodies’ development phases in the vertical direction, since AI (impedance) is petrophysically considered a tool for distinguishing the reef limestone and the clastic rocks within the formation (limestone exhibits a relatively high impedance than clastic rock). With this method, the existence of multiple phases of the Lower Permian reef-bank bodies along the eastern margin of the Pre-Caspian Basin has been confirmed. These reef-bank bodies are considered good subsalt exploration targets due to their lateral connectivity from south to north, large distribution range and large scale.

Single rotating stars and the formation of bipolar planetary nebula

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

García-Segura, G.; Villaver, E.; Langer, N.

2014-03-10

We have computed new stellar evolution models that include the effects of rotation and magnetic torques under different hypotheses. The goal is to test whether a single star can sustain the rotational velocities needed in the envelope for magnetohydrodynamical(MHD) simulations to shape bipolar planetary nebulae (PNe) when high mass-loss rates take place. Stellar evolution models with main sequence masses of 2.5 and 5 M {sub ☉} and initial rotational velocities of 250 km s{sup –1} have been followed through the PNe formation phase. We find that stellar cores have to be spun down using magnetic torques in order to reproducemore » the rotation rates observed for white dwarfs. During the asymptotic giant branch phase and beyond, the magnetic braking of the core has a practically null effect on increasing the rotational velocity of the envelope since the stellar angular momentum is efficiently removed by the wind. We have also tested the best possible case scenarios in rather non-physical contexts to give enough angular momentum to the envelope. We find that we cannot get the envelope of a single star to rotate at the speeds needed for MHD simulations to form bipolar PNe. We conclude that single stellar rotators are unlikely to be the progenitors of bipolar PNe under the current MHD model paradigm.« less

Transformation of BCC and B2 High Temperature Phases to HCP and Orthorhombic Structures in the Ti-Al-Nb System. Part II: Experimental TEM Study of Microstructures

PubMed Central

Bendersky, L. A.; Boettinger, W. J.

1993-01-01

Possible transformation paths that involve no long range diffusion and their corresponding microstructural details were predicted by Bendersky, Roytburd, and Boettinger [J. Res. Natl. Inst. Stand. Technol. 98, 561 (1993)] for Ti-Al-Nb alloys cooled from the high temperature BCC/B2 phase field into close-packed orthorhombic or hexagonal phase fields. These predictions were based on structural and symmetry relations between the known phases. In the present paper experimental TEM results show that two of the predicted transformation paths are indeed followed for different alloy compositions. For Ti-25Al-12.5Nb (at%), the path includes the formation of intermediate hexagonal phases, A3 and DO19, and subsequent formation of a metastable domain structure of the low-temperature O phase. For alloys close to Ti-25Al-25Nb (at%), the path involves an intermediate B19 structure and subsequent formation of a translational domain structure of the O phase. The path selection depends on whether B2 order forms in the high temperature cubic phase prior to transformation to the close-packed structure. The paper also analyzes the formation of a two-phase modulated microstructure during long term annealing at 700 °C. The structure forms by congruent ordering of the DO19 phase to the O phase, and then reprecipitation of the DO19 phase, possibly by a spinodal mechanism. The thermodynamics underlying the path selection and the two-phase formation are also discussed. PMID:28053488

PuLSE: Quality control and quantification of peptide sequences explored by phage display libraries.

PubMed

Shave, Steven; Mann, Stefan; Koszela, Joanna; Kerr, Alastair; Auer, Manfred

2018-01-01

The design of highly diverse phage display libraries is based on assumption that DNA bases are incorporated at similar rates within the randomized sequence. As library complexity increases and expected copy numbers of unique sequences decrease, the exploration of library space becomes sparser and the presence of truly random sequences becomes critical. We present the program PuLSE (Phage Library Sequence Evaluation) as a tool for assessing randomness and therefore diversity of phage display libraries. PuLSE runs on a collection of sequence reads in the fastq file format and generates tables profiling the library in terms of unique DNA sequence counts and positions, translated peptide sequences, and normalized 'expected' occurrences from base to residue codon frequencies. The output allows at-a-glance quantitative quality control of a phage library in terms of sequence coverage both at the DNA base and translated protein residue level, which has been missing from toolsets and literature. The open source program PuLSE is available in two formats, a C++ source code package for compilation and integration into existing bioinformatics pipelines and precompiled binaries for ease of use.

Spatial analysis of biomineralization associated gene expression from the mantle organ of the pearl oyster Pinctada maxima

PubMed Central

2011-01-01

Background Biomineralization is a process encompassing all mineral containing tissues produced within an organism. One of the most dynamic examples of this process is the formation of the mollusk shell, comprising a variety of crystal phases and microstructures. The organic component incorporated within the shell is said to dictate this architecture. However general understanding of how this process is achieved remains ambiguous. The mantle is a conserved organ involved in shell formation throughout molluscs. Specifically the mantle is thought to be responsible for secreting the protein component of the shell. This study employs molecular approaches to determine the spatial expression of genes within the mantle tissue to further the elucidation of the shell biomineralization. Results A microarray platform was custom generated (PmaxArray 1.0) from the pearl oyster Pinctada maxima. PmaxArray 1.0 consists of 4992 expressed sequence tags (ESTs) originating from mantle tissue. This microarray was used to analyze the spatial expression of ESTs throughout the mantle organ. The mantle was dissected into five discrete regions and analyzed for differential gene expression with PmaxArray 1.0. Over 2000 ESTs were determined to be differentially expressed among the tissue sections, identifying five major expression regions. In situ hybridization validated and further localized the expression for a subset of these ESTs. Comparative sequence similarity analysis of these ESTs revealed a number of the transcripts were novel while others showed significant sequence similarities to previously characterized shell related genes. Conclusions This investigation has mapped the spatial distribution for over 2000 ESTs present on PmaxArray 1.0 with reference to specific locations of the mantle. Expression profile clusters have indicated at least five unique functioning zones in the mantle. Three of these zones are likely involved in shell related activities including formation of nacre, periostracum and calcitic prismatic microstructure. A number of novel and known transcripts have been identified from these clusters. The development of PmaxArray 1.0, and the spatial map of its ESTs expression in the mantle has begun characterizing the molecular mechanisms linking the organics and inorganics of the molluscan shell. PMID:21936921

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.

Fault and fluid systems in supra-subduction zones: The Troodos ophiolite

NASA Astrophysics Data System (ADS)

Quandt, Dennis; Micheuz, Peter; Kurz, Walter; Krenn, Kurt

2017-04-01

The Troodos massif on the island of Cyprus represents a well-preserved and complete supra-subduction zone (SSZ) ophiolite. It includes an extrusive sequence that is subdivided into Upper (UPL) and Lower Pillow Lavas (LPL). These volcanic rocks contain mineralized fractures (veins) and vesicles that record fluid availability probably related to slab dehydration and deformation subsequent to a period of subduction initiation in the framework of a SSZ setting. Here, we present electron microprobe element mappings and cathodoluminescence studies of vein minerals as well as analyses of fluid inclusions entrapped in zeolite, calcite and quartz from veins and vesicles of the Pillow Lavas of the Troodos ophiolite. Two different zeolite type assemblages, interpreted as alteration products of compositional varying volcanic glasses, occur: (1) Na-zeolites analcime and natrolite from the UPL that require lower formation temperatures, higher Na/Ca ratios and pH values than (2) Ca-zeolites heulandite and mordenite from the LPL which indicate temporal or spatial varying fluid compositions and conditions. Calcite represents a late stage phase in incompletely sealed blocky type (1) assemblage and in syntaxial quartz veins. Additionally, calcite occurs as major phase in syntaxial and blocky veins of UPL and LPL. These syntaxial quartz and calcite veins are assumed to be related to tectonic extension. Chalcedony is associated with quartz and occurs in typical veins and vesicles of the LPL. In addition, the presence of neptunian dykes in veins suggests that seawater penetrated fractures throughout the extrusive sequence. Thus, circulation in an open system via advective transport is favored while diffusion in a closed system is a subordinate, local and late stage phenomenon. Calcite veins and quartz vesicles contain primary, partly re-equilibrated two phase (liquid, vapor) fluid inclusions. The chemical system of all studied inclusions in both host minerals is restricted to aqueous chemistry with salinities below 5 mass% based on last melting of ice between -3 and -0.8° C. Homogenization around 100-200° C occurs always to the liquid phase indicative for a pressure dominated fluid origin. Well preserved zonation textures in blocky calcite veins consisting of partly decrepitated but also re-equilibrated large fluid inclusions are related to Mn-rich areas. This fluid inclusion generation shows also homogenization to the liquid phase and points to minimum temperature conditions for formation of Mn-enriched areas of about 220° C. Calcite microstructures within the veins are characterized by type I and II twins as well as undulatory extinction and subgrain boundaries indicative for deformation temperatures of approximately 200-250° C, with differential stresses of about 50 MPa. We acknowledge financial support by the Austrian Research Fund (P27982-N29) to W. Kurz

Overcoming S-Phase Checkpoint-Mediated Resistance: Sequence-Dependent Synergy of Gemcitabine and SN-38 In Human Carcinoma Cell Lines*

PubMed Central

Gálvez-Peralta, Marina; Dai, Nga T.; Loegering, David A.; Flatten, Karen; Safgren, Stephanie; Wagner, Jill; Ames, Matthew M.; Karnitz, Larry M.; Kaufmann, Scott H.

2008-01-01

Although agents that inhibit DNA synthesis are widely used in the treatment of cancer, the optimal method for combining such agents and the mechanism of their synergy is poorly understood. The present study examined the effects of combining gemcitabine and SN-38 (the active metabolite of irinotecan), two S phase-selective agents that individually have broad antitumor activity, in human cancer cells in vitro. Colony forming assays revealed that simultaneous treatment of Ovcar-5 ovarian cancer cells or BxPC-3 pancreatic cancer cells with gemcitabine and SN-38 resulted in antagonistic effects. In contrast, sequential treatment with the two agents in either order resulted in synergistic antiproliferative effects, although the mechanism of synergy varied with the sequence. In particular, SN-38 arrested cells in S phase, enhanced the accumulation of gemcitabine metabolites and diminished checkpoint kinase 1, thereby sensitizing cells in the SN-38 → gemcitabine sequence. Gemcitabine treatment followed by removal allowed prolonged progression through S phase, contributing to synergy of the gemcitabine → SN-38 sequence. Collectively, these results suggest that S phase selective agents might exhibit more cytotoxicity when administered sequentially rather than simultaneously. PMID:18509065

Self-organizing approach for meta-genomes.

PubMed

Zhu, Jianfeng; Zheng, Wei-Mou

2014-12-01

We extend the self-organizing approach for annotation of a bacterial genome to analyze the raw sequencing data of the human gut metagenome without sequence assembling. The original approach divides the genomic sequence of a bacterium into non-overlapping segments of equal length and assigns to each segment one of seven 'phases', among which one is for the noncoding regions, three for the direct coding regions to indicate the three possible codon positions of the segment starting site, and three for the reverse coding regions. The noncoding phase and the six coding phases are described by two frequency tables of the 64 triplet types or 'codon usages'. A set of codon usages can be used to update the phase assignment and vice versa. An iteration after an initialization leads to a convergent phase assignment to give an annotation of the genome. In the extension of the approach to a metagenome, we consider a mixture model of a number of categories described by different codon usages. The Illumina Genome Analyzer sequencing data of the total DNA from faecal samples are then examined to understand the diversity of the human gut microbiome. Copyright © 2014 Elsevier Ltd. All rights reserved.

Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II.

PubMed

Lu, Huasong; Yu, Dan; Hansen, Anders S; Ganguly, Sourav; Liu, Rongdiao; Heckert, Alec; Darzacq, Xavier; Zhou, Qiang

2018-06-01

Hyperphosphorylation of the C-terminal domain (CTD) of the RPB1 subunit of human RNA polymerase (Pol) II is essential for transcriptional elongation and mRNA processing 1-3 . The CTD contains 52 heptapeptide repeats of the consensus sequence YSPTSPS. The highly repetitive nature and abundant possible phosphorylation sites of the CTD exert special constraints on the kinases that catalyse its hyperphosphorylation. Positive transcription elongation factor b (P-TEFb)-which consists of CDK9 and cyclin T1-is known to hyperphosphorylate the CTD and negative elongation factors to stimulate Pol II elongation 1,4,5 . The sequence determinant on P-TEFb that facilitates this action is currently unknown. Here we identify a histidine-rich domain in cyclin T1 that promotes the hyperphosphorylation of the CTD and stimulation of transcription by CDK9. The histidine-rich domain markedly enhances the binding of P-TEFb to the CTD and functional engagement with target genes in cells. In addition to cyclin T1, at least one other kinase-DYRK1A 6 -also uses a histidine-rich domain to target and hyperphosphorylate the CTD. As a low-complexity domain, the histidine-rich domain also promotes the formation of phase-separated liquid droplets in vitro, and the localization of P-TEFb to nuclear speckles that display dynamic liquid properties and are sensitive to the disruption of weak hydrophobic interactions. The CTD-which in isolation does not phase separate, despite being a low-complexity domain-is trapped within the cyclin T1 droplets, and this process is enhanced upon pre-phosphorylation by CDK7 of transcription initiation factor TFIIH 1-3 . By using multivalent interactions to create a phase-separated functional compartment, the histidine-rich domain in kinases targets the CTD into this environment to ensure hyperphosphorylation and efficient elongation of Pol II.

Stratigraphy and Melt Compositions of the 3.6 and 6.7 ka Plinian Eruptions of Hudson Volcano, Chile.

NASA Astrophysics Data System (ADS)

Carey, S.; Scasso, R.; Kratzmann, D.; Naranjo, J.; Bande, A.

2005-12-01

Fallout deposits from two major Holocene eruptions of Hudson Volcano in southern Chile (3.6 ka and 6.7 ka BP, Naranjo and Stern, 1998) provide new evidence for multiple phases, including subplinian to plinian discharges and episodes of phreatomagmatic activity. Four phases have been identified for the 3.6 ka eruption. The melt was trachydacitic and did not exhibit any significant variation throughout the fall sequence. Phase one (P1) produced a commonly reverse graded, lapilli fall deposit. Phase two (P2) also produced a reverse graded, coarse lapilli fall layer. Phase three (P3) deposited a massive, poorly-sorted, silty-ash layer with pumice and minor accretionary lapilli. The final phase of the eruption (P4) laid down a commonly normal graded, coarse lapilli fall deposit. Phases P1, P2 and P4 represent fallout from high altitude plumes with minor intensity fluctuations, whereas P3 resulted from magma/water interactions and a lower eruption column. Isopach maps show a shift in the main dispersal axis for the 3.6 ka phreatomagmatic ashfall (P3), relative to the lapilli deposits. Phases 1, 2 and 4 trend generally to the east, whereas the axis for the P3 fallout trends northeast. This is likely caused by dispersal of material at different altitudes during the eruption and not a general change in the predominant wind direction. Three major phases (P1 to P3) were identified for the 6.7 ka eruption. The initial phase (P1) produced a commonly reverse graded, coarse lapilli fall deposit. The second phase (P2) produced a thick, distinctive accretionary lapilli-rich, silty-ash layer with accretionary lapilli diameters up to 2.3 cm at 35 kms from the volcano. The final phase (P3) laid down an often normal graded, coarse lapilli fall unit. The melt phase was also trachydacitic in composition and relatively uniform during the eruption, but less evolved than the magma erupted during the 3.6 ka event. The accretionary lapilli layer (P2) has been correlated with a widespread tephra in southern Patagonia, 900km to the south of Hudson volcano with an estimated bulk volume more than 18 km3 making this one of the largest Holocene eruptions in southern South America (Naranjo et al. 2001). The occurrence of extensive, fine grained accretionary lapilli-bearing beds within these two plinian eruption sequences may be related to magma/meltwater interactions triggered by eruption discharge through the summit glacier of Hudson volcano, probably related to the formation of its last superimposed or partially nested caldera (Orihashi et al., 2004).

Aromatic sulfonation with sulfur trioxide: mechanism and kinetic model.

PubMed

Moors, Samuel L C; Deraet, Xavier; Van Assche, Guy; Geerlings, Paul; De Proft, Frank

2017-01-01

Electrophilic aromatic sulfonation of benzene with sulfur trioxide is studied with ab initio molecular dynamics simulations in gas phase, and in explicit noncomplexing (CCl 3 F) and complexing (CH 3 NO 2 ) solvent models. We investigate different possible reaction pathways, the number of SO 3 molecules participating in the reaction, and the influence of the solvent. Our simulations confirm the existence of a low-energy concerted pathway with formation of a cyclic transition state with two SO 3 molecules. Based on the simulation results, we propose a sequence of elementary reaction steps and a kinetic model compatible with experimental data. Furthermore, a new alternative reaction pathway is proposed in complexing solvent, involving two SO 3 and one CH 3 NO 2 .

Investigation of island formation due to RMPs in DIII-D plasmas with the SIESTA resistive MHD equilibrium code

NASA Astrophysics Data System (ADS)

Hirshman, S. P.; Shafer, M. W.; Seal, S. K.; Canik, J. M.

2016-04-01

> The SIESTA magnetohydrodynamic (MHD) equilibrium code has been used to compute a sequence of ideally stable equilibria resulting from numerical variation of the helical resonant magnetic perturbation (RMP) applied to an axisymmetric DIII-D plasma equilibrium. Increasing the perturbation strength at the dominant , resonant surface leads to lower MHD energies and increases in the equilibrium island widths at the (and sidebands) surfaces, in agreement with theoretical expectations. Island overlap at large perturbation strengths leads to stochastic magnetic fields which correlate well with the experimentally inferred field structure. The magnitude and spatial phase (around the dominant rational surfaces) of the resonant (shielding) component of the parallel current are shown to change qualitatively with the magnetic island topology.

Influence of the Heterogeneous Nucleation Sites on the Kinetics of Intermetallic Phase Formation in Aged Duplex Stainless Steel

NASA Astrophysics Data System (ADS)

Melo, Elis Almeida; Magnabosco, Rodrigo

2017-11-01

The aim of this work is to study the influence of the heterogeneous nucleation site quantity, observed in different ferrite and austenite grain size samples, on the phase transformations that result in intermetallic phases in a UNS S31803 duplex stainless steel (DSS). Solution treatment was conducted for 1, 24, 96, or 192 hours at 1373 K (1100 °C) to obtain different ferrite and austenite grain sizes. After solution treatment, isothermal aging treatments for 5, 8, 10, 20, 30, or 60 minutes at 1123 K (850 °C) were performed to verify the influence of different amounts of heterogeneous nucleation sites in the kinetics of intermetallic phase formation. The sample solution treated for 1 hour, with the highest surface area between matrix phases, was the one that presented, after 60 minutes at 1123 K (850 °C), the smaller volume fraction of ferrite (indicative of greater intermetallic phase formation), higher volume of sigma (that was present in coral-like and compact morphologies), and chi phase. It was not possible to identify which was the first nucleated phase, sigma or chi. It was also observed that the phase formation kinetics is higher for the sample solution treated for 1 hour. It was evidenced that, from a certain moment on, the chi phase begins to be consumed due to the sigma phase formation, and the austenite/ferrite interface presents higher S V for all solution treatment times. It was also observed that intermetallic phases form preferably in austenite-ferrite interfaces, although the higher occupation rate occurs at triple junction ferrite-ferrite-ferrite. It was verified that there was no saturation of nucleation sites in any interface type nor triple junction, and the equilibrium after 1 hour of aging at 1123 K (850 °C) was not achieved. It was then concluded that sigma phase formation is possibly controlled by diffusional processes, without saturation of nucleation sites.

Dynamic learning and context-dependence in sequential, attribute-based, stated-preference valuation questions

Treesearch

Thomas P. Holmes; Kevin J. Boyle

2005-01-01

A hybrid stated-preference model is presented that combines the referendum contingent valuation response format with an experimentally designed set of attributes. A sequence of valuation questions is asked to a random sample in a mailout mail-back format. Econometric analysis shows greater discrimination between alternatives in the final choice in the sequence, and the...

Sequencing Adventure Activities: A New Perspective.

ERIC Educational Resources Information Center

Bisson, Christian

Sequencing in adventure education involves putting activities in an order appropriate to the needs of the group. Contrary to the common assumption that each adventure sequence is unique, a review of literature concerning five sequencing models reveals a certain universality. These models present sequences that move through four phases: group…

H-Bond Self-Assembly: Folding versus Duplex Formation.

PubMed

Núñez-Villanueva, Diego; Iadevaia, Giulia; Stross, Alexander E; Jinks, Michael A; Swain, Jonathan A; Hunter, Christopher A

2017-05-17

Linear oligomers equipped with complementary H-bond donor (D) and acceptor (A) sites can interact via intermolecular H-bonds to form duplexes or fold via intramolecular H-bonds. These competing equilibria have been quantified using NMR titration and dilution experiments for seven systems featuring different recognition sites and backbones. For all seven architectures, duplex formation is observed for homo-sequence 2-mers (AA·DD) where there are no competing folding equilibria. The corresponding hetero-sequence AD 2-mers also form duplexes, but the observed self-association constants are strongly affected by folding equilibria in the monomeric states. When the backbone is flexible (five or more rotatable bonds separating the recognition sites), intramolecular H-bonding is favored, and the folded state is highly populated. For these systems, the stability of the AD·AD duplex is 1-2 orders of magnitude lower than that of the corresponding AA·DD duplex. However, for three architectures which have more rigid backbones (fewer than five rotatable bonds), intramolecular interactions are not observed, and folding does not compete with duplex formation. These systems are promising candidates for the development of longer, mixed-sequence synthetic information molecules that show sequence-selective duplex formation.

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.

PubMed

Habegger, Lukas; Sboner, Andrea; Gianoulis, Tara A; Rozowsky, Joel; Agarwal, Ashish; Snyder, Michael; Gerstein, Mark

2011-01-15

The advent of next-generation sequencing for functional genomics has given rise to quantities of sequence information that are often so large that they are difficult to handle. Moreover, sequence reads from a specific individual can contain sufficient information to potentially identify and genetically characterize that person, raising privacy concerns. In order to address these issues, we have developed the Mapped Read Format (MRF), a compact data summary format for both short and long read alignments that enables the anonymization of confidential sequence information, while allowing one to still carry out many functional genomics studies. We have developed a suite of tools (RSEQtools) that use this format for the analysis of RNA-Seq experiments. These tools consist of a set of modules that perform common tasks such as calculating gene expression values, generating signal tracks of mapped reads and segmenting that signal into actively transcribed regions. Moreover, the tools can readily be used to build customizable RNA-Seq workflows. In addition to the anonymization afforded by MRF, this format also facilitates the decoupling of the alignment of reads from downstream analyses. RSEQtools is implemented in C and the source code is available at http://rseqtools.gersteinlab.org/.

Flexible theta sequence compression mediated via phase precessing interneurons

PubMed Central

Chadwick, Angus; van Rossum, Mark CW; Nolan, Matthew F

2016-01-01

Encoding of behavioral episodes as spike sequences during hippocampal theta oscillations provides a neural substrate for computations on events extended across time and space. However, the mechanisms underlying the numerous and diverse experimentally observed properties of theta sequences remain poorly understood. Here we account for theta sequences using a novel model constrained by the septo-hippocampal circuitry. We show that when spontaneously active interneurons integrate spatial signals and theta frequency pacemaker inputs, they generate phase precessing action potentials that can coordinate theta sequences in place cell populations. We reveal novel constraints on sequence generation, predict cellular properties and neural dynamics that characterize sequence compression, identify circuit organization principles for high capacity sequential representation, and show that theta sequences can be used as substrates for association of conditioned stimuli with recent and upcoming events. Our results suggest mechanisms for flexible sequence compression that are suited to associative learning across an animal’s lifespan. DOI: http://dx.doi.org/10.7554/eLife.20349.001 PMID:27929374

KMOS3D Reveals Low-level Star Formation Activity in Massive Quiescent Galaxies at 0.7 < z < 2.7

NASA Astrophysics Data System (ADS)

Belli, Sirio; Genzel, Reinhard; Förster Schreiber, Natascha M.; Wisnioski, Emily; Wilman, David J.; Wuyts, Stijn; Mendel, J. Trevor; Beifiori, Alessandra; Bender, Ralf; Brammer, Gabriel B.; Burkert, Andreas; Chan, Jeffrey; Davies, Rebecca L.; Davies, Ric; Fabricius, Maximilian; Fossati, Matteo; Galametz, Audrey; Lang, Philipp; Lutz, Dieter; Momcheva, Ivelina G.; Nelson, Erica J.; Saglia, Roberto P.; Tacconi, Linda J.; Tadaki, Ken-ichi; Übler, Hannah; van Dokkum, Pieter

2017-05-01

We explore the Hα emission in the massive quiescent galaxies observed by the KMOS3D survey at 0.7 < z < 2.7. The Hα line is robustly detected in 20 out of 120 UVJ-selected quiescent galaxies, and we classify the emission mechanism using the Hα line width and the [N II]/Hα line ratio. We find that AGNs are likely to be responsible for the line emission in more than half of the cases. We also find robust evidence for star formation activity in nine quiescent galaxies, which we explore in detail. The Hα kinematics reveal rotating disks in five of the nine galaxies. The dust-corrected Hα star formation rates are low (0.2-7 M ⊙ yr-1), and place these systems significantly below the main sequence. The 24 μm-based, infrared luminosities, instead, overestimate the star formation rates. These galaxies present a lower gas-phase metallicity compared to star-forming objects with similar stellar mass, and many of them have close companions. We therefore conclude that the low-level star formation activity in these nine quiescent galaxies is likely to be fueled by inflowing gas or minor mergers, and could be a sign of rejuvenation events. Based on observations collected at the European Southern Observatory under programs 092.A-0091, 093.A-0079, 094.A-0217, 095.A-0047, 096.A-0025, and 097.A-0028.

Sequential processing of quantitative phase images for the study of cell behaviour in real-time digital holographic microscopy.

PubMed

Zikmund, T; Kvasnica, L; Týč, M; Křížová, A; Colláková, J; Chmelík, R

2014-11-01

Transmitted light holographic microscopy is particularly used for quantitative phase imaging of transparent microscopic objects such as living cells. The study of the cell is based on extraction of the dynamic data on cell behaviour from the time-lapse sequence of the phase images. However, the phase images are affected by the phase aberrations that make the analysis particularly difficult. This is because the phase deformation is prone to change during long-term experiments. Here, we present a novel algorithm for sequential processing of living cells phase images in a time-lapse sequence. The algorithm compensates for the deformation of a phase image using weighted least-squares surface fitting. Moreover, it identifies and segments the individual cells in the phase image. All these procedures are performed automatically and applied immediately after obtaining every single phase image. This property of the algorithm is important for real-time cell quantitative phase imaging and instantaneous control of the course of the experiment by playback of the recorded sequence up to actual time. Such operator's intervention is a forerunner of process automation derived from image analysis. The efficiency of the propounded algorithm is demonstrated on images of rat fibrosarcoma cells using an off-axis holographic microscope. © 2014 The Authors Journal of Microscopy © 2014 Royal Microscopical Society.

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.

The role of Mesozoic sedimentary basin tapers on the formation of Cenozoic crustal shortening structures and foredeep in the western Sichuan Basin, China

NASA Astrophysics Data System (ADS)

Wang, M.

2017-12-01

The foreland basin records important clues of tectonic and sedimentary process of mountain-building, thus to explore its dynamic mechanism on the formation is an important issue of the mountain-basin interaction. The Longmen Shan fold-and-thrust belt and its adjacent Sichuan basin located in the eastern margin of Tibetan Plateau, are one of the most-concerned regions of studying modern mountain-building and seismic process, and are also a natural laboratory of studying the dynamics of the formation and development of foreland basin. However, it still need further explore on the mechanics of the development of the Cenozoic foreland basin and thrust-belts in the western Sichuan Basin. The Longmen Shan thrust belt has experienced multi-stages of tectonics evolution, foreland basin formation and topography growth since Late Triassic, and whether the early formed basin architecture and large Mesozoic sedimentary basin taper can influence the formation and development of the Cenozoic foreland basin and thrust belts? To solve these issues, this project aim to focus on the Cenozoic foreland basin and internal crustal shortening structures in the western Sichuan basin, on the basis of growth critical wedge taper theory. We will reconstruct the shape of multi-phases of sedimentary basin tapers, the temporal-spatial distribution of crustal shortening and thrusting sequences, and analyze the control mechanism of Mesozoic sedimentary basin taper on the formation of Cenozoic foreland basins, and final explore the interaction between the tectonics geomorphology, stress field and dynamic propagation of foreland basin.

The Cold Side of Galaxy Formation: Dense Gas Through Cosmic Time

NASA Astrophysics Data System (ADS)

Riechers, Dominik A.; ngVLA Galaxy Assembly through Cosmic Time Science Working Group, ngVLA Galaxy Ecosystems Science Working Group

2018-01-01

The processes that lead to the formation and evolution of galaxies throughout the history of the Universe involve the complex interplay between hierarchical merging of dark matter halos, accretion of primordial and recycled gas, transport of gas within galaxy disks, accretion onto central super-massive black holes, and the formation of molecular clouds which subsequently collapse and fragment. The resulting star formation and black hole accretion provide large sources of energy and momentum that light up galaxies and lead to feedback. The ngVLA will be key to further understand how gas is accreted onto galaxies, and the processes that regulate the growth of galaxies through cosmic history. It will reveal how and on which timescales star formation and black hole accretion impact the gas in galaxies, and how the physical properties and chemical state of the gas change as gas cycles between different phases for different galaxy populations over a broad range in redshifts. The ngVLA will have the capability to carry out unbiased, large cosmic volume surveys at virtually any redshift down to an order of magnitude lower gas masses than currently possible in the critical low-level CO lines, thus exposing the evolution of gaseous reservoirs from the earliest epochs to the peak of the cosmic history of star formation. It will also image routinely and systematically the sub-kiloparsec scale distribution and kinematic structure of molecular gas in both normal main-sequence galaxies and large starbursts. The ngVLA thus is poised to revolutionize our understanding of galaxy evolution through cosmic time.

Protocol optimization of sacroiliac joint MR Imaging at 3 Tesla: Impact of coil design and motion resistant sequences on image quality.

PubMed

Gondim Teixeira, P A; Bravetti, M; Hossu, G; Lecocq, S; Petit, D; Loeuille, D; Blum, A

2017-12-01

To evaluate the impact of coil design and motion-resistant sequences on the quality of sacroiliac magnetic resonance imaging (MRI) examination in patients with spondyloarthropathy. One hundred and twenty-one patients with suspected sacroiliitis and referred for MRI of the sacroiliac joints were retrospectively evaluated with MRI at 3-Tesla. There were 78 women and 43 men with a mean age of 36.7±11.5 (SD) years (range: 15.8-78.4 years). Conventional and motion-resistant fat-saturated fast-spin echo T2-weighted sequences were performed with two different coils. Image quality was subjectively evaluated by two independent readers (R1 and R2) using a four-point scale. Confidence in the identification of bone marrow edema pattern (BMEP) was also evaluated subjectively using a three-point scale. Phased array body coil yielded improved image quality compared to surface coil (14.1 to 30.4% for R1 and 14.6 to 25.7% for R2; P<0.0001). The impact of the sequence type on quality was also statistically significant (P=0.0046). BMEP was identified in 40 patients and best inter-reader agreement was obtained using the combination of phased-array body coil with motion-resistant T2-weighted sequence (kappa 0.990). The smallest number of indeterminate BMEP zones was seen on MRI set acquired with the phased-array body coil and motion-resistant T2-weighted sequence. Phased array body coil and motion-resistant T2-weighted sequences perform better than surface coil and conventional T2-weighted sequences for the evaluation of sacroiliac joints, increasing confidence in the identification of BMEP. Copyright © 2017 Editions françaises de radiologie. Published by Elsevier Masson SAS. All rights reserved.

Similar star formation rate and metallicity variability time-scales drive the fundamental metallicity relation

NASA Astrophysics Data System (ADS)

Torrey, Paul; Vogelsberger, Mark; Hernquist, Lars; McKinnon, Ryan; Marinacci, Federico; Simcoe, Robert A.; Springel, Volker; Pillepich, Annalisa; Naiman, Jill; Pakmor, Rüdiger; Weinberger, Rainer; Nelson, Dylan; Genel, Shy

2018-06-01

The fundamental metallicity relation (FMR) is a postulated correlation between galaxy stellar mass, star formation rate (SFR), and gas-phase metallicity. At its core, this relation posits that offsets from the mass-metallicity relation (MZR) at a fixed stellar mass are correlated with galactic SFR. In this Letter, we use hydrodynamical simulations to quantify the time-scales over which populations of galaxies oscillate about the average SFR and metallicity values at fixed stellar mass. We find that Illustris and IllustrisTNG predict that galaxy offsets from the star formation main sequence and MZR oscillate over similar time-scales, are often anticorrelated in their evolution, evolve with the halo dynamical time, and produce a pronounced FMR. Our models indicate that galaxies oscillate about equilibrium SFR and metallicity values - set by the galaxy's stellar mass - and that SFR and metallicity offsets evolve in an anticorrelated fashion. This anticorrelated variability of the metallicity and SFR offsets drives the existence of the FMR in our models. In contrast to Illustris and IllustrisTNG, we speculate that the SFR and metallicity evolution tracks may become decoupled in galaxy formation models dominated by feedback-driven globally bursty SFR histories, which could weaken the FMR residual correlation strength. This opens the possibility of discriminating between bursty and non-bursty feedback models based on the strength and persistence of the FMR - especially at high redshift.

SPATIALLY RESOLVED STAR FORMATION MAIN SEQUENCE OF GALAXIES IN THE CALIFA SURVEY

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

Cano-Díaz, M.; Sánchez, S. F.; Zibetti, S.

2016-04-20

The “main sequence of galaxies”–defined in terms of the total star formation rate ψ versus the total stellar mass M {sub *}—is a well-studied tight relation that has been observed at several wavelengths and at different redshifts. All earlier studies have derived this relation from integrated properties of galaxies. We recover the same relation from an analysis of spatially resolved properties, with integral field spectroscopic (IFS) observations of 306 galaxies from the CALIFA survey. We consider the SFR surface density in units of log( M {sub ⊙} yr{sup −1} Kpc{sup −2}) and the stellar mass surface density in units ofmore » log( M {sub ⊙} Kpc{sup −2}) in individual spaxels that probe spatial scales of 0.5–1.5 Kpc. This local relation exhibits a high degree of correlation with small scatter ( σ = 0.23 dex), irrespective of the dominant ionization source of the host galaxy or its integrated stellar mass. We highlight (i) the integrated star formation main sequence formed by galaxies whose dominant ionization process is related to star formation, for which we find a slope of 0.81 ± 0.02; (ii) for the spatially resolved relation obtained with the spaxel analysis, we find a slope of 0.72 ± 0.04; and (iii) for the integrated main sequence, we also identified a sequence formed by galaxies that are dominated by an old stellar population, which we have called the retired galaxies sequence.« less

The origin of diverse α-element abundances in galaxy discs

NASA Astrophysics Data System (ADS)

Mackereth, J. Ted; Crain, Robert A.; Schiavon, Ricardo P.; Schaye, Joop; Theuns, Tom; Schaller, Matthieu

2018-07-01

Spectroscopic surveys of the Galaxy reveal that its disc stars exhibit a spread in [α/Fe] at fixed [Fe/H], manifest at some locations as a bimodality. The origin of these diverse, and possibly distinct, stellar populations in the Galactic disc is not well understood. We examine the Fe and α-element evolution of 133 Milky Way-like galaxies from the EAGLE simulation, to investigate the origin and diversity of their [α/Fe]-[Fe/H] distributions. We find that bimodal [α/Fe] distributions arise in galaxies whose gas accretion histories exhibit episodes of significant infall at both early and late times, with the former fostering more intense star formation than the latter. The shorter characteristic consumption time-scale of gas accreted in the earlier episode suppresses its enrichment with iron synthesized by Type Ia SNe, resulting in the formation of a high-[α/Fe] sequence. We find that bimodality in [α/Fe] similar to that seen in the Galaxy is rare, appearing in approximately 5 per cent of galaxies in our sample. We posit that this is a consequence of an early gas accretion episode requiring the mass accretion history of a galaxy's dark matter halo to exhibit a phase of atypically rapid growth at early epochs. The scarcity of EAGLE galaxies exhibiting distinct sequences in the [α/Fe]-[Fe/H] plane may therefore indicate that the Milky Way's elemental abundance patterns, and its accretion history, are not representative of the broader population of ˜L⋆ disc galaxies.

The origin of diverse α-element abundances in galaxy discs

NASA Astrophysics Data System (ADS)

Mackereth, J. Ted; Crain, Robert A.; Schiavon, Ricardo P.; Schaye, Joop; Theuns, Tom; Schaller, Matthieu

2018-04-01

Spectroscopic surveys of the Galaxy reveal that its disc stars exhibit a spread in [α/Fe] at fixed [Fe/H], manifest at some locations as a bimodality. The origin of these diverse, and possibly distinct, stellar populations in the Galactic disc is not well understood. We examine the Fe and α-element evolution of 133 Milky Way-like galaxies from the EAGLE simulation, to investigate the origin and diversity of their [α/Fe]-[Fe/H] distributions. We find that bimodal [α/Fe] distributions arise in galaxies whose gas accretion histories exhibit episodes of significant infall at both early and late times, with the former fostering more intense star formation than the latter. The shorter characteristic consumption timescale of gas accreted in the earlier episode suppresses its enrichment with iron synthesised by Type Ia SNe, resulting in the formation of a high-[α/Fe] sequence. We find that bimodality in [α/Fe] similar to that seen in the Galaxy is rare, appearing in approximately 5 percent of galaxies in our sample. We posit that this is a consequence of an early gas accretion episode requiring the mass accretion history of a galaxy's dark matter halo to exhibit a phase of atypically-rapid growth at early epochs. The scarcity of EAGLE galaxies exhibiting distinct sequences in the [α/Fe]-[Fe/H] plane may therefore indicate that the Milky Way's elemental abundance patterns, and its accretion history, are not representative of the broader population of ˜L⋆ disc galaxies.

A ceramic/slag interface as an analog for accretion of hot refractory objects and rim formation

NASA Technical Reports Server (NTRS)

Paque, J. M.; Bunch, T. E.

1994-01-01

Refractory inclusions or Ca-Al-rich inclusions (CAI's) from carbonaceous chondrites span a wide range of bulk compositions that cannot be explained either by segregation from a gas of solar composition at different points in the condensation sequence or by fractional crystallization from a parent liquid. CAI's are commonly rimmed by Wark-Lovering (W-L) rims, a series of nearly monomineralic layers that have been a source of controversy since the variety of rim sequences occurring on different types of CAI's from Allende were described. The origin of these distinctive features has not yet been resolved, with proponents of accretion, condensation, flash heating, ablation, evaporation, etc. Rims have generated considerable interest because they potentially contain clues to conditions experienced by CAI's after the formation of the inclusion and prior to incorporation into the parent body. Ceramic bricks in contact with hot steel slag may produce reaction products in rimlike fashion similar to those found in CAI's. The similarity between the mineralogy of blast furnace slags and CAI's has long been recognized, with both containing unusual phases not found in terrestrial materials. We provide here a comparison between a ceramic brick/slag multiple-layered interface and a multiple-layered interface between a melilite-perovskite object and a melilite-spinel object in the Allende inclusion USNM 4691-1. These results have implications in interpreting the origin of rims and the textures and compositions of CAI's.

Aerobic granulation in a sequencing batch reactor (SBR) for industrial wastewater treatment.

PubMed

Inizan, M; Freval, A; Cigana, J; Meinhold, J

2005-01-01

Aerobic granulation seems to be an a attractive process for COD removal from industrial wastewater, characterised by a high content of soluble organic compounds. In order to evaluate the practical aspects of the process, comparative experimental tests are performed on synthetic and on industrial wastewater, originating from pharmaceutical industry. Two pilot plants are operated as sequencing batch bubble columns. Focus was put on the feasibility of the process for high COD removal and on its operational procedure. For both wastewaters, a rapid formation of aerobic granules is observed along with a high COD removal rate. Granule characteristics are quite similar with respect to the two types of wastewater. It seems that filamentous bacteria are part of the granule structure and that phosphorus precipitation can play an important role in granule formation. For both wastewaters similar removal performances for dissolved biodegradable COD are observed (> 95%). However, a relatively high concentration of suspended solids in the outlet deteriorates the performance with regard to total COD removal. Biomass detachment seems to play a non-negligible role in the current set-up. After a stable operational phase the variation of the pharmaceutical wastewater caused a destabilisation and loss of the granules, despite the control for balanced nutrient supply. The first results with real industrial wastewater demonstrate the feasibility of this innovative process. However, special attention has to be paid to the critical aspects such as granule stability as well as the economic competitiveness, which both will need further investigation and evaluation.

OPTICAL–INFRARED PROPERTIES OF FAINT 1.3 mm SOURCES DETECTED WITH ALMA

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

Hatsukade, Bunyo; Yabe, Kiyoto; Ohta, Kouji

2015-09-10

We report optical-infrared (IR) properties of faint 1.3 mm sources (S{sub 1.3mm} = 0.2–1.0 mJy) detected with the Atacama Large Millimeter/submillimeter Array (ALMA) in the Subaru/XMM-Newton Deep Survey field. We searched for optical/IR counterparts of eight ALMA-detected sources (≥4.0σ, the sum of the probability of spurious source contamination is ∼1) in a K-band source catalog. Four ALMA sources have K-band counterpart candidates within a 0.″4 radius. Comparison between ALMA-detected and undetected K-band sources in the same observing fields shows that ALMA-detected sources tend to be brighter, more massive, and more actively forming stars. While many of the ALMA-identified submillimeter-bright galaxiesmore » (SMGs) in previous studies lie above the sequence of star-forming galaxies in the stellar mass–star formation rate plane, our ALMA sources are located in the sequence, suggesting that the ALMA-detected faint sources are more like “normal” star-forming galaxies rather than “classical” SMGs. We found a region where multiple ALMA sources and K-band sources reside in a narrow photometric redshift range (z ∼ 1.3–1.6) within a radius of 5″ (42 kpc if we assume z = 1.45). This is possibly a pre-merging system and we may be witnessing the early phase of formation of a massive elliptical galaxy.« less

Automated array assembly, phase 2

NASA Technical Reports Server (NTRS)

Daiello, R. V.

1980-01-01

A manufacturing sequence which is capable of mass producing silicon solar cells is described. The sequence was arrived at after the evaluation of many processes and three related manufacturing sequences which are discussed.

Palaeoenvironments during MIS 3 and MIS 2 inferred from lacustrine intercalations in the loess-palaeosol sequence at Bobingen (southern Germany)

NASA Astrophysics Data System (ADS)

Mayr, Christoph; Matzke-Karasz, Renate; Stojakowits, Philipp; Lowick, Sally E.; Zolitschka, Bernd; Heigl, Tanja; Mollath, Richard; Theuerkauf, Marian; Weckend, Marc-Oliver; Bäumler, Rupert; Gregor, Hans-Joachim

2017-12-01

Recently exposed loess-palaeosol sequences in the northern Alpine foreland close to Bobingen (southern Germany) were investigated with a multi-proxy approach combining isotopic, geochemical, lithological, and micropalaeontological methods. Luminescence ages date the sections into the Middle and Upper Würmian periods corresponding to Marine Isotope Stages 3 and 2. A gleyic soil horizon at the base was dated to 45 ka and provided a palynoflora dominated by Poaceae, Cyperaceae, and Pinus, as well as frequent aquatic taxa. Lacustrine conditions prevailed after the gley formation until 30 ka, providing a comparatively diverse lacustrine fauna dominated by aquatic gastropods and the ostracod species Candona candida. At the transition to the Upper Würm, climatic conditions became harsh, indicated by accelerated deposition of more coarse-grained loess, organic geochemical indicators, and scarceness of biotic remains. Two tundra-gley horizons in the Upper Würm point to short phases of climatic amelioration with higher humidity also evidenced by reoccurrence of ostracod and aquatic gastropod remains. We propose that these climatic ameliorations were coincident with the Greenland interstadials 4 and 2.

Influence of NiO on the crystallization kinetics of near stoichiometric cordierite glasses nucleated with TiO2

NASA Astrophysics Data System (ADS)

Goel, Ashutosh; Shaaban, Essam R.; Ribeiro, Manuel J.; Melo, Francisco C. L.; Ferreira, José M. F.

2007-09-01

This work presents the effect of NiO on the thermal behavior and the crystallization kinetics of glasses lying near the stoichiometric cordierite composition nucleated with TiO2. Three glasses with NiO content varying between 1 and 5 mol% have been synthesized in Pt crucibles. Activation energies for structural relaxation and viscous flow have been calculated using the data obtained from differential thermal analysis (DTA). Kinetic fragility of the glasses along with other thermal parameters has been calculated. Non-isothermal crystallization kinetic studies have been employed to study the mechanism of crystallization in all three glasses. The crystallization sequence in the glasses has been followed by x-ray diffraction analysis of the heat treated glass samples in the temperature range of 800-1200 °C. μ-cordierite has been observed to be the first crystalline phase in all the glass samples after heat treatment at 850 °C, while NiO plays an important role in determining the crystallization sequence at higher temperatures, leading to the formation of α-cordierite.

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

WANG,YIFENG; XU,HUIFANG

Correctly identifying the possible alteration products and accurately predicting their occurrence in a repository-relevant environment are the key for the source-term calculation in a repository performance assessment. Uraninite in uranium deposits has long been used as a natural analog to spent fuel in a repository because of their chemical and structural similarity. In this paper, a SEM/AEM investigation has been conducted on a partially alternated uraninite sample from a uranium ore deposit of Shinkolobwe of Congo. The mineral formation sequences were identified: uraninite {yields} uranyl hydrates {yields} uranyl silicates {yields} Ca-uranyl silicates or uraninite {yields} uranyl silicates {yields} Ca-uranyl silicates.more » Reaction-path calculations were conducted for the oxidative dissolution of spent fuel in a representative Yucca Mountain groundwater. The predicted sequence is in general consistent with the SEM observations. The calculations also show that uranium carbonate minerals are unlikely to become major solubility-controlling mineral phases in a Yucca Mountain environment. Some discrepancies between model predictions and field observations are observed. Those discrepancies may result from poorly constrained thermodynamic data for uranyl silicate minerals.« less

From starburst to quiescence: testing active galactic nucleus feedback in rapidly quenching post-starburst galaxies

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

Yesuf, Hassen M.; Faber, S. M.; Trump, Jonathan R.

Post-starbursts are galaxies in transition from the blue cloud to the red sequence. Although they are rare today, integrated over time they may be an important pathway to the red sequence. This work uses Sloan Digital Sky Survey, the Galaxy Evolution Explorer, and Wide-field Infrared Survey Explorer observations to identify the evolutionary sequence from starbursts to fully quenched post-starbursts (QPSBs) in the narrow mass range log M(M {sub ☉}) = 10.3-10.7, and identifies 'transiting' post-starbursts (TPSBs) which are intermediate between these two populations. In this mass range, ∼0.3% of galaxies are starbursts, ∼0.1% are QPSBs, and ∼0.5% are the transitingmore » types in between. The TPSBs have stellar properties that are predicted for fast-quenching starbursts and morphological characteristics that are already typical of early-type galaxies. The active galactic nucleus (AGN) fraction, as estimated from optical line ratios, of these post-starbursts is about three times higher (≳ 36% ± 8%) than that of normal star forming galaxies of the same mass, but there is a significant delay between the starburst phase and the peak of nuclear optical AGN activity (median age difference of ≳ 200 ± 100 Myr), in agreement with previous studies. The time delay is inferred by comparing the broadband near-NUV-to-optical photometry with stellar population synthesis models. We also find that starbursts and post-starbursts are significantly more dust obscured than normal star forming galaxies in the same mass range. About 20% of the starbursts and 15% of the TPSBs can be classified as 'dust-obscured galaxies' (DOGs), with a near-UV-to-mid-IR flux ratio of ≳ 900, while only 0.8% of normal galaxies are DOGs. The time delay between the starburst phase and AGN activity suggests that AGNs do not play a primary role in the original quenching of starbursts but may be responsible for quenching later low-level star formation by removing gas and dust during the post-starburst phase.« less

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.

SequenceCEROSENE: a computational method and web server to visualize spatial residue neighborhoods at the sequence level.

PubMed

Heinke, Florian; Bittrich, Sebastian; Kaiser, Florian; Labudde, Dirk

2016-01-01

To understand the molecular function of biopolymers, studying their structural characteristics is of central importance. Graphics programs are often utilized to conceive these properties, but with the increasing number of available structures in databases or structure models produced by automated modeling frameworks this process requires assistance from tools that allow automated structure visualization. In this paper a web server and its underlying method for generating graphical sequence representations of molecular structures is presented. The method, called SequenceCEROSENE (color encoding of residues obtained by spatial neighborhood embedding), retrieves the sequence of each amino acid or nucleotide chain in a given structure and produces a color coding for each residue based on three-dimensional structure information. From this, color-highlighted sequences are obtained, where residue coloring represent three-dimensional residue locations in the structure. This color encoding thus provides a one-dimensional representation, from which spatial interactions, proximity and relations between residues or entire chains can be deduced quickly and solely from color similarity. Furthermore, additional heteroatoms and chemical compounds bound to the structure, like ligands or coenzymes, are processed and reported as well. To provide free access to SequenceCEROSENE, a web server has been implemented that allows generating color codings for structures deposited in the Protein Data Bank or structure models uploaded by the user. Besides retrieving visualizations in popular graphic formats, underlying raw data can be downloaded as well. In addition, the server provides user interactivity with generated visualizations and the three-dimensional structure in question. Color encoded sequences generated by SequenceCEROSENE can aid to quickly perceive the general characteristics of a structure of interest (or entire sets of complexes), thus supporting the researcher in the initial phase of structure-based studies. In this respect, the web server can be a valuable tool, as users are allowed to process multiple structures, quickly switch between results, and interact with generated visualizations in an intuitive manner. The SequenceCEROSENE web server is available at https://biosciences.hs-mittweida.de/seqcerosene.

The effects of stimulated star formation on the evolution of the galaxy. III - The chemical evolution of nonlinear systems

NASA Technical Reports Server (NTRS)

Shore, Steven N.; Ferrini, Federico; Palla, Francesco

1987-01-01

The evolution of models for star formation in galaxies with disk and halo components is discussed. Two phases for the halo (gas and stars) and three for the disk (including clouds) are used in these calculations. The star-formation history is followed using nonlinear phase-coupling models which completely determine the populations of the phases as a function of time. It is shown that for a wide range of parameters, including the effects of both spontaneous and stimulated star formation and mass exchange between the spatial components of the system, the observed chemical history of the galaxy can easily be obtained. The most sensitive parameter in the detailed metallicity and star-formation history for the system is the rate of return of gas to the diffuse phase upon stellar death.

Extrasolar binary planets. I. Formation by tidal capture during planet-planet scattering

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

Ochiai, H.; Nagasawa, M.; Ida, S., E-mail: nagasawa.m.ad@m.titech.ac.jp

2014-08-01

We have investigated (1) the formation of gravitationally bounded pairs of gas-giant planets (which we call 'binary planets') from capturing each other through planet-planet dynamical tide during their close encounters and (2) the subsequent long-term orbital evolution due to planet-planet and planet-star quasi-static tides. For the initial evolution in phase 1, we carried out N-body simulations of the systems consisting of three Jupiter-mass planets taking into account the dynamical tide. The formation rate of the binary planets is as much as 10% of the systems that undergo orbital crossing, and this fraction is almost independent of the initial stellarcentric semimajormore » axes of the planets, while ejection and merging rates sensitively depend on the semimajor axes. As a result of circularization by the planet-planet dynamical tide, typical binary separations are a few times the sum of the physical radii of the planets. After the orbital circularization, the evolution of the binary system is governed by long-term quasi-static tide. We analytically calculated the quasi-static tidal evolution in phase 2. The binary planets first enter the spin-orbit synchronous state by the planet-planet tide. The planet-star tide removes angular momentum of the binary motion, eventually resulting in a collision between the planets. However, we found that the binary planets survive the tidal decay for the main-sequence lifetime of solar-type stars (∼10 Gyr), if the binary planets are beyond ∼0.3 AU from the central stars. These results suggest that the binary planets can be detected by transit observations at ≳ 0.3 AU.« less

HerMES: The Far-infrared Emission from Dust-obscured Galaxies

NASA Astrophysics Data System (ADS)

Calanog, J. A.; Wardlow, J.; Fu, Hai; Cooray, A.; Assef, R. J.; Bock, J.; Casey, C. M.; Conley, A.; Farrah, D.; Ibar, E.; Kartaltepe, J.; Magdis, G.; Marchetti, L.; Oliver, S. J.; Pérez-Fournon, I.; Riechers, D.; Rigopoulou, D.; Roseboom, I. G.; Schulz, B.; Scott, Douglas; Symeonidis, M.; Vaccari, M.; Viero, M.; Zemcov, M.

2013-09-01

Dust-obscured galaxies (DOGs) are an ultraviolet-faint, infrared-bright galaxy population that reside at z ~ 2 and are believed to be in a phase of dusty star-forming and active galactic nucleus (AGN) activity. We present far-infrared (far-IR) observations of a complete sample of DOGs in the 2 deg2 of the Cosmic Evolution Survey. The 3077 DOGs have langzrang = 1.9 ± 0.3 and are selected from 24 μm and r + observations using a color cut of r + - [24] >= 7.5 (AB mag) and S 24 >= 100 μJy. Based on the near-IR spectral energy distributions, 47% are bump DOGs (star formation dominated) and 10% are power-law DOGs (AGN-dominated). We use SPIRE far-IR photometry from the Herschel Multi-tiered Extragalactic Survey to calculate the IR luminosity and characteristic dust temperature for the 1572 (51%) DOGs that are detected at 250 μm (>=3σ). For the remaining 1505 (49%) that are undetected, we perform a median stacking analysis to probe fainter luminosities. Herschel-detected and undetected DOGs have average luminosities of (2.8 ± 0.4) × 1012 L ⊙ and (0.77 ± 0.08) × 1012 L ⊙, and dust temperatures of (33 ± 7) K and (37 ± 5) K, respectively. The IR luminosity function for DOGs with S 24 >= 100 μJy is calculated, using far-IR observations and stacking. DOGs contribute 10%-30% to the total star formation rate (SFR) density of the universe at z = 1.5-2.5, dominated by 250 μm detected and bump DOGs. For comparison, DOGs contribute 30% to the SFR density for all z = 1.5-2.5 galaxies with S 24 >= 100 μJy. DOGs have a large scatter about the star formation main sequence and their specific SFRs show that the observed phase of star formation could be responsible for their total observed stellar mass at z ~ 2.

Determination of haplotypes at structurally complex regions using emulsion haplotype fusion PCR.

PubMed

Tyson, Jess; Armour, John A L

2012-12-11

Genotyping and massively-parallel sequencing projects result in a vast amount of diploid data that is only rarely resolved into its constituent haplotypes. It is nevertheless this phased information that is transmitted from one generation to the next and is most directly associated with biological function and the genetic causes of biological effects. Despite progress made in genome-wide sequencing and phasing algorithms and methods, problems assembling (and reconstructing linear haplotypes in) regions of repetitive DNA and structural variation remain. These dynamic and structurally complex regions are often poorly understood from a sequence point of view. Regions such as these that are highly similar in their sequence tend to be collapsed onto the genome assembly. This is turn means downstream determination of the true sequence haplotype in these regions poses a particular challenge. For structurally complex regions, a more focussed approach to assembling haplotypes may be required. In order to investigate reconstruction of spatial information at structurally complex regions, we have used an emulsion haplotype fusion PCR approach to reproducibly link sequences of up to 1kb in length to allow phasing of multiple variants from neighbouring loci, using allele-specific PCR and sequencing to detect the phase. By using emulsion systems linking flanking regions to amplicons within the CNV, this led to the reconstruction of a 59kb haplotype across the DEFA1A3 CNV in HapMap individuals. This study has demonstrated a novel use for emulsion haplotype fusion PCR in addressing the issue of reconstructing structural haplotypes at multiallelic copy variable regions, using the DEFA1A3 locus as an example.

An Attempt at Blocking of Position Learning by Training with Reward-Memory Associations

ERIC Educational Resources Information Center

Burns, Richard A.; Johnson, Kendra S.

2006-01-01

Rats were runway trained with sequences of rewards that changed in 3 phases. In Phase 1 (24 days), the sequences were NP', SNP', and P'SNP' (n = 3), or NS', PNS', and S'PNS', where P and P' refer to 4 and 8 plain Noyes pellets, and S and S' are 4 and 8 sucrose pellets. N was a 30-s confinement in the goal without reward. In Phase 2 (14 days) the…

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

Medina, J., E-mail: judit.medina@cenim.csic.es

The effects of calcium, manganese and cerium-rich mischmetal additions on the microstructure and texture of the extruded Mg−6Zn−1Y (wt.%) alloy have been investigated. The microstructure of the alloys consisted of a magnesium matrix embedding second phase particles aligned along the extrusion direction. The nature and volume fraction of the second phases depended on the alloying element. Thus, Ce-rich mischmetal promoted the formation of T-phase while calcium additions resulted in the formation of a ternary Mg−Zn−Ca compound. Only, manganese additions did not affect the existence of the I-phase present in the ternary alloy. The texture was measured and it was foundmore » that calcium addition has a significant effect weakening the extrusion texture. - Highlights: •In-situ HEXRD and DSC techniques are employed to identify phase transformations. •The existence of I-phase is not altered by manganese addition to Mg93Zn6Y1 (wt.%). •Calcium addition promotes Mg{sub 6}Zn{sub 3}Ca{sub 2} formation instead of I-phase. •Mischmetal addition induces the formation of coarse T-phase particles. •Texture depends on the nature of second phases and therefore of the extrusion pressure.« less

Regional stratigraphy, sedimentology, and tectonic significance of Oligocene-Miocene sedimentary and volcanic rocks, northern Baja California, Mexico

NASA Astrophysics Data System (ADS)

Dorsey, Rebecca J.; Burns, Beverly

1994-01-01

Upper Oligocene (?) to middle Miocene sedimentary and volcanic rocks in northern Baja California were deposited along the western margin of North America during subduction of the Guadalupe plate and southward migration of the Rivera Triple Junction. Regional mapping and compilation of stratigraphic data reveal a sequence of three regionally traceable stratigraphic units. (1) Oligocene (?) to lower Miocene Mesa Formation: basal quartz-rich fluvial sandstone, grus, conglomerate, and accessory facies, whose detrital compositions reflect the composition of local pre-Tertiary basement rock. (2) Lower to middle Miocene Comondú Formation: laterally variable sequence of volcaniclastic conglomerate, breccia, sandstone, tuff and minor volcanic flow units. (3) Widespread mesa-capping rhyolite tuff, typically welded and crystal-rich, probably upper Miocene in age. The Mesa Formation overlies a highly irregular and deeply dissected erosional surface developed on pre-Tertiary basement rock. The shift from pre-Mesa erosion to widespread (though localized) deposition and valley-filling records the final phase of late Cretaceous to middle Tertiary regional subsidence and eastward transgression that resulted from slow cooling and thermal contraction of Cretaceous arc crust during a temporal gap in magmatic activity along the western Cordilleran margin. Nonmarine sediments of the Mesa Formation were deposited in small, steep-walled paleovalleys and basins that gradually filled and evolved to form through-going, low-energy ephemeral stream systems. The gradational upward transition from the Mesa to Comondú Formation records the early to middle Miocene onset of subduction-related arc magmatism in eastern Baja California and related westward progradation of alluvial volcaniclastic aprons shed from high-standing eruptive volcanic centers. Pre-existing streams were choked with the new influx of volcanic detritus, causing the onset of rapid sediment deposition by stream flows and dilute to viscous sediment gravity flows. Deposits of the Comondú Formation thin and fine systematically westward, from proximal volcanic conglomerate and breccia with thin basalt and andesite flows in the east, to distal volcaniclastic fluvial sandstone in the west. These proximal—distal relationships help to define the location and paleogeography of active arc-flanking volcaniclastic alluvial aprons of the Miocene magmatic arc in northern Baja California. A substantial late Miocene drop in regional base level (relative sea level) is best attributed to regional uplift caused by the renewal of magmatic and thermal activity in northern Baja California, which has continued to the present day.

Long Read Alignment with Parallel MapReduce Cloud Platform

PubMed Central

Al-Absi, Ahmed Abdulhakim; Kang, Dae-Ki

2015-01-01

Genomic sequence alignment is an important technique to decode genome sequences in bioinformatics. Next-Generation Sequencing technologies produce genomic data of longer reads. Cloud platforms are adopted to address the problems arising from storage and analysis of large genomic data. Existing genes sequencing tools for cloud platforms predominantly consider short read gene sequences and adopt the Hadoop MapReduce framework for computation. However, serial execution of map and reduce phases is a problem in such systems. Therefore, in this paper, we introduce Burrows-Wheeler Aligner's Smith-Waterman Alignment on Parallel MapReduce (BWASW-PMR) cloud platform for long sequence alignment. The proposed cloud platform adopts a widely accepted and accurate BWA-SW algorithm for long sequence alignment. A custom MapReduce platform is developed to overcome the drawbacks of the Hadoop framework. A parallel execution strategy of the MapReduce phases and optimization of Smith-Waterman algorithm are considered. Performance evaluation results exhibit an average speed-up of 6.7 considering BWASW-PMR compared with the state-of-the-art Bwasw-Cloud. An average reduction of 30% in the map phase makespan is reported across all experiments comparing BWASW-PMR with Bwasw-Cloud. Optimization of Smith-Waterman results in reducing the execution time by 91.8%. The experimental study proves the efficiency of BWASW-PMR for aligning long genomic sequences on cloud platforms. PMID:26839887

Long Read Alignment with Parallel MapReduce Cloud Platform.

PubMed

Al-Absi, Ahmed Abdulhakim; Kang, Dae-Ki

2015-01-01

Genomic sequence alignment is an important technique to decode genome sequences in bioinformatics. Next-Generation Sequencing technologies produce genomic data of longer reads. Cloud platforms are adopted to address the problems arising from storage and analysis of large genomic data. Existing genes sequencing tools for cloud platforms predominantly consider short read gene sequences and adopt the Hadoop MapReduce framework for computation. However, serial execution of map and reduce phases is a problem in such systems. Therefore, in this paper, we introduce Burrows-Wheeler Aligner's Smith-Waterman Alignment on Parallel MapReduce (BWASW-PMR) cloud platform for long sequence alignment. The proposed cloud platform adopts a widely accepted and accurate BWA-SW algorithm for long sequence alignment. A custom MapReduce platform is developed to overcome the drawbacks of the Hadoop framework. A parallel execution strategy of the MapReduce phases and optimization of Smith-Waterman algorithm are considered. Performance evaluation results exhibit an average speed-up of 6.7 considering BWASW-PMR compared with the state-of-the-art Bwasw-Cloud. An average reduction of 30% in the map phase makespan is reported across all experiments comparing BWASW-PMR with Bwasw-Cloud. Optimization of Smith-Waterman results in reducing the execution time by 91.8%. The experimental study proves the efficiency of BWASW-PMR for aligning long genomic sequences on cloud platforms.