Geologic Structures in Crater Walls on Vesta

NASA Technical Reports Server (NTRS)

Mittlefehldt, David W.; Beck, A. W.; Ammannito, E.; Carsenty, U.; DeSanctis, M. C.; LeCorre, L.; McCoy, T. J.; Reddy, V.; Schroeder, S. E.

2012-01-01

The Framing Camera (FC) on the Dawn spacecraft has imaged most of the illuminated surface of Vesta with a resolution of apporpx. 20 m/pixel through different wavelength filters that allow for identification of lithologic units. The Visible and Infrared Mapping Spectrometer (VIR) has imaged the surface at lower spatial resolution but high spectral resolution from 0.25 to 5 micron that allows for detailed mineralogical interpretation. The FC has imaged geologic structures in the walls of fresh craters and on scarps on the margin of the Rheasilvia basin that consist of cliff-forming, competent units, either as blocks or semi-continuous layers, hundreds of m to km below the rims. Different units have different albedos, FC color ratios and VIR spectral characteristics, and different units can be juxtaposed in individual craters. We will describe different examples of these competent units and present preliminary interpretations of the structures. A common occurrence is of blocks several hundred m in size of high albedo (bright) and low albedo (dark) materials protruding from crater walls. In many examples, dark material deposits lie below coherent bright material blocks. In FC Clementine color ratios, bright material is green indicating deeper 1 m pyroxene absorption band. VIR spectra show these to have deeper and wider 1 and 2 micron pyroxene absorption bands than the average vestan surface. The associated dark material has subdued pyroxene absorption features compared to the average vestan surface. Some dark material deposits are consistent with mixtures of HED materials with carbonaceous chondrites. This would indicate that some dark material deposits in crater walls are megabreccia blocks. The same would hold for bright material blocks found above them. Thus, these are not intact crustal units. Marcia crater is atypical in that the dark material forms a semi-continuous, thin layer immediately below bright material. Bright material occurs as one or more layers. In one region, there is an apparent angular unconformity between the bright material and the dark material where bright material layers appear to be truncated against the underlying dark layer. One crater within the Rheasilvia basin contains two distinct types of bright materials outcropping on its walls, one like that found elsewhere on Vesta and the other an anomalous block 200 m across. This material has the highest albedo; almost twice that of the vestan average. Unlike all other bright materials, this block has a subdued 1 micron pyroxene absorption band in FC color ratios. These data indicate that this block represents a distinct vestan lithology that is rarely exposed.

Morphology and Proton Transport in Sulfonated Block Copolymer and Mesoporous Polymer Electrolyte Membranes

NASA Astrophysics Data System (ADS)

Chen, Chelsea; Wong, David; Beers, Keith; Balsara, Nitash

2013-03-01

In an effort to understand the fundamentals of proton transport in polymer electrolyte membranes (PEMs), we have developed a series of poly(styrene-b-ethylene-b-styrene) (SES) membranes. The SES membranes were subsequently sulfonated to yield proton conducting S-SES membranes. We examine the effects of sulfonation level, temperature and thermal history on the morphology of S-SES membranes in both dry and hydrated states. The effects of these parameters on water uptake and proton transport characteristics of the membranes are also examined. Furthermore, building upon the strategy we deployed in sulfonating the SES membranes, we fabricated mesoporous S-SES membranes, with pores lined up with the proton conducting channels. These membranes have three distinct phases: structural block, proton-conducting block, and void. We examine the effects of pore size, domain structure and sulfonation level on water uptake and proton conductivity of the mesoporous PEMs at different temperatures. This work is funded by Department of Energy.

Influence of topographically patterned angled guidelines on directed self-assembly of block copolymers

NASA Astrophysics Data System (ADS)

Rebello, Nathan; Sethuraman, Vaidyanathan; Blachut, Gregory; Ellison, Christopher J.; Willson, C. Grant; Ganesan, Venkat

2017-11-01

Single chain in mean-field Monte Carlo simulations were employed to study the self-assembly of block copolymers (BCP) in thin films that use trapezoidal guidelines to direct the orientation and alignment of lamellar patterns. The present study explored the influence of sidewall interactions and geometry of the trapezoidal guidelines on the self-assembly of perpendicularly oriented lamellar morphologies. When both the sidewall and the top surface exhibit preferential interactions to the same block of the BCP, trapezoidal guidelines with intermediate taper angles were found to result in less defective perpendicularly orientated morphologies. Similarly, when the sidewall and top surface are preferential to distinct blocks of the BCP, intermediate tapering angles were found to be optimal in promoting defect free structures. Such results are rationalized based on the energetics arising in the formation of perpendicularly oriented lamella on patterned substrates.

On structure-exploiting trust-region regularized nonlinear least squares algorithms for neural-network learning.

PubMed

Mizutani, Eiji; Demmel, James W

2003-01-01

This paper briefly introduces our numerical linear algebra approaches for solving structured nonlinear least squares problems arising from 'multiple-output' neural-network (NN) models. Our algorithms feature trust-region regularization, and exploit sparsity of either the 'block-angular' residual Jacobian matrix or the 'block-arrow' Gauss-Newton Hessian (or Fisher information matrix in statistical sense) depending on problem scale so as to render a large class of NN-learning algorithms 'efficient' in both memory and operation costs. Using a relatively large real-world nonlinear regression application, we shall explain algorithmic strengths and weaknesses, analyzing simulation results obtained by both direct and iterative trust-region algorithms with two distinct NN models: 'multilayer perceptrons' (MLP) and 'complementary mixtures of MLP-experts' (or neuro-fuzzy modular networks).

Manipulating the ABCs of self-assembly via low-χ block polymer design

PubMed Central

Chang, Alice B.; Lee, Byeongdu; Garland, Carol M.; Jones, Simon C.; Matsen, Mark W.

2017-01-01

Block polymer self-assembly typically translates molecular chain connectivity into mesoscale structure by exploiting incompatible blocks with large interaction parameters (χij). In this article, we demonstrate that the converse approach, encoding low-χ interactions in ABC bottlebrush triblock terpolymers (χAC ≲ 0), promotes organization into a unique mixed-domain lamellar morphology, which we designate LAMP. Transmission electron microscopy indicates that LAMP exhibits ACBC domain connectivity, in contrast to conventional three-domain lamellae (LAM3) with ABCB periods. Complementary small-angle X-ray scattering experiments reveal a strongly decreasing domain spacing with increasing total molar mass. Self-consistent field theory reinforces these observations and predicts that LAMP is thermodynamically stable below a critical χAC, above which LAM3 emerges. Both experiments and theory expose close analogies to ABA′ triblock copolymer phase behavior, collectively suggesting that low-χ interactions between chemically similar or distinct blocks intimately influence self-assembly. These conclusions provide fresh opportunities for block polymer design with potential consequences spanning all self-assembling soft materials. PMID:28588139

Three-dimensional lithospheric electrical structure of Southern Granulite Terrain, India and its tectonic implications

NASA Astrophysics Data System (ADS)

Patro, Prasanta K.; Sarma, S. V. S.; Naganjaneyulu, K.

2014-01-01

crustal as well as the upper mantle lithospheric electrical structure of the Southern Granulite Terrain (SGT) is evaluated, using the magnetotelluric (MT) data from two parallel traverses: one is an 500 km long N-S trending traverse across SGT and another a 200 km long traverse. Data space Occam 3-D inversion was used to invert the MT data. The electrical characterization of lithospheric structure in SGT shows basically a highly resistive (several thousands of Ohm meters) upper crustal layer overlying a moderately resistive (a few hundred Ohm meters) lower crustal layer which in turn is underlain by the upper mantle lithosphere whose resistivity shows significant changes along the traverse. The highly resistive upper crustal layer is interspersed with four major conductive features with three of them cutting across the crustal column, bringing out a well-defined crustal block structure in SGT with individual highly resistive blocks showing correspondence to the geologically demarcated Salem, Madurai, and Trivandrum blocks. The 3-D model also brought out a well-defined major crustal conductor located in the northern half of the Madurai block. The electrical characteristics of this south dipping conductor and its close spatial correlation with two of the major structural elements, viz., Karur-Oddanchatram-Kodaikanal Shear Zone and Karur-Kamban-Painavu-Trichur Shear Zone, suggest that this conductive feature is closely linked to the subduction-collision tectonic processes in the SGT, and it is inferred that the Archean Dharwar craton/neoproterozoic SGT terrain boundary lies south of the Palghat-Cauvery shear zone. The results also showed that the Achankovil shear zone is characterized by a well-defined north dipping conductive feature. The resistive block adjoining this conductor on the southern side, representing the Trivandrum block, is shown to be downthrown along this north dipping crustal conductor relative to the Madurai block, suggesting a northward movement of Trivandrum block colliding against the Madurai block. The lithospheric upper mantle electrical structure of the SGT up to a depth of 100 km may be broadly divided into two distinctly different segments, viz., northern and southern segments. The northern lithospheric segment, over a major part, is characterized by a thick resistive upper mantle, while the southern one is characterized by a dominantly conductive medium suggesting a relatively thinned lithosphere in the southern segment.

Substrate effect on nanoporous structure of silica wires by channel-confined self-assembly of block-copolymer and sol-gel precursors

DOE PAGES

Hu, Michael Z.; Lai, Peng

2015-09-22

Nanoporous silica wires of various wire diameters were developed by space-confined molecular self-assembly of triblock copolymer ethylene/propylene/ethylene (P123) and silica alkoxide precursor (tetraethylorthosilicate, TEOS). Two distinctive hard-templating substrates, anodized aluminum oxide (AAO) and track-etched polycarbonate (EPC), with channel diameters in the range between 10 nm and 200 nm were employed for space-confinement of soft molecular self-assembly driven by the block-copolymer microphase separation. It was observed in the scanning and transmission electron microscope (STEM) studies that the substrate geometry and material characteristics had pronounced effects on the structure and morphology of the silica nanowires. A substrate wall effect was proposed tomore » explain the ordering and orientation of the intra-wire mesostructure. Circular and spiral nanostructures were found only in wires formed in AAO substrate, not in EPC. Pore-size differences and distinctive wall morphologies of the nanowires relating to the substrates were discussed. It was shown that the material and channel wall characteristics of different substrates play key roles in the ordering and morphology of the intra-wire nanostructures.« less

Distinct Photovoltaic Performance of Hierarchical Nanostructures Self-Assembled from Multiblock Copolymers.

PubMed

Xu, Zhanwen; Lin, Jiaping; Zhang, Liangshun; Wang, Liquan; Wang, Gengchao; Tian, Xiaohui; Jiang, Tao

2018-06-14

We applied a multi-scale approach coupling dissipative particle dynamics method with a drift-diffusion model to elucidate the photovoltaic properties of multiblock copolymers consisting of alternating electron donor and acceptor blocks. A series of hierarchical lamellae-in-lamellar structures were obtained from the self-assembly of the multiblock copolymers. A distinct improvement in photovoltaic performance upon the morphology transformation from lamella to lamellae-in-lamella was observed. The hierarchical lamellae-in-lamellar structures significantly enhanced exciton dissociation and charge carrier transport, which consequently contributed to the improved photovoltaic performance. Based on our theoretical calculations, the hierarchical nanostructures can achieve a much enhanced energy conversion efficiency, improved by around 25% compared with that of general ones, through structure modulation on number and size of the small-length-scale domains. Our findings are supported by recent experimental evidence and yield guidelines for designing hierarchical materials with improved photovoltaic properties.

The sympathetic postganglionic fibre and the block by bretylium; the block prevented by hexamethonium and imitated by mecamylamine

PubMed Central

Burn, J. H.; Gibbons, W. R.

1964-01-01

Acetylcholine, in the presence of atropine, has an action like that of sympathetic stimulation. When injected into the splenic artery it causes contraction of the spleen, but this action is blocked by hexamethonium; stimulation of the splenic nerves, however, is still effective. Thus hexamethonium distinguishes between sympathetic nerve stimulation and the action of acetylcholine. If bretylium is used instead of hexamethonium, there is no such distinction, for bretylium blocks the response to nerve stimulation as well as that to acetylcholine. It appeared that hexamethonium might block the action of acetylcholine by preventing its entry into the sympathetic fibre. Acetylcholine has some structural similarity to bretylium, since acetylcholine is a derivative of trimethylammonium and bretylium is a derivative of dimethylethylammonium. It has been found that hexamethonium, pentolinium and hemicholinium (HC-3), which are all bis-quaternary compounds, block the action of bretylium, presumably by preventing its entry into the fibre. Consistent with the view that ability to enter the fibre is important is the observation that mecamylamine and pempidine, which are ganglion-blocking agents, but not either mono- or bis-quaternary compounds, often abolish the response to stimulation of the sympathetic postganglionic fibre. PMID:14211685

Molecular dynamics study of the encapsulation capability of a PCL-PEO based block copolymer for hydrophobic drugs with different spatial distributions of hydrogen bond donors and acceptors.

PubMed

Patel, Sarthak K; Lavasanifar, Afsaneh; Choi, Phillip

2010-03-01

Molecular dynamics simulation was used to study the potential of using a block copolymer containing three poly(epsilon-caprolactone) (PCL) blocks of equal length connected to one end of a poly(ethylene oxide) (PEO) block, designated as PEO-b-3PCL, to encapsulate two classes of hydrophobic drugs with distinctively different molecular structures. In particular, the first class of drugs consisted of two cucurbitacin drugs (CuB and CuI) that contain multiple hydrogen bond donors and acceptors evenly distributed on their molecules while the other class of drugs (fenofibrate and nimodipine) contain essentially only clustered hydrogen bond acceptors. In the case of cucurbitacin drugs, the results showed that PEO-b-3PCL lowered the Flory-Huggins interaction parameters (chi) considerably (i.e., increased the drug solubility) compared to the linear di-block copolymer PEO-b-PCL with the same PCL/PEO (w/w) ratio of 1.0. However, the opposite effect was observed for fenofibrate and nimodipine. Analysis of the intermolecular interactions indicates that the number of hydrogen bonds formed between the three PCL blocks and cucurbitacin drugs is significantly higher than that of the linear di-block copolymer. On the other hand, owing to the absence of hydrogen bond donors and the clustering of the hydrogen bond acceptors on the fenofibrate and nimodipine molecules, this significantly reduces the number of hydrogen bonds formed in the multi-PCL block environment, leading to unfavourable chi values. The findings of the present work suggest that multi-hydrophobic block architecture could potentially increase the drug loading for hydrophobic drugs with structures containing evenly distributed multiple hydrogen bond donors and acceptors. (c) 2009 Elsevier Ltd. All rights reserved.

Polymer-directed synthesis of metal oxide-containing nanomaterials for electrochemical energy storage

NASA Astrophysics Data System (ADS)

Mai, Yiyong; Zhang, Fan; Feng, Xinliang

2013-12-01

Metal oxide-containing nanomaterials (MOCNMs) of controllable structures at the nano-scale have attracted considerable interest because of their great potential applications in electrochemical energy storage devices, such as lithium-ion batteries (LIBs) and supercapacitors. Among many structure-directing agents, polymers and macromolecules, including block copolymers (BCPs) and graphene, exhibit distinct advantages in the template-assisted synthesis of MOCNMs. In this feature article, we introduce the controlled preparation of MOCNMs employing BCPs and graphene as structure-directing agents. Typical synthetic strategies are presented for the control of structures and sizes as well as the improvement of physical properties and electrochemical performance of MOCNMs in LIBs and supercapacitors.

Polymer-directed synthesis of metal oxide-containing nanomaterials for electrochemical energy storage.

PubMed

Mai, Yiyong; Zhang, Fan; Feng, Xinliang

2014-01-07

Metal oxide-containing nanomaterials (MOCNMs) of controllable structures at the nano-scale have attracted considerable interest because of their great potential applications in electrochemical energy storage devices, such as lithium-ion batteries (LIBs) and supercapacitors. Among many structure-directing agents, polymers and macromolecules, including block copolymers (BCPs) and graphene, exhibit distinct advantages in the template-assisted synthesis of MOCNMs. In this feature article, we introduce the controlled preparation of MOCNMs employing BCPs and graphene as structure-directing agents. Typical synthetic strategies are presented for the control of structures and sizes as well as the improvement of physical properties and electrochemical performance of MOCNMs in LIBs and supercapacitors.

Self-assembly strategies for the synthesis of functional nanostructured materials

NASA Astrophysics Data System (ADS)

Perego, M.; Seguini, G.

2016-06-01

Self-assembly is the autonomous organization of components into patterns or structures without human intervention. This is the approach followed by nature to generate living cells and represents one of the practical strategies to fabricate ensembles of nanostructures. In static self-assembly the formation of ordered structures could require energy but once formed the structures are stable. The introduction of additional regular features in the environment could be used to template the self-assembly guiding the organization of the components and determining the final structure they form. In this regard self-assembly of block copolymers represents a potent platform for fundamental studies at the nanoscale and for application-driven investigation as a tool to fabricate functional nanostructured materials. Block copolymers can hierarchically assemble into chemically distinct domains with size and periodicity on the order of 10nm or below, offering a potentially inexpensive route to generate large-area nanostructured materials. The final structure characteristics of these materials are dictated by the properties of the elementary block copolymers, like chain length, volume fraction or degree of block incompatibility. Modern synthetic chemistry offers the possibility to design these macromolecules with very specific length scales and geometries, directly embodying in the block copolymers the code that drives their self- assembling process. The understanding of the kinetics and thermodynamics of the block copolymer self-assembly process in the bulk phase as well as in thin films represents a fundamental prerequisite toward the exploitation of these materials. Incorporating block copolymer into device fabrication procedures or directly into devices, as active elements, will lead to the development of a new generation of devices fabricated using the fundamental law of nature to our advantage in order to minimize cost and power consumption in the fabrication process. Moreover the capability to precisely organize these nano-objects on appropriate substrates is the key point to support the technological development of new device concepts with predictable characteristics based on these nano-materials. In the next coming years this area of research, at the intersection between fundamental science and technology, is expected to disclose additional insights in the physics of the self-assembly process and to delineate unforeseen applications for these exciting materials.

Manipulating the ABCs of self-assembly via low-χ block polymer design

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

Chang, Alice B.; Bates, Christopher M.; Lee, Byeongdu

Block polymer self-assembly typically translates molecular chain connectivity into mesoscale structure by exploiting incompatible blocks with large interaction parameters (χ ij). In this report, we demonstrate that the converse approach, encoding low-χ interactions in ABC bottlebrush triblock terpolymers (χ AC ≲ 0), promotes organization into a unique mixed-domain lamellar morphology which we designate LAM P. Transmission electron microscopy indicates that LAMP exhibits ACBC domain connectivity, in contrast to conventional three-domain lamellae (LAM 3) with ABCB periods. Complementary small angle X-ray scattering experiments reveal a strongly decreasing domain spacing with increasing total molar mass. Self-consistent field theory reinforces these observations andmore » predicts that LAM P is thermodynamically stable below a critical χ AC, above which LAM 3 emerges. Both experiments and theory expose close analogies to ABA triblock copolymer phase behavior, collectively suggesting that low-χ interactions between chemically similar or distinct blocks intimately influence self-assembly. Furthermore, these conclusions provide new opportunities in block polymer design with potential consequences spanning all self-assembling soft materials.« less

Manipulating the ABCs of self-assembly via low-χ block polymer design

DOE PAGES

Chang, Alice B.; Bates, Christopher M.; Lee, Byeongdu; ...

2017-06-06

Block polymer self-assembly typically translates molecular chain connectivity into mesoscale structure by exploiting incompatible blocks with large interaction parameters (χ ij). In this report, we demonstrate that the converse approach, encoding low-χ interactions in ABC bottlebrush triblock terpolymers (χ AC ≲ 0), promotes organization into a unique mixed-domain lamellar morphology which we designate LAM P. Transmission electron microscopy indicates that LAMP exhibits ACBC domain connectivity, in contrast to conventional three-domain lamellae (LAM 3) with ABCB periods. Complementary small angle X-ray scattering experiments reveal a strongly decreasing domain spacing with increasing total molar mass. Self-consistent field theory reinforces these observations andmore » predicts that LAM P is thermodynamically stable below a critical χ AC, above which LAM 3 emerges. Both experiments and theory expose close analogies to ABA triblock copolymer phase behavior, collectively suggesting that low-χ interactions between chemically similar or distinct blocks intimately influence self-assembly. Furthermore, these conclusions provide new opportunities in block polymer design with potential consequences spanning all self-assembling soft materials.« less

Mechanical analysis of the dry stone walls built by the Incas

NASA Astrophysics Data System (ADS)

Castro, Jaime; Vallejo, Luis E.; Estrada, Nicolas

2017-06-01

In this paper, the retaining walls in the agricultural terraces built by the Incas are analyzed from a mechanical point of view. In order to do so, ten different walls from the Lower Agricultural Sector of Machu Picchu, Perú, were selected using images from Google Street View and Google Earth Pro. Then, these walls were digitalized and their mechanical stability was evaluated. Firstly, it was found that these retaining walls are characterized by two distinctive features: disorder and a block size distribution with a large size span, i.e., the particle size varies from blocks that can be carried by one person to large blocks weighing several tons. Secondly, it was found that, thanks to the large span of the block size distribution, the factor of safety of the Inca retaining walls is remarkably close to those that are recommended in modern geotechnical design standards. This suggests that these structures were not only functional but also highly optimized, probably as a result of a careful trial and error procedure.

Chemical structure-guided design of dynapyrazoles, cell-permeable dynein inhibitors with a unique mode of action

PubMed Central

Steinman, Jonathan B; Santarossa, Cristina C; Miller, Rand M; Yu, Lola S; Serpinskaya, Anna S; Furukawa, Hideki; Morimoto, Sachie; Tanaka, Yuta; Nishitani, Mitsuyoshi; Asano, Moriteru; Zalyte, Ruta; Ondrus, Alison E; Johnson, Alex G; Ye, Fan; Nachury, Maxence V; Fukase, Yoshiyuki; Aso, Kazuyoshi; Foley, Michael A; Gelfand, Vladimir I; Chen, James K; Carter, Andrew P; Kapoor, Tarun M

2017-01-01

Cytoplasmic dyneins are motor proteins in the AAA+ superfamily that transport cellular cargos toward microtubule minus-ends. Recently, ciliobrevins were reported as selective cell-permeable inhibitors of cytoplasmic dyneins. As is often true for first-in-class inhibitors, the use of ciliobrevins has in part been limited by low potency. Moreover, suboptimal chemical properties, such as the potential to isomerize, have hindered efforts to improve ciliobrevins. Here, we characterized the structure of ciliobrevins and designed conformationally constrained isosteres. These studies identified dynapyrazoles, inhibitors more potent than ciliobrevins. At single-digit micromolar concentrations dynapyrazoles block intraflagellar transport in the cilium and lysosome motility in the cytoplasm, processes that depend on cytoplasmic dyneins. Further, we find that while ciliobrevins inhibit both dynein's microtubule-stimulated and basal ATPase activity, dynapyrazoles strongly block only microtubule-stimulated activity. Together, our studies suggest that chemical-structure-based analyses can lead to inhibitors with improved properties and distinct modes of inhibition. DOI: http://dx.doi.org/10.7554/eLife.25174.001 PMID:28524820

Microwave spectroscopy of biomolecular building blocks.

PubMed

Alonso, José L; López, Juan C

2015-01-01

Microwave spectroscopy, considered as the most definitive gas phase structural probe, is able to distinguish between different conformational structures of a molecule, because they have unique spectroscopic constants and give rise to distinct individual rotational spectra.Previously, application of this technique was limited to molecular specimens possessing appreciable vapor pressures, thus discarding the possibility of studying many other molecules of biological importance, in particular those with high melting points, which had a tendency to undergo thermal reactions, and ultimately degradation, upon heating.Nowadays, the combination of laser ablation with Fourier transform microwave spectroscopy techniques, in supersonic jets, has enabled the gas-phase study of such systems. In this chapter, these techniques, including broadband spectroscopy, as well as results of their application into the study of the conformational panorama and structure of biomolecular building blocks, such as amino acids, nucleic bases, and monosaccharides, are briefly discussed, and with them, the tools for conformational assignation - rotational constants, nuclear quadrupole coupling interaction, and dipole moment.

Semiconductor nanowires: A platform for nanoscience and nanotechnology

PubMed Central

Lieber, Charles M.

2012-01-01

Advances in nanoscience and nanotechnology critically depend on the development of nanostructures whose properties are controlled during synthesis. We focus on this critical concept using semiconductor nanowires, which provide the capability through design and rational synthesis to realize unprecedented structural and functional complexity in building blocks as a platform material. First, a brief review of the synthesis of complex modulated nanowires in which rational design and synthesis can be used to precisely control composition, structure, and, most recently, structural topology is discussed. Second, the unique functional characteristics emerging from our exquisite control of nanowire materials are illustrated using several selected examples from nanoelectronics and nano-enabled energy. Finally, the remarkable power of nanowire building blocks is further highlighted through their capability to create unprecedented, active electronic interfaces with biological systems. Recent work pushing the limits of both multiplexed extracellular recording at the single-cell level and the first examples of intracellular recording is described, as well as the prospects for truly blurring the distinction between nonliving nanoelectronic and living biological systems. PMID:22707850

A novel metal-organic coordination polymer with unprecedented floor-like structural configuration consisting of two kinds of independent building blocks of triple- and double-stranded braids

NASA Astrophysics Data System (ADS)

Che, Yun-Xia; Luo, Feng; Zheng, Ji-Min

2007-02-01

This paper presents a novel and distinctive metal-organic compound, {[Cd 4(bet) 4Cl 6(H 2O) 4][Cd 2Cl 6]} n (bet=(CH 3) 3NCH 2CO 2, namely betaine) 1, assembled from two independent building blocks of triple- and double-stranded braids, and characterized by an unprecedented floor-like structural configuration. Furthermore, IR, element analysis, and TG-DTA were employed to characterize it. Compound 1 belongs to triclinic system, space group P-1, a = 6.704(2) Å, b = 9.338(3) Å, c = 20.056(7) Å, α = 101.409(5)°, β = 96.650(5)°, γ = 93.148(5)°, V = 1218.5(7) Å 3, Z = 1, R1 = 0.0340, ωR2 = 0.1017.

Geology of the north end of the Ruby Range, southwestern Montana

USGS Publications Warehouse

Tysdal, Russell G.

1970-01-01

This study consists of two parts: stratigraphy and sedimentation, and structure of rocks in the northern one-third of the Ruby Range of southwestern Montana. Detailed studies of Cambrian marine dolomite rocks in the Red Lion Formation and in the upper part of the Pilgrim Limestone resulted in their division into distinct rock units, termed lithofacies. These lithofacies contain features suggestive of subtidal, intertidal, and supratidal environments similar to those presently forming in the Persian Gulf. Stromatolltic structures occurring in the uppermost part of the Red Lion Formation are similar to those presently forming in Shark Bay, Australia. The Ruby Range within the map area is broken into a series of northwest-plunging basement (Precambrian metamorphic rock) blocks, differentially uplifted during the Cretaceous-Tertiary orogenic period. These blocks are bordered by upthrust faults, which are nearly vertical in their lower segments and are .low-angle in their uppermost parts. Asymmetrical folds in Paleozoic sedimentary rocks formed in response to the differential uplift of the blocks; thus they too plunge to the northwest. Displaced masses of rock border the range on the three sides within the map area and are interpreted as gravity-slide features resulting from uplift of the range. Normal faulting began blocking out the present range margins by Oligocene time.

Overlapping and Divergent Actions of Structurally Distinct Histone Deacetylase Inhibitors in Cardiac Fibroblasts

PubMed Central

Schuetze, Katherine B.; Stratton, Matthew S.; Blakeslee, Weston W.; Wempe, Michael F.; Wagner, Florence F.; Holson, Edward B.; Kuo, Yin-Ming; Andrews, Andrew J.; Gilbert, Tonya M.; Hooker, Jacob M.

2017-01-01

Inhibitors of zinc-dependent histone deacetylases (HDACs) profoundly affect cellular function by altering gene expression via changes in nucleosomal histone tail acetylation. Historically, investigators have employed pan-HDAC inhibitors, such as the hydroxamate trichostatin A (TSA), which simultaneously targets members of each of the three zinc-dependent HDAC classes (classes I, II, and IV). More recently, class- and isoform-selective HDAC inhibitors have been developed, providing invaluable chemical biology probes for dissecting the roles of distinct HDACs in the control of various physiologic and pathophysiological processes. For example, the benzamide class I HDAC-selective inhibitor, MGCD0103 [N-(2-aminophenyl)-4-[[(4-pyridin-3-ylpyrimidin-2-yl)amino]methyl] benzamide], was shown to block cardiac fibrosis, a process involving excess extracellular matrix deposition, which often results in heart dysfunction. Here, we compare the mechanisms of action of structurally distinct HDAC inhibitors in isolated primary cardiac fibroblasts, which are the major extracellular matrix–producing cells of the heart. TSA, MGCD0103, and the cyclic peptide class I HDAC inhibitor, apicidin, exhibited a common ability to enhance histone acetylation, and all potently blocked cardiac fibroblast cell cycle progression. In contrast, MGCD0103, but not TSA or apicidin, paradoxically increased expression of a subset of fibrosis-associated genes. Using the cellular thermal shift assay, we provide evidence that the divergent effects of HDAC inhibitors on cardiac fibroblast gene expression relate to differential engagement of HDAC1- and HDAC2-containing complexes. These findings illustrate the importance of employing multiple compounds when pharmacologically assessing HDAC function in a cellular context and during HDAC inhibitor drug development. PMID:28174211

Hissar-Alai and the Pamirs: Junction and Position in the System of Mobile Belts of Central Asia

NASA Astrophysics Data System (ADS)

Leonov, M. G.; Rybin, A. K.; Batalev, V. Yu.; Matyukov, V. E.; Shchelochkov, G. G.

2018-01-01

The position of the Pamirs and the Hissar-Alai mountainous system in the structure of Central Asia and features of their junction are considered. It is shown that their outer contours and tectonic infrastructure are significantly distinct in the planar pattern: latitudinally linear and arched for the Hissar-Alai and the Pamirs, respectively. These structures logically match those of the Central Asian and Alpine-Himalayan belts, respectively. The Pamir orogen is a relatively autonomous structural element of the crust, which is located discordantly relative to the country lithospheric blocks. Most of the Pamirs (at least, the Northern and Central) probably form a giant allochthon on the ancient basement of the Tarim and Afghan-Tajik blocks. The junction zone of these two "hard" crustal segments is reflected in the transverse Transpamir threshold, which is expressed in the relief, deep structure, and seismicity. The specific geological structure of the junction zone of the Pamirs and Hissar-Alai (systems of the Tarim, Alai, and Afghan-Tajik troughs) is shown. It suggested that this zone is a damper, which significantly neutralizes the dynamic influence of the Pamir and the southernmost elements of the Pamir-Punjab syntax on Hissar-Alai structures.

Synthesis, structure, and excited state kinetics of heteroleptic Cu(i) complexes with a new sterically demanding phenanthroline ligand

DOE PAGES

Kohler, Lars; Hadt, Ryan G.; Hayes, Dugan; ...

2017-09-25

In this paper we describe the synthesis of a new phenanthroline ligand, 2,9-di(2,4,6-tri-isopropyl-phenyl)-1,10-phenanthroline (bL2) and its use as the blocking ligand in the preparation of two new heteroleptic Cu(I)diimine complexes. Analysis of the CuHETPHEN single crystal structures shows a distinct distortion from an ideal tetrahedral geometry around the Cu(I) center, forced by the secondary phenanthroline ligand rotating to accommodate the isopropyl groups of bL2. The increased steric bulk of bL2 as compared to the more commonly used 2,9-dimesityl-1,10-phenanthroline blocking ligand prohibits intramolecular ligand–ligand interaction, which is unique among CuHETPHEN complexes. The ground state optical and redox properties of CuHETPHEN complexesmore » are responsive to the substitution on the blocking ligand even though the differences in structure are far removed from the Cu(I) center. Transient optical spectroscopy was used to understand the excited state kinetics in both coordinating and non-coordinating solvents following visible excitation. Substitution of the blocking phenanthroline ligand has a significant impact on the 3MLCT decay and can be used to increase the excited state lifetime by 50%. Electronic structure calculations established relationships between ground and excited state properties, and general entatic state concepts are discussed for copper photosensitizers. This work contributes to the growing library of CuHETPHEN complexes and broadens the fundamental understanding of their ground and excited state properties.« less

Complex and hierarchical micelle architectures from diblock copolymers using living, crystallization-driven polymerizations.

PubMed

Gädt, Torben; Ieong, Nga Sze; Cambridge, Graeme; Winnik, Mitchell A; Manners, Ian

2009-02-01

Block copolymers consist of two or more chemically distinct polymer segments, or blocks, connected by a covalent link. In a selective solvent for one of the blocks, core-corona micelle structures are formed. We demonstrate that living polymerizations driven by the epitaxial crystallization of a core-forming metalloblock represent a synthetic tool that can be used to generate complex and hierarchical micelle architectures from diblock copolymers. The use of platelet micelles as initiators enables the formation of scarf-like architectures in which cylindrical micelle tassels of controlled length are grown from specific crystal faces. A similar process enables the fabrication of brushes of cylindrical micelles on a crystalline homopolymer substrate. Living polymerizations driven by heteroepitaxial growth can also be accomplished and are illustrated by the formation of tri- and pentablock and scarf architectures with cylinder-cylinder and platelet-cylinder connections, respectively, that involve different core-forming metalloblocks.

Granitoids of the Ufalei block (South Urals): Sr-Nd isotope systematics, geodynamic position and genetic reconstructions

NASA Astrophysics Data System (ADS)

Ronkin, Yu. L.; Shardakova, G. Yu.; Maslov, A. V.; Shagalov, E. S.; Lepikhina, O. P.

2009-04-01

Petrogeochemical and isotopic-geochronological signatures in granitoids developed in structures with complex geological history represent an important feature for reconstructing paleogeodynamic settings. Granitoids are widespread in the western slope of the Urals, where the Uralian Orogen contacts via a collage of different-age blocks of the east European Platform. The Ufalei block located in the Central Urals megazone at the junction between the South and Middle Urals’ segments represents one such boundary structure with multistage geological evolution. The isotopic ages obtained by different methods for acid igneous rocks range from 1290 to 245 Ma. We determined close Rb-Sr and Sm-Nd ages (317 Ma) for granites of the Nizhnii Ufalei Massif. By their petrochemical parameters, granitoids and host granite-gneisses differ principally from each other: the former are close to subduction-related, while the latter, to continental-riftogenic varieties. The primary ratio (87Sr/86Sr)0 = 0.70428 and ɛNd ≈ +4 values indicate significant contribution of oceanic (island-arc?) material to the substrate, which served as a source for granites of the Nizhnii Ufalei Massif. Model Nd ages of granites vary from 641 to 550 Ma. Distinct oceanic rocks and varieties with such ages are missing from the surrounding structures. New isotopic dates obtained for ultramafic and mafic rocks from different zones of the Urals related to the Cadomian cycle imply development of unexposed Upper Riphean-Vendian “oceanic” rocks in the central part of the Ufalei block, which played a substantial role in the formation of the Nizhnii Ufalei granitoids. Such rocks could be represented, for example, by fragments of the Precambrian Timanide-type ophiolite association. The analysis of original materials combined with published data point to the heterogeneous composition and structure of the Ufalei block and a significant part of the western segment of the Central Uralian Uplift and extremely complex geological history of the region coupling the Uralian Orogen with the East European Platform in the present-day structure.

Synthesis and studies of polypeptide materials: Self-assembled block copolypeptide amphiphiles, DNA-condensing block copolypeptides and membrane-interactive random copolypeptides

NASA Astrophysics Data System (ADS)

Wyrsta, Michael Dmytro

A new class of transition metal initiators for the controlled polymerization of alpha-aminoacid-N-carboxyanhydrides (alpha-NCAs), has been developed by Deming et al. This discovery has allowed for the synthesis of well-defined "protein-like" polymers. Using this chemistry we have made distinct block/random copolypeptides for biomedical applications. Drug delivery, gene delivery, and antimicrobial polymers were the focus of our research efforts. The motivation for the synthesis and study of synthetic polypeptide based materials comes from proteins. Natural proteins are able to adopt a staggeringly large amount of uniquely well-defined folded structures. These structures account for the diversity in properties of proteins. As catalysts (enzymes) natural proteins perform some of the most difficult chemistry with ease and precision at ambient pressures and temperatures. They also exhibit incredible structural properties that directly result from formation of complex hierarchical assemblies. Self-assembling block copolymers were synthesized with various compositions and architectures. In general, di- and tri-block amphiphiles were studied for their self-assembling properties. Both spherical and tubular vesicles were found to assemble from di- and tri-block amphiphiles, respectively. In addition to self-assembly, pH responsiveness was engineered into these amphiphiles by the incorporation of basic residues (lysine) into the hydrophobic block. Another form of self-assembly studied was the condensation of DNA using cationic block copolymers. It was found that cationic block copolymers could condense DNA into compact, ordered, water-soluble aggregates on the nanoscale. These aggregates sufficiently protected DNA from nucleases and yet were susceptible to proteases. These studies form the basis of a gene delivery platform. The ease with which NCAs are polymerized renders them completely amenable to parallel synthetic methods. We have employed this technique to discover new antimicrobial polypeptides. The polymers studied were themselves the antimicrobial agent, not a self-assembled aggregate that contained antibiotics. It was found that powerful antibacterial polymers could be readily prepared with simple binary compositions. Antibacterial activity was sensitive to copolymer composition, bacterial cell-wall type, and insensitive to chain length (within reason).

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

Kohler, Lars; Hadt, Ryan G.; Hayes, Dugan

In this paper we describe the synthesis of a new phenanthroline ligand, 2,9-di(2,4,6-tri-isopropyl-phenyl)-1,10-phenanthroline (bL2) and its use as the blocking ligand in the preparation of two new heteroleptic Cu(I)diimine complexes. Analysis of the CuHETPHEN single crystal structures shows a distinct distortion from an ideal tetrahedral geometry around the Cu(I) center, forced by the secondary phenanthroline ligand rotating to accommodate the isopropyl groups of bL2. The increased steric bulk of bL2 as compared to the more commonly used 2,9-dimesityl-1,10-phenanthroline blocking ligand prohibits intramolecular ligand–ligand interaction, which is unique among CuHETPHEN complexes. The ground state optical and redox properties of CuHETPHEN complexesmore » are responsive to the substitution on the blocking ligand even though the differences in structure are far removed from the Cu(I) center. Transient optical spectroscopy was used to understand the excited state kinetics in both coordinating and non-coordinating solvents following visible excitation. Substitution of the blocking phenanthroline ligand has a significant impact on the 3MLCT decay and can be used to increase the excited state lifetime by 50%. Electronic structure calculations established relationships between ground and excited state properties, and general entatic state concepts are discussed for copper photosensitizers. This work contributes to the growing library of CuHETPHEN complexes and broadens the fundamental understanding of their ground and excited state properties.« less

75 FR 16424 - Proposed Information Collection; Comment Request; Census Coverage Measurement Final Housing Unit...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-01

... unit is a block cluster, which consists of one or more geographically contiguous census blocks. As in... a number of distinct processes, ranging from forming block clusters, selecting the block clusters... sample of block clusters, while the E Sample is the census of housing units and enumerations in the same...

Effects of the amino acid sequence on thermal conduction through β-sheet crystals of natural silk protein.

PubMed

Zhang, Lin; Bai, Zhitong; Ban, Heng; Liu, Ling

2015-11-21

Recent experiments have discovered very different thermal conductivities between the spider silk and the silkworm silk. Decoding the molecular mechanisms underpinning the distinct thermal properties may guide the rational design of synthetic silk materials and other biomaterials for multifunctionality and tunable properties. However, such an understanding is lacking, mainly due to the complex structure and phonon physics associated with the silk materials. Here, using non-equilibrium molecular dynamics, we demonstrate that the amino acid sequence plays a key role in the thermal conduction process through β-sheets, essential building blocks of natural silks and a variety of other biomaterials. Three representative β-sheet types, i.e. poly-A, poly-(GA), and poly-G, are shown to have distinct structural features and phonon dynamics leading to different thermal conductivities. A fundamental understanding of the sequence effects may stimulate the design and engineering of polymers and biopolymers for desired thermal properties.

Pyridine-pyrimidine amides that prevent HGF-induced epithelial scattering by two distinct mechanisms.

PubMed

Siddiqui-Jain, Adam; Hoj, Jacob P; Hargiss, J Blade; Hoj, Taylor H; Payne, Carter J; Ritchie, Collin A; Herron, Steven R; Quinn, Colette; Schuler, Jeffrey T; Hansen, Marc D H

2017-09-01

Stimulation of cultured epithelial cells with scatter factor/hepatocyte growth factor (HGF) results in individual cells detaching and assuming a migratory and invasive phenotype. Epithelial scattering recapitulates cancer progression and studies have implicated HGF signaling as a driver of cancer metastasis. Inhibitors of HGF signaling have been proposed to act as anti-cancer agents. We previously screened a small molecule library for compounds that block HGF-induced epithelial scattering. Most hits identified in this screen exhibit anti-mitotic properties. Here we assess the biological mechanism of a compound that blocks HGF-induced scattering with limited anti-mitotic activity. Analogs of this compound have one of two distinct activities: inhibiting either cell migration or cell proliferation with cell cycle arrest in G2/M. Each activity bears unique structure-activity relationships. The mechanism of action of anti-mitotic compounds is by inhibition of microtubule polymerization; these compounds entropically and enthalpically bind tubulin in the colchicine binding site, generating a conformational change in the tubulin dimer. Copyright © 2017 Elsevier Ltd. All rights reserved.

Fast iterative solution of the Bethe-Salpeter eigenvalue problem using low-rank and QTT tensor approximation

NASA Astrophysics Data System (ADS)

Benner, Peter; Dolgov, Sergey; Khoromskaia, Venera; Khoromskij, Boris N.

2017-04-01

In this paper, we propose and study two approaches to approximate the solution of the Bethe-Salpeter equation (BSE) by using structured iterative eigenvalue solvers. Both approaches are based on the reduced basis method and low-rank factorizations of the generating matrices. We also propose to represent the static screen interaction part in the BSE matrix by a small active sub-block, with a size balancing the storage for rank-structured representations of other matrix blocks. We demonstrate by various numerical tests that the combination of the diagonal plus low-rank plus reduced-block approximation exhibits higher precision with low numerical cost, providing as well a distinct two-sided error estimate for the smallest eigenvalues of the Bethe-Salpeter operator. The complexity is reduced to O (Nb2) in the size of the atomic orbitals basis set, Nb, instead of the practically intractable O (Nb6) scaling for the direct diagonalization. In the second approach, we apply the quantized-TT (QTT) tensor representation to both, the long eigenvectors and the column vectors in the rank-structured BSE matrix blocks, and combine this with the ALS-type iteration in block QTT format. The QTT-rank of the matrix entities possesses almost the same magnitude as the number of occupied orbitals in the molecular systems, No

Merging Bottom-Up with Top-Down: Continuous Lamellar Networks and Block Copolymer Lithography

NASA Astrophysics Data System (ADS)

Campbell, Ian Patrick

Block copolymer lithography is an emerging nanopatterning technology with capabilities that may complement and eventually replace those provided by existing optical lithography techniques. This bottom-up process relies on the parallel self-assembly of macromolecules composed of covalently linked, chemically distinct blocks to generate periodic nanostructures. Among the myriad potential morphologies, lamellar structures formed by diblock copolymers with symmetric volume fractions have attracted the most interest as a patterning tool. When confined to thin films and directed to assemble with interfaces perpendicular to the substrate, two-dimensional domains are formed between the free surface and the substrate, and selective removal of a single block creates a nanostructured polymeric template. The substrate exposed between the polymeric features can subsequently be modified through standard top-down microfabrication processes to generate novel nanostructured materials. Despite tremendous progress in our understanding of block copolymer self-assembly, continuous two-dimensional materials have not yet been fabricated via this robust technique, which may enable nanostructured material combinations that cannot be fabricated through bottom-up methods. This thesis aims to study the effects of block copolymer composition and processing on the lamellar network morphology of polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA) and utilize this knowledge to fabricate continuous two-dimensional materials through top-down methods. First, block copolymer composition was varied through homopolymer blending to explore the physical phenomena surrounding lamellar network continuity. After establishing a framework for tuning the continuity, the effects of various processing parameters were explored to engineer the network connectivity via defect annihilation processes. Precisely controlling the connectivity and continuity of lamellar networks through defect engineering and optimizing the block copolymer lithography process thus enabled the top-down fabrication of continuous two-dimensional gold networks with nanoscale properties. The lamellar structure of these networks was found to confer unique mechanical properties on the nanowire networks and suggests that materials templated via this method may be excellent candidates for integration into stretchable and flexible devices.

The Emerging Field of RNA Nanotechnology

PubMed Central

Guo, Peixuan

2011-01-01

RNA can be designed and manipulated just like DNA while having different rules for base-pairing and displaying functions similar to proteins. The large variety of loops and motifs in RNA allow them to fold into numerous complicated structures. This diversity provides a platform for identifying viable building blocks for particle assemblies, substrate binding and manufacture engineering. RNA thermal stability allows production of multivalent nanostructures with defined stoichiometry. Here we review the unique qualities of RNA nanotechnology and their distinct properties inside the body. We describe techniques for constructing RNA nanoparticles from different building blocks and their applications in nanomedicine. Finally, we discuss challenges in predicting and synthesizing RNA and offer some perspectives on the yield and cost of RNA production. PMID:21102465

A simple theory of molecular organization in fullerene-containing liquid crystals

NASA Astrophysics Data System (ADS)

Peroukidis, S. D.; Vanakaras, A. G.; Photinos, D. J.

2005-10-01

Systematic efforts to synthesize fullerene-containing liquid crystals have produced a variety of successful model compounds. We present a simple molecular theory, based on the interconverting shape approach [Vanakaras and Photinos, J. Mater. Chem. 15, 2002 (2005)], that relates the self-organization observed in these systems to their molecular structure. The interactions are modeled by dividing each molecule into a number of submolecular blocks to which specific interactions are assigned. Three types of blocks are introduced, corresponding to fullerene units, mesogenic units, and nonmesogenic linkage units. The blocks are constrained to move on a cubic three-dimensional lattice and molecular flexibility is allowed by retaining a number of representative conformations within the block representation of the molecule. Calculations are presented for a variety of molecular architectures including twin mesogenic branch monoadducts of C60, twin dendromesogenic branch monoadducts, and conical (badminton shuttlecock) multiadducts of C60. The dependence of the phase diagrams on the interaction parameters is explored. In spite of its many simplifications and the minimal molecular modeling used (three types of chemically distinct submolecular blocks with only repulsive interactions), the theory accounts remarkably well for the phase behavior of these systems.

Genetic characterization of Russian honey bee stock selected for improved resistance to Varroa destructor.

PubMed

Bourgeois, A Lelania; Rinderer, Thomas E

2009-06-01

Maintenance of genetic diversity among breeding lines is important in selective breeding and stock management. The Russian Honey Bee Breeding Program has strived to maintain high levels of heterozygosity among its breeding lines since its inception in 1997. After numerous rounds of selection for resistance to tracheal and varroa mites and improved honey production, 18 lines were selected as the core of the program. These lines were grouped into three breeding blocks that were crossbred to improve overall heterozygosity levels of the population. Microsatellite DNA data demonstrated that the program has been successful. Heterozygosity and allelic richness values are high and there are no indications of inbreeding among the three blocks. There were significant levels of genetic structure measured among the three blocks. Block C was genetically distinct from both blocks A and B (F(ST) = 0.0238), whereas blocks A and B did not differ from each other (F(ST) = 0.0074). The same pattern was seen for genic (based on numbers of alleles) differentiation. Genetic distance, as measured by chord distance, indicates that all of the 18 lines are equally distant, with minimal clustering. The data indicate that the overall design of the breeding program has been successful in maintaining high levels of diversity and avoiding problems associated with inbreeding.

Distortion of Local Atomic Structures in Amorphous Ge-Sb-Te Phase Change Materials

NASA Astrophysics Data System (ADS)

Hirata, A.; Ichitsubo, T.; Guan, P. F.; Fujita, T.; Chen, M. W.

2018-05-01

The local atomic structures of amorphous Ge-Sb-Te phase-change materials have yet to be clarified and the rapid crystal-amorphous phase change resulting in distinct optical contrast is not well understood. We report the direct observation of local atomic structures in amorphous Ge2Sb2Te5 using "local" reverse Monte Carlo modeling dedicated to an angstrom-beam electron diffraction analysis. The results corroborated the existence of local structures with rocksalt crystal-like topology that were greatly distorted compared to the crystal symmetry. This distortion resulted in the breaking of ideal octahedral atomic environments, thereby forming local disordered structures that basically satisfied the overall amorphous structure factor. The crystal-like distorted octahedral structures could be the main building blocks in the formation of the overall amorphous structure of Ge-Sb-Te.

Cloud computing-based TagSNP selection algorithm for human genome data.

PubMed

Hung, Che-Lun; Chen, Wen-Pei; Hua, Guan-Jie; Zheng, Huiru; Tsai, Suh-Jen Jane; Lin, Yaw-Ling

2015-01-05

Single nucleotide polymorphisms (SNPs) play a fundamental role in human genetic variation and are used in medical diagnostics, phylogeny construction, and drug design. They provide the highest-resolution genetic fingerprint for identifying disease associations and human features. Haplotypes are regions of linked genetic variants that are closely spaced on the genome and tend to be inherited together. Genetics research has revealed SNPs within certain haplotype blocks that introduce few distinct common haplotypes into most of the population. Haplotype block structures are used in association-based methods to map disease genes. In this paper, we propose an efficient algorithm for identifying haplotype blocks in the genome. In chromosomal haplotype data retrieved from the HapMap project website, the proposed algorithm identified longer haplotype blocks than an existing algorithm. To enhance its performance, we extended the proposed algorithm into a parallel algorithm that copies data in parallel via the Hadoop MapReduce framework. The proposed MapReduce-paralleled combinatorial algorithm performed well on real-world data obtained from the HapMap dataset; the improvement in computational efficiency was proportional to the number of processors used.

Cloud Computing-Based TagSNP Selection Algorithm for Human Genome Data

PubMed Central

Hung, Che-Lun; Chen, Wen-Pei; Hua, Guan-Jie; Zheng, Huiru; Tsai, Suh-Jen Jane; Lin, Yaw-Ling

2015-01-01

Single nucleotide polymorphisms (SNPs) play a fundamental role in human genetic variation and are used in medical diagnostics, phylogeny construction, and drug design. They provide the highest-resolution genetic fingerprint for identifying disease associations and human features. Haplotypes are regions of linked genetic variants that are closely spaced on the genome and tend to be inherited together. Genetics research has revealed SNPs within certain haplotype blocks that introduce few distinct common haplotypes into most of the population. Haplotype block structures are used in association-based methods to map disease genes. In this paper, we propose an efficient algorithm for identifying haplotype blocks in the genome. In chromosomal haplotype data retrieved from the HapMap project website, the proposed algorithm identified longer haplotype blocks than an existing algorithm. To enhance its performance, we extended the proposed algorithm into a parallel algorithm that copies data in parallel via the Hadoop MapReduce framework. The proposed MapReduce-paralleled combinatorial algorithm performed well on real-world data obtained from the HapMap dataset; the improvement in computational efficiency was proportional to the number of processors used. PMID:25569088

Overlapping and Divergent Actions of Structurally Distinct Histone Deacetylase Inhibitors in Cardiac Fibroblasts.

PubMed

Schuetze, Katherine B; Stratton, Matthew S; Blakeslee, Weston W; Wempe, Michael F; Wagner, Florence F; Holson, Edward B; Kuo, Yin-Ming; Andrews, Andrew J; Gilbert, Tonya M; Hooker, Jacob M; McKinsey, Timothy A

2017-04-01

Inhibitors of zinc-dependent histone deacetylases (HDACs) profoundly affect cellular function by altering gene expression via changes in nucleosomal histone tail acetylation. Historically, investigators have employed pan-HDAC inhibitors, such as the hydroxamate trichostatin A (TSA), which simultaneously targets members of each of the three zinc-dependent HDAC classes (classes I, II, and IV). More recently, class- and isoform-selective HDAC inhibitors have been developed, providing invaluable chemical biology probes for dissecting the roles of distinct HDACs in the control of various physiologic and pathophysiological processes. For example, the benzamide class I HDAC-selective inhibitor, MGCD0103 [ N -(2-aminophenyl)-4-[[(4-pyridin-3-ylpyrimidin-2-yl)amino]methyl] benzamide], was shown to block cardiac fibrosis, a process involving excess extracellular matrix deposition, which often results in heart dysfunction. Here, we compare the mechanisms of action of structurally distinct HDAC inhibitors in isolated primary cardiac fibroblasts, which are the major extracellular matrix-producing cells of the heart. TSA, MGCD0103, and the cyclic peptide class I HDAC inhibitor, apicidin, exhibited a common ability to enhance histone acetylation, and all potently blocked cardiac fibroblast cell cycle progression. In contrast, MGCD0103, but not TSA or apicidin, paradoxically increased expression of a subset of fibrosis-associated genes. Using the cellular thermal shift assay, we provide evidence that the divergent effects of HDAC inhibitors on cardiac fibroblast gene expression relate to differential engagement of HDAC1- and HDAC2-containing complexes. These findings illustrate the importance of employing multiple compounds when pharmacologically assessing HDAC function in a cellular context and during HDAC inhibitor drug development. Copyright © 2017 by The American Society for Pharmacology and Experimental Therapeutics.

Influence of habitat structure on fish assemblage of an artificial reef in southern Brazil.

PubMed

Hackradt, Carlos Werner; Félix-Hackradt, Fabiana Cézar; García-Charton, José Antonio

2011-12-01

Habitat complexity strongly influences reef fish community composition. An understanding of the underlying reasons for this relationship is important for evaluating the suitability of artificial reef (AR) habitats as a marine resource management tool. We studied the influence of AR habitat structure on fish assemblage composition off the southern coast of Brazil. We found that reef blocks with greater area and number of holes possessed the greatest fish species richness and abundance. Reef blocks with greater complexity had higher abundance of almost 30% of fish species present. Natural reef (NR) and AR were different in their fish species composition, trophic structure and categories of water column occupancy by fish (spatial categories). Although NR was more diverse and harboured more trophic levels, AR presented the higher abundances and the presence of distinct fish species that underlined their importance at a regional scale. The greater availability of sheltering habitat where hard substrate is scarce, together with their frequent use by economically important species, make AR a useful tool for coastal management when certain ecological conditions are met. Copyright © 2011 Elsevier Ltd. All rights reserved.

Geodynamic movements and deformations of the Sudetic structural unit of the Bohemian Massif

NASA Astrophysics Data System (ADS)

Schenk, V.; Jechumtálová, Z.; Schenková, Z.; Kottnauer, P.

2003-04-01

The African plate pushes to European orogenic Alpine structures that transfer the compression further to Variscan structural units, including the Bohemian Massif. Central parts of the Bohemian Massif are relatively deep-seated and, therefore, some of marginal parts of the Massif and its border geological structures should be affected intensively and moved distinctly with respect to the central parts. The geodynamical GPS network EAST SUDETEN is located just over the area mentioned above, i.e. it covers both kinetically quasi-effected and quasi-non-effected structural blocks. GPS data observed already for six annual campaigns (1997-2002) were processed and movement vectors of individual network sites were assessed. Applied data processing did not allow errors in the horizontal direction 2 mm and in the vertical direction 5-6 mm to be exceeded. Since time series of coordinate changes for several network sites gave rather pronounce movement trends, preliminary deformations among individual structural blocks were evaluated and compared to other geological, geophysical and geodetic materials. The investigation has been supported by the Grant Agency of the Czech Republic, projects 205/97/0679 and 205/01/0480, and by the research programme of the Ministry of Education, Youth and Sport of the Czech Republic, project LN00A005 "Dynamics of the Earth".

New Insights into Tectonics of the Saint Elias, Alaska, Region Based on Local Seismicity and Tomography

NASA Astrophysics Data System (ADS)

Ruppert, N. A.; Zabelina, I.; Freymueller, J. T.

2013-12-01

Saint Elias Mountains in southern Alaska are manifestation of ongoing tectonic processes that include collision of the Yakutat block with and subduction of the Yakutat block and Pacific plate under the North American plate. Interaction of these tectonic blocks and plates is complex and not well understood. In 2005 and 2006 a network of 22 broadband seismic sites was installed in the region as part of the SainT Elias TEctonics and Erosion Project (STEEP), a five-year multi-disciplinary study that addressed evolution of the highest coastal mountain range on Earth. High quality seismic data provides unique insights into earthquake occurrence and velocity structure of the region. Local earthquake data recorded between 2005 and 2010 became a foundation for detailed study of seismotectonic features and crustal velocities. The highest concentration of seismicity follows the Chugach-St.Elias fault, a major on land tectonic structure in the region. This fault is also delineated in tomographic images as a distinct contrast between lower velocities to the south and higher velocities to the north. The low-velocity region corresponds to the rapidly-uplifted and exhumed sediments on the south side of the range. Earthquake source parameters indicate high degree of compression and undertrusting processes along the coastal area, consistent with multiple thrust structures mapped from geological studies in the region. Tomographic inversion reveals velocity anomalies that correlate with sedimentary basins, volcanic features and subducting Yakutat block. We will present precise earthquake locations and source parameters recorded with the STEEP and regional seismic network along with the results of P- and S-wave tomographic inversion.

Chemical Interactions and Their Role in the Microphase Separation of Block Copolymer Thin Films

PubMed Central

Farrell, Richard A.; Fitzgerald, Thomas G.; Borah, Dipu; Holmes, Justin D.; Morris, Michael A.

2009-01-01

The thermodynamics of self-assembling systems are discussed in terms of the chemical interactions and the intermolecular forces between species. It is clear that there are both theoretical and practical limitations on the dimensions and the structural regularity of these systems. These considerations are made with reference to the microphase separation that occurs in block copolymer (BCP) systems. BCP systems self-assemble via a thermodynamic driven process where chemical dis-affinity between the blocks driving them part is balanced by a restorative force deriving from the chemical bond between the blocks. These systems are attracting much interest because of their possible role in nanoelectronic fabrication. This form of self-assembly can obtain highly regular nanopatterns in certain circumstances where the orientation and alignment of chemically distinct blocks can be guided through molecular interactions between the polymer and the surrounding interfaces. However, for this to be possible, great care must be taken to properly engineer the interactions between the surfaces and the polymer blocks. The optimum methods of structure directing are chemical pre-patterning (defining regions on the substrate of different chemistry) and graphoepitaxy (topographical alignment) but both centre on generating alignment through favourable chemical interactions. As in all self-assembling systems, the problems of defect formation must be considered and the origin of defects in these systems is explored. It is argued that in these nanostructures equilibrium defects are relatively few and largely originate from kinetic effects arising during film growth. Many defects also arise from the confinement of the systems when they are ‘directed’ by topography. The potential applications of these materials in electronics are discussed. PMID:19865513

Distinct Element Modeling of the Large Block Test

NASA Astrophysics Data System (ADS)

Carlson, S. R.; Blair, S. C.; Wagoner, J. L.

2001-12-01

The Yucca Mountain Site Characterization Project is investigating Yucca Mountain, Nevada as a potential nuclear waste repository site. As part of this effort, the Large Block, a 3m x 3m x 4.5m rectangular prism of Topopah Spring tuff, was excavated at Fran Ridge near Yucca Mountain. The Large Block was heated to a peak temperature of 145\\deg C along a horizontal plane 2.75m below the top of the block over a period of about one-year. Displacements were measured in three orthogonal directions with an array of six Multiple Point Borehole Extensometers (MPBX) and were numerically simulated in three dimensions with 3DEC, a distinct element code. The distinct element method was chosen to incorporate discrete fractures in the simulations. The model domain was extended 23m below the ground surface and, in the subsurface, 23m outward from each vertical face so that fixed displacement boundary conditions could be applied well away from the heated portion of the block. A single continuum model and three distinct element models, incorporating six to twenty eight mapped fractures, were tested. Two thermal expansion coefficients were tested for the six-fracture model: a higher value taken from laboratory measurements and a lower value from an earlier field test. The MPBX data show that the largest displacements occurred in the upper portion of the block despite the higher temperatures near the center. The continuum model was found to under-predict the MPBX displacements except in the east west direction near the base of the block. The high thermal expansion model over-predicted the MPBX displacements except in the north south direction near the top of the block. The highly fractured model under-predicted most of the MPBX displacements and poorly simulated the cool-down portion of the test. Although no model provided the single best fit to all of the MPBX data, the six and seven fracture models consistently provided good fits and in most cases showed much improvement over the other three models. Both provided particularly good fits to the east west displacements in the upper portion of the block throughout the entire test. This exercise demonstrates that distinct element models can surpass continuum models in their ability to simulate fractured rock mass deformation, but care needs to be taken in the selection of fractures incorporated in the models. *This work was performed under the auspices of the U.S. Department of Energy by the University of California, Lawrence Livermore National Laboratory under contract No. W-7405-Eng-48.

An interpretation of the tectonostratigraphic framework of the Murray Basin region of southeastern Australia, based on an examination of airborne magnetic patterns

NASA Astrophysics Data System (ADS)

Brown, C. M.; Tucker, D. H.; Anfiloff, V.

1988-11-01

New pixel map representations of regional total magnetic intensity data reveal previously unknown characteristics of the basement concealed beneath thin Cainozoic sediments of the Murray Basin in southeastern Australia. Interpretations of magnetic patterns in terms of structural features allow a revised interpretation of the nature of the tectonostratigraphic framework underlying and flanking the basin. The magnetic data indicate that arcuate or curvilinear structural trends under the Murray Basin do not conform with those of the exposed Lachlan Fold Belt to the east and suggest that the basement concealed beneath the basin, together with that exposed in the Victorian Highlands to the south, forms a distinct composite tectonostratigraphic terrane. Beneath the southwestern Murray Basin ?Proterozoic-Lower Cambrian metasediments of the Padthaway Ridge of the Kanmantoo Fold Belt display a northwesterly trending structural grain and a previously unsuspected continuity of structural trend with Adelaidean-Cambrian rocks of the Mount Lofty Ranges to the west. In the south, Cambrian volcanics of the Black Range and Stavely greenstone belts have similar magnetic response and appear to be components of a single elongate and strongly magnetic domain which extends to the northwest for at least 400 km (Stavely Belt). To the north a similar but entirely concealed northeasterly trending magnetic domain can also be interpreted as volcanics (Lake Wintlow Belt). Together these two magnetic domains appear to form an arcuate zone of volcanics, with a concave-to-the-east configuration, located at a possible suture between the Lachlan and Kanmantoo Fold Belts beneath the western Murray Basin. In the south the magnetic imagery indicates that metasediments of the ?Cambro-Ordovician Stawell Belt produce magnetic patterns distinct from those produced by the metasediments of the adjacent Ordovician Bendigo Belt, which can itself be subdivided into a number of areas of distinct magnetic pattern. Magnetic domains can be interpreted in terms of concealed Proterozoic and Palaeozoic structural belts and tectonostratigraphic terranes. Reconstructions suggest that much of the Murray Basin may be underlain by a former microcontinental block or rifted marginal plateau of Precambrian crust, now welded to the Precambrian craton to the west. Deformation of the Kanmantoo and Adelaide Fold Belts adjacent to and beneath the western and southwestern margins of the basin, can be attributed to Late Cambrian-Early Ordovician convergence between the microcontinental block and the craton. Volcanics of the arcuate Stavely and Lake Wintlow Belts are interpreted to be located at the suture between the microcontinental block and the craton. In addition, the presence of concave-to-the-east, curvilinear magnetic trends in the Cambro-Ordovician metasedimentary belts beneath the Murray Basin suggests that these successions, as well as the volcanics of the Heathcote and Mount Wellington Belts, may form allochthonous sheets. These were possibly emplaced from the east during Late Ordovician-Devonian deformation, possibly related to convergence of a further microcontinental block underlying the adjacent Lachlan Fold Belt to the east of the Murray Basin.

Comparative evaluation of structured oil systems: Shellac oleogel, HPMC oleogel, and HIPE gel.

PubMed

Patel, Ashok R; Dewettinck, Koen

2015-11-01

In lipid-based food products, fat crystals are used as building blocks for creating a crystalline network that can trap liquid oil into a 3D gel-like structure which in turn is responsible for the desirable mouth feel and texture properties of the food products. However, the recent ban on the use of trans-fat in the US, coupled with the increasing concerns about the negative health effects of saturated fat consumption, has resulted in an increased interest in the area of identifying alternative ways of structuring edible oils using non-fat-based building blocks. In this paper, we give a brief account of three alternative approaches where oil structuring was carried out using wax crystals (shellac), polymer strands (hydrophilic cellulose derivative), and emulsion droplets as structurants. These building blocks resulted in three different types of oleogels that showed distinct rheological properties and temperature functionalities. The three approaches are compared in terms of the preparation process (ease of processing), properties of the formed systems (microstructure, rheological gel strength, temperature response, effect of water incorporation, and thixotropic recovery), functionality, and associated limitations of the structured systems. The comparative evaluation is made such that the new researchers starting their work in the area of oil structuring can use this discussion as a general guideline. Various aspects of oil binding for three different building blocks were studied in this work. The practical significance of this study includes (i) information on the preparation process and the concentrations of structuring agents required for efficient gelation and (ii) information on the behavior of oleogels to temperature, applied shear, and presence of water. This information can be very useful for selecting the type of structuring agents keeping the final applications in mind. For detailed information on the actual edible applications (bakery, chocolate, and spreads) which are based on the oleogel systems described in this manuscript, the readers are advised to refer our recent papers published elsewhere. (Food & Function 2014, 5, 645-652 and Food & Function 2014, 5, 2833-2841).

Multilayer block copolymer meshes by orthogonal self-assembly

PubMed Central

Tavakkoli K. G., Amir; Nicaise, Samuel M.; Gadelrab, Karim R.; Alexander-Katz, Alfredo; Ross, Caroline A.; Berggren, Karl K.

2016-01-01

Continued scaling-down of lithographic-pattern feature sizes has brought templated self-assembly of block copolymers (BCPs) into the forefront of nanofabrication research. Technologies now exist that facilitate significant control over otherwise unorganized assembly of BCP microdomains to form both long-range and locally complex monolayer patterns. In contrast, the extension of this control into multilayers or 3D structures of BCP microdomains remains limited, despite the possible technological applications in next-generation devices. Here, we develop and analyse an orthogonal self-assembly method in which multiple layers of distinct-molecular-weight BCPs naturally produce nanomesh structures of cylindrical microdomains without requiring layer-by-layer alignment or high-resolution lithographic templating. The mechanisms for orthogonal self-assembly are investigated with both experiment and simulation, and we determine that the control over height and chemical preference of templates are critical process parameters. The method is employed to produce nanomeshes with the shapes of circles and Y-intersections, and is extended to produce three layers of orthogonally oriented cylinders. PMID:26796218

Ballistic Blocks Surrounding Kilauea's Caldera

NASA Astrophysics Data System (ADS)

Swanson, D.; Zolkos, S.; Haravitch, B.

2010-12-01

Thousands of lithic blocks dot the surface around Kilauea’s caldera, erupted ballistically at the end of the 1790 eruption or soon thereafter. Most of the blocks occur in the western and southern sectors, probably reflecting the proximity of vents on the caldera floor. We mapped the ejecta field, measuring most of the blocks with nominal diameters ((a+b+c)/3) more than 75 cm and many of the smaller ones, noting distinctive lithologies. The distributions, sizes, and lithologies suggest 7-8 different ballistic bursts from 3-4 generalized vent areas. We measured 15 blocks with nominal diameters (ND) of 150-201 cm, 169 blocks with ND 100-149 cm, 308 blocks with ND 75-99 cm, 684 blocks with ND 50-74 cm, and 545 blocks with ND 25-49 cm. The smaller blocks were measured only in outlying areas, where they were the largest in the neighborhood, but they occur throughout the field. Twelve blocks with ND >150 cm lie within 1.7 km west and south of the center of Halema`uma`u; a vent near this location likely erupted the blocks. Three of the largest blocks, however, are 2.2-2.7 km north of Halema`uma`u and probably came from a more northerly vent. This interpretation is supported by the distributions of all blocks with ND >100 cm, which define at least 4, and possibly 5, different dispersal lobes; three cluster near Halema`uma`u, one is slightly north, and the one with the three large blocks is still farther north. The blocks have typical lithologies for Kilauea’s summit, including coarse basalt or fine gabbro derived from the centers of thick flows, solidified lakes, or small intrusions. Three lithologies are distinctive and help define 3, possibly 4, discrete bursts. Blocks of fine-grained basalt riddled with segregation veins occur only in a lobe 1.3 km wide reaching as far as 1.8 km southwest of Halema`uma`u; this lobe overlaps slightly with one defined by block size but is mostly distinct and probably indicates a separate burst. A cluster of blocks with puffy, somewhat fluidal rinds forms a distinct lobe 800 m wide out to 1.8 km southeast of Halema`uma`u. The cluster also contains many cored bombs and a few juvenile bombs and lapilli without cores. This is the only ballistic lobe that contains much juvenile material, though older fall and surge deposits of 1790 and pre1790 vintage also carry cored bombs and juvenile lapilli. This lobe is coextensive with one defined by block size. The largest ballistic lobe has abundant, commonly oxidized blocks of olivine-rich basalt, some verging on picrite. The main lobe, about 900 m wide, extends 0.9-3.6 km southeast of Halema`uma`u; three olivine-rich blocks between 100 and 150 cm ND occur 2.4 to 3.3 km out. A possible second lobe of olivine-rich blocks occurs out to 1.6 km due south of Halema`uma`u. The lobes indicate a directionality and inclined ejection angle for at least some of the ballistic eruptions, as was true for the observed, but much smaller, ballistic eruptions in 1924. The scarcity of juvenile ejecta argues for phreatic eruptions that were likely initiated at or below the water table, today about 600 m below the caldera rim. If so, some ballistic blocks weighing a few tonnes were thrown at least 600 m above the vent. The dynamics of these explosive eruptions are under study.

SCA with rotation to distinguish common and distinctive information in linked data.

PubMed

Schouteden, Martijn; Van Deun, Katrijn; Pattyn, Sven; Van Mechelen, Iven

2013-09-01

Often data are collected that consist of different blocks that all contain information about the same entities (e.g., items, persons, or situations). In order to unveil both information that is common to all data blocks and information that is distinctive for one or a few of them, an integrated analysis of the whole of all data blocks may be most useful. Interesting classes of methods for such an approach are simultaneous-component and multigroup factor analysis methods. These methods yield dimensions underlying the data at hand. Unfortunately, however, in the results from such analyses, common and distinctive types of information are mixed up. This article proposes a novel method to disentangle the two kinds of information, by making use of the rotational freedom of component and factor models. We illustrate this method with data from a cross-cultural study of emotions.

Real-time three-dimensional ultrasound-assisted axillary plexus block defines soft tissue planes.

PubMed

Clendenen, Steven R; Riutort, Kevin; Ladlie, Beth L; Robards, Christopher; Franco, Carlo D; Greengrass, Roy A

2009-04-01

Two-dimensional (2D) ultrasound is commonly used for regional block of the axillary brachial plexus. In this technical case report, we described a real-time three-dimensional (3D) ultrasound-guided axillary block. The difference between 2D and 3D ultrasound is similar to the difference between plain radiograph and computer tomography. Unlike 2D ultrasound that captures a planar image, 3D ultrasound technology acquires a 3D volume of information that enables multiple planes of view by manipulating the image without movement of the ultrasound probe. Observation of the brachial plexus in cross-section demonstrated distinct linear hyperechoic tissue structures (loose connective tissue) that initially inhibited the flow of the local anesthesia. After completion of the injection, we were able to visualize the influence of arterial pulsation on the spread of the local anesthesia. Possible advantages of this novel technology over current 2D methods are wider image volume and the capability to manipulate the planes of the image without moving the probe.

Hidden Markov model approach for identifying the modular framework of the protein backbone.

PubMed

Camproux, A C; Tuffery, P; Chevrolat, J P; Boisvieux, J F; Hazout, S

1999-12-01

The hidden Markov model (HMM) was used to identify recurrent short 3D structural building blocks (SBBs) describing protein backbones, independently of any a priori knowledge. Polypeptide chains are decomposed into a series of short segments defined by their inter-alpha-carbon distances. Basically, the model takes into account the sequentiality of the observed segments and assumes that each one corresponds to one of several possible SBBs. Fitting the model to a database of non-redundant proteins allowed us to decode proteins in terms of 12 distinct SBBs with different roles in protein structure. Some SBBs correspond to classical regular secondary structures. Others correspond to a significant subdivision of their bounding regions previously considered to be a single pattern. The major contribution of the HMM is that this model implicitly takes into account the sequential connections between SBBs and thus describes the most probable pathways by which the blocks are connected to form the framework of the protein structures. Validation of the SBBs code was performed by extracting SBB series repeated in recoding proteins and examining their structural similarities. Preliminary results on the sequence specificity of SBBs suggest promising perspectives for the prediction of SBBs or series of SBBs from the protein sequences.

Consensus structures of the Mo(v) sites of sulfite-oxidizing enzymes derived from variable frequency pulsed EPR spectroscopy, isotopic labelling and DFT calculations.

PubMed

Enemark, John H

2017-10-10

Sulfite-oxidizing enzymes from eukaryotes and prokaryotes have five-coordinate distorted square-pyramidal coordination about the molybdenum atom. The paramagnetic Mo(v) state is easily generated, and over the years four distinct CW EPR spectra have been identified, depending upon enzyme source and the reaction conditions, namely high and low pH (hpH and lpH), phosphate inhibited (P i ) and sulfite (or blocked). Extensive studies of these paramagnetic forms of sulfite-oxidizing enzymes using variable frequency pulsed electron spin echo (ESE) spectroscopy, isotopic labeling and density functional theory (DFT) calculations have led to the consensus structures that are described here. Errors in some of the previously proposed structures are corrected.

Programming Hierarchical Self-Assembly of Patchy Particles into Colloidal Crystals via Colloidal Molecules.

PubMed

Morphew, Daniel; Shaw, James; Avins, Christopher; Chakrabarti, Dwaipayan

2018-03-27

Colloidal self-assembly is a promising bottom-up route to a wide variety of three-dimensional structures, from clusters to crystals. Programming hierarchical self-assembly of colloidal building blocks, which can give rise to structures ordered at multiple levels to rival biological complexity, poses a multiscale design problem. Here we explore a generic design principle that exploits a hierarchy of interaction strengths and employ this design principle in computer simulations to demonstrate the hierarchical self-assembly of triblock patchy colloidal particles into two distinct colloidal crystals. We obtain cubic diamond and body-centered cubic crystals via distinct clusters of uniform size and shape, namely, tetrahedra and octahedra, respectively. Such a conceptual design framework has the potential to reliably encode hierarchical self-assembly of colloidal particles into a high level of sophistication. Moreover, the design framework underpins a bottom-up route to cubic diamond colloidal crystals, which have remained elusive despite being much sought after for their attractive photonic applications.

On topological RNA interaction structures.

PubMed

Qin, Jing; Reidys, Christian M

2013-07-01

Recently a folding algorithm of topological RNA pseudoknot structures was presented in Reidys et al. (2011). This algorithm folds single-stranded γ-structures, that is, RNA structures composed by distinct motifs of bounded topological genus. In this article, we set the theoretical foundations for the folding of the two backbone analogues of γ structures: the RNA γ-interaction structures. These are RNA-RNA interaction structures that are constructed by a finite number of building blocks over two backbones having genus at most γ. Combinatorial properties of γ-interaction structures are of practical interest since they have direct implications for the folding of topological interaction structures. We compute the generating function of γ-interaction structures and show that it is algebraic, which implies that the numbers of interaction structures can be computed recursively. We obtain simple asymptotic formulas for 0- and 1-interaction structures. The simplest class of interaction structures are the 0-interaction structures, which represent the two backbone analogues of secondary structures.

Are Abstract and Concrete Concepts Organized Differently? Evidence from the Blocked Translation Paradigm

ERIC Educational Resources Information Center

Zhang, Xiaohong; Han, Zaizhu; Bi, Yanchao

2013-01-01

Using the blocked-translation paradigm with healthy participants, we examined Crutch and Warrington's hypothesis that concrete and abstract concepts are organized by distinct principles: concrete concepts by semantic similarities and abstract ones by associations. In three experiments we constructed two types of experimental blocking (similar…

Finite Frequency Traveltime Tomography of Lithospheric and Upper Mantle Structures beneath the Cordillera-Craton Transition in Southwestern Canada

NASA Astrophysics Data System (ADS)

Chen, Y.; Gu, Y. J.; Hung, S. H.

2014-12-01

Based on finite-frequency theory and cross-correlation teleseismic relative traveltime data from the USArray, Canadian National Seismograph Network (CNSN) and Canadian Rockies and Alberta Network (CRANE), we present a new tomographic model of P-wave velocity perturbations for the lithosphere and upper mantle beneath the Cordillera-cration transition region in southwestern Canada. The inversion procedure properly accounts for the finite-volume sensitivities of measured travel time residuals, and the resulting model shows a greater resolution of upper mantle velocity heterogeneity beneath the study area than earlier approaches based on the classical ray-theoretical approach. Our model reveals a lateral change of P velocities from -0.5% to 0.5% down to ~200-km depth in a 50-km wide zone between the Alberta Basin and the foothills of the Rocky Mountains, which suggests a sharp structural gradient along the Cordillera deformation front. The stable cratonic lithosphere, delineated by positive P-velocity perturbations of 0.5% and greater, extends down to a maximum depth of ~180 km beneath the Archean Loverna Block (LB). In comparison, the mantle beneath the controversial Medicine Hat Block (MHB) exhibits significantly higher velocities in the uppermost mantle and a shallower (130-150 km depth) root, generally consistent with the average depth of the lithosphere-asthenosphere boundary beneath Southwest Western Canada Sedimentary Basin (WCSB). The complex shape of the lithospheric velocities under the MHB may be evidence of extensive erosion or a partial detachment of the Precambrian lithospheric root. Furthermore, distinct high velocity anomalies in LB and MHB, which are separated by 'normal' mantle block beneath the Vulcan structure (VS), suggest different Archean assembly and collision histories between these two tectonic blocks.

Aeromagnetic and aeromagnetic-based geologic maps of the Coastal Belt, Franciscan Complex, northern California

USGS Publications Warehouse

Langenheim, V.E.; Jachens, R.C.; McLaughlin, R.J.

2011-01-01

The Coastal belt of the Franciscan Complex represents a Late Cretaceous to Miocene accretionary prism and overlying slope deposits. Its equivalents may extend from the offshore outer borderland of southern California to north of the Mendocino Triple Junction under the Eel River Basin and in the offshore of Cascadia. The Coastal belt is exposed on land in northern California, yet its structure and stratigraphy are incompletely known because of discontinuous exposure, structural disruption, and lithologically non-distinctive clastic rocks. The intent of this report is to make available, in map form, aeromagnetic data covering the Coastal belt that provide a new dataset to aid in mapping, understanding, and interpreting the incompletely understood geology and structure in northern California.The newly merged aeromagnetic data over the Coastal belt of the Franciscan Complex reveal long, linear anomalies that indicate remarkably coherent structure within a terrane where mapping at the surface indicates complex deformation and that has been described as "broken formation" and, even locally as "mélange". The anomalies in the Coastal belt are primarily sourced by volcanic-rich graywackes and exotic blocks of basalt. Some anomalies along the contact of the Coastal belt with the Central belt are likely caused by local interleaving of components of the Coast Ranges ophiolite. These data can be used to map additional exotic blocks within the Coastal belt and to distinguish lithologically indistinct graywackes within the Coastal terrane. Using anomaly asymmetry allows projection of these "layers" into the subsurface. This analysis indicates predominant northeast dips consistent with tectonic interleaving of blocks within a subduction zone.

Modification of graphene oxide with amphiphilic double-crystalline block copolymer polyethylene-b-poly(ethylene oxide) with assistance of supercritical CO2 and its further functionalization.

PubMed

Zheng, Xiaoli; Xu, Qun; He, Linghao; Yu, Ning; Wang, Shanshan; Chen, Zhimin; Fu, JianWei

2011-05-19

Graphene oxide (GO) sheets were noncovalently modified with an amphiphilic double-crystalline block copolymer, polyethylene-b-poly(ethylene oxide) (PE-b-PEO) with assistance of supercritical CO(2) (SC CO(2)) in this work. The resulting PE-b-PEO/GO nanohybrids were characterized by transmission electron microscopy (TEM), wide-angle X-ray diffraction (WAXD), Fourier transform infrared spectroscopy (FTIR), and Raman spectra. Distinct morphologies of PE-b-PEO decorating on the surface of GO were obtained in different solvent systems and at different SC CO(2) pressures. We found that the solvent system and the SC CO(2) have significant influence on the crystallization, aggregation, or assembly behaviors of PE-b-PEO molecular chains on the GO sheets. The formation mechanism of the distinct nanohybrid structures is attributed to a relevant easy heteronucleation and the limited crystal growth of the block polymer on the surface of GO. The resulting modified GO sheets could find a broad spectrum of applications not only in producing graphene-based nanocomposites but also being used as a template to fabricate multifunctional structures due to the unique properties of PE-b-PEO. As a proof-of-concept, we further decorated the GO sheets with the as-prepared Au nanoparticles (Au NPs) and CdTe nanoparticles (CdTe NPs) with PE-b-PEO as the interlinker. Using the thiol-terminated PE-b-PEO as an interlinker, Au NPs can be densely assembled on the surface of GO via robust Au-S bonds. Furthermore, the photoluminescence quenching of CdTe NPs was more notable for PE-b-PEO/GO-CdTe hybrid compared to the GO-CdTe hybrid, suggesting that the electron transfer from the CdTe NPs to the GO sheets was enhanced with the PE-b-PEO interlinker. The availability of these affordable graphene-based multifunctional structures and their fundamental properties will open up new opportunities for nanoscience and nanotechnology and accelerate their applications. © 2011 American Chemical Society

The variation of crustal structure along the Song Ma Shear Zone, Northern Vietnam

NASA Astrophysics Data System (ADS)

Su, Chien-Min; Wen, Strong; Tang, Chi-Chia; Yeh, Yu-Lien; Chen, Chau-Huei

2018-06-01

Northern Vietnam is divided into two regions by suture zone. The southwestern region belongs to the Indochina block, and the northeastern region is a portion of the South China block with distinct geological characteristics. From previous studies, the closing the Paleotethys led the collision between the Indochina and South China blocks, and this collision form the suture zone in the Middle Triassic. In the Tertiary, Indian and Eurasian plates started to collide, and this collision caused the extrusion of the Indochina block along the suture zone and a clockwise rotation. Metamorphic rocks associated with the subduction process have been found at the Song Ma Shear Zone (SMSZ) from geological surveys, which indicated that the SMSZ is a possible boundary between the South China and Indochina block. However, according to previous study, there is an argument of whether the SMSZ is a subduction zone of the South China and Indochina plates or not. In this study, we applied the H-κ and the common conversion point (CCP) stacking method using teleseismic converted waves recorded by a seismic broadband array to obtain the Moho depth, VP/VS ratio and the crustal structure along the SMSZ. The CCP results are further used to identify whether the fault extends through the entire crust or not. We have selected two profiles along the SMSZ and a profile across the SMSZ for imaging lateral variations of impedance from stacking. According to H-κ stacking results, crustal thickness vary from 26.0 to 29.3 km, and the average of VP/VS ratio is about 1.77. Finally, the CCP results also show the heterogeneity of crust among the SMSZ. These evidences might support that SMSZ is the suture zone between the South China and Indochina plates.

New insights into the phenotypic covariance structure of the anthropoid cranium

PubMed Central

Makedonska, Jana

2014-01-01

In complex organisms, suites of non-random, highly intercorrelated phenotypic traits, organized according to their developmental history and forming semi-autonomous units (i.e. modules), have the potential to impose constraints on morphological diversification or to improve evolvability. Because of its structural, developmental and functional complexity, the cranium is arguably one of the best models for studying the interplay between developmental history and the need for various parts of a structure to specialize in different functions. This study evaluated the significance of two specific types of developmental imprints in the adult anthropoid cranium, those imposed by ossification pattern (i.e. ossification with and without a pre-existing cartilaginous phase) and those imposed by tissue origin (i.e. tissues derived principally from neural-crest vs. those derived from paraxial mesoderm). Specifically, this study tests the hypothesis that the face and the basicranium form two distinct modules with higher within-unit trait integration magnitudes compared with the cranium as a whole. Data on 12 anthropoid primate species were collected in the form of 23-dimensional landmarks digitized on cranial surface models that sample the basicranium as well as regions of functional importance during feeding. The presence of a significant modularity imprint in the adult cranium was assessed using a between-region within-species comparison of multivariate correlations (RV coefficients) obtained with partial least-squares, using within-module within-species eigenvalue variance (EV), and using cluster analyses and non-metric multidimensional scaling. In addition to addressing the validity of the cranial modularity hypothesis in anthropoids, this study addressed methodological aspects of the interspecific comparison of morphological integration, namely the effect of sample size and the effect of landmark number on integration magnitudes. Two methodological findings that are of significance to research in morphological integration are that: (i) a smaller sample size increases integration magnitude, but preserves the pattern of variation of integration magnitudes from block to block within species; and that (ii) the number of landmarks per cranial block does not significantly impact block integration magnitude measured as EV. Results from the analyses testing for cranial modularity imprints in the adult anthropoid cranium show that some facial landmarks covary more strongly with basicranial landmarks than with other facial landmarks. Cluster methods, non-metric multidimensional scaling and, to an extent, RV results show that the rostral and the zygomatic landmarks covary more strongly with the basicranial landmarks than they do with the molar landmarks. However, the rostral–zygomatic–basicranial block, the molar block, the facial block, the basicranial block and the other analyzed cranial and facial blocks are not more integrated than the cranium. Thus, the morphological variation in the adult anthropoid cranium is not significantly constrained by at least two of the potential developmental sources of its covariance structure. PMID:25406861

Nanoparticle Superlattice Engineering with DNA

NASA Astrophysics Data System (ADS)

Macfarlane, Robert J.; Lee, Byeongdu; Jones, Matthew R.; Harris, Nadine; Schatz, George C.; Mirkin, Chad A.

2011-10-01

A current limitation in nanoparticle superlattice engineering is that the identities of the particles being assembled often determine the structures that can be synthesized. Therefore, specific crystallographic symmetries or lattice parameters can only be achieved using specific nanoparticles as building blocks (and vice versa). We present six design rules that can be used to deliberately prepare nine distinct colloidal crystal structures, with control over lattice parameters on the 25- to 150-nanometer length scale. These design rules outline a strategy to independently adjust each of the relevant crystallographic parameters, including particle size (5 to 60 nanometers), periodicity, and interparticle distance. As such, this work represents an advance in synthesizing tailorable macroscale architectures comprising nanoscale materials in a predictable fashion.

Schematic construction of flanged nanobearings from double-walled carbon nanotubes.

PubMed

Shenai, Prathamesh Mahesh; Zhao, Yang

2010-08-01

The performance of nanobearings constructed from double walled carbon nanotubes is considered to be crucially dependent on the initial rotational speed. Wearless rotation ceases for a nanobearing operating beyond a certain angular velocity. We propose a new design of nanobearings by manipulation of double walled carbon nanotubes leading to a flanged structure which possesses a built-in hindrance to the intertube oscillation without obstructing rotational motion. Through blocking the possible leakage path for rotational kinetic energy to the intertube oscillatory motion, the flanged bearing lowers its dissipative tendency when set into motion. Using molecular dynamics, it is shown that on account of its distinctive structure, the flanged bearing has superior operating characteristics and a broader working domain.

The evolution of a Gondwanan collisional orogen: A structural and geochronological appraisal from the Southern Granulite Terrane, South India

NASA Astrophysics Data System (ADS)

Plavsa, Diana; Collins, Alan S.; Foden, John D.; Clark, Chris

2015-05-01

Gondwana amalgamated along a suite of Himalayan-scale collisional orogens, the roots of which lace the continents of Africa, South America, and Antarctica. The Southern Granulite Terrane of India is a generally well-exposed, exhumed, Gondwana-forming orogen that preserves a record of the tectonic evolution of the eastern margin of the East African Orogen during the Ediacaran-Cambrian (circa 600-500 Ma) as central Gondwana formed. The deformation associated with the closure of the Mozambique Ocean and collision of the Indian and East African/Madagascan cratonic domains is believed to have taken place along the southern margin of the Salem Block (the Palghat-Cauvery Shear System, PCSS) in the Southern Granulite Terrane. Investigation of the structural fabrics and the geochronology of the high-grade shear zones within the PCSS system shows that the Moyar-Salem-Attur shear zone to the north of the PCSS system is early Paleoproterozoic in age and associated with dextral strike-slip motion, while the Cauvery shear zone (CSZ) to the south of the PCSS system can be loosely constrained to circa 740-550 Ma and is associated with dip-slip dextral transpression and north side-up motion. To the south of the proposed suture zone (the Cauvery shear zone), the structural fabrics of the Northern Madurai Block suggest four deformational events (D1-D4), some of which are likely to be contemporaneous. The timing of high pressure-ultrahigh temperature metamorphism and deformation (D1-D3) in the Madurai Block (here interpreted as the southern extension of Azania) is constrained to circa 550-500 Ma and interpreted as representing collisional orogeny and subsequent orogenic collapse of the eastern margin of the East African Orogen. The disparity in the nature of the structural fabrics and the timing of the deformation in the Salem and the Madurai Blocks suggest that the two experienced distinct tectonothermal events prior to their amalgamation along the Cauvery shear zone during the Ediacaran/Cambrian.

Atomic structure of the Y complex of the nuclear pore

DOE PAGES

Kelley, Kotaro; Knockenhauer, Kevin E.; Kabachinski, Greg; ...

2015-03-30

The nuclear pore complex (NPC) is the principal gateway for transport into and out of the nucleus. Selectivity is achieved through the hydrogel-like core of the NPC. The structural integrity of the NPC depends on ~15 architectural proteins, which are organized in distinct subcomplexes to form the >40-MDa ring-like structure. In this paper, we present the 4.1-Å crystal structure of a heterotetrameric core element ('hub') of the Y complex, the essential NPC building block, from Myceliophthora thermophila. Using the hub structure together with known Y-complex fragments, we built the entire ~0.5-MDa Y complex. Our data reveal that the conserved coremore » of the Y complex has six rather than seven members. Finally, evolutionarily distant Y-complex assemblies share a conserved core that is very similar in shape and dimension, thus suggesting that there are closely related architectural codes for constructing the NPC in all eukaryotes.« less

Freezing polystyrene-b-poly(2-vinylpyridine) micelle nanoparticles with different nanostructures and sizes.

PubMed

Fan, Hailong; Jin, Zhaoxia

2014-04-28

Herein we report how to control the nanostructures and sizes of polystyrene-b-poly(2-vinylpyridine) (PS-b-P2VP) nanoparticles via manipulating freezing in solvent-exchange. By characterizing and analyzing the distinct structural features of the obtained nanoparticles, we recognized that micelle self-assembly happens in the precipitation of PS-b-P2VP when water is added into the block copolymer (BCP) solution. Solvent properties significantly influence micelle types that are vesicles in acetone/H2O and spherical micelles in tetrahydrofuran/H2O, respectively, thus further inducing different frozen nanostructures of the obtained nanoparticles, onion-like in acetone/H2O and large compound micelles in tetrahydrofuran/H2O. By changing the concentration of the block copolymers and the Vsolvent/VH2O ratio to modify the freezing stage at which block copolymer micelles are frozen, we can further control the size of the nanoparticles. Moreover, small molecules (phosphotungstic acid, pyrene, 1-pyrenebutyric acid) can be trapped into the block copolymer nanoparticles via the freezing process. Their distribution in the nanoparticles relies not only on the solvent property, but also on their interactions with block copolymers. The hybrid nanoparticles with ordered distribution of small molecules can be further changed to partially-void nanoparticles. Our study demonstrated that manipulating the freezing of block copolymers in the solvent exchange process is a simple and controllable fabrication method to generate BCP nanoparticles with different architectures.

Tectonic geomorphology of the New Madrid seismic zone based on imaging of digital topographic data

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

Mayer, L.

1993-03-01

Topographic analysis using digital elevation data of the New Madrid region focuses on topographic features that occur at several spatial scales and can be used to delineate distinct anomalies. In this region, topographic anomalies occur as domal or elongate uplifts and bowl-shaped depressions approximately 1--10 km in size, topographic lineaments, and differences in topographic blocking across 50 km long boundaries. In order to fully explain these topographic anomalies, tectonic processes may be required. Imaging is based on digital topographic data from USGS 30 arc-second, 3 arc-second, and 30 m resolutions. Imaging of these data uses standard imaging processing techniques tomore » examine topography within the contexts of geomorphological hypothesis testing. A good example is the use of thresholding to highlight areas of unusually high elevation given the hypothesis of fluvial landscape architecture. Thresholding delineates topographic features such as the Tiptonville dome which is strongly believed to be tectonic in origin. To determine the pattern of topographic blocking, defined as a pattern that topography assumes when constrained by active forces other than erosion alone, low frequency passing spatial convolutions are used as filters and the resulting data are sliced into blocks according to pseudoelevations that produce a stable block pattern. The resultant blocks are analyzed according to its structural pattern of block size and block orientation. This analysis suggests that a topographic boundary cuts across the Mississippi embayment from near the Newport pluton on the west, to the area south of Memphis on east.« less

Using tethered triblock copolymers to mediate the interaction between substrates

NASA Astrophysics Data System (ADS)

Chern, Shyh-Shi; Zhulina, Ekaterina B.; Pickett, Galen T.; Balazs, Anna C.

1998-04-01

Using scaling analysis and a self-consistent field (SCF) theory, we compress two copolymer-coated surfaces and isolate conditions that yield multiple, distinct minima in the interaction profile. We focus on planar surfaces that are coated with ABC triblock copolymers. Tethered to the surface by the last monomer in the C block, the copolymers are grafted at relatively low densities. The surrounding solution is a poor solvent for both the A and C blocks, and is a good solvent for the B blocks. Through scaling theory, we pinpoint the parameters that yield two minima in the interaction profile. The SCF calculations reveal the changes in the morphology of the polymers as the layers are compressed. Through both studies, we determine how the morphological changes give rise to the observed surface interactions. The results provide guidelines for creating polymer-coated colloidal systems that can form two stable crystal structures. Such systems could be used for bistable, optical switches. The findings also yield a prescription for creating systems that exhibit additional minima in the free energy of interaction.

Timing of terrane accretion in eastern and east-central Maine

NASA Astrophysics Data System (ADS)

Ludman, Allan

1986-05-01

The Norumbega fault zone is often cited as a post-Acadian suture between exotic blocks, even though stratigraphic, structural, and metamorphic data indicate that there is little offset of the Silurian-Devonian strata that the zone cuts in eastern Maine. Similarly, the Kingman fault zone has been shown by gravity and geochemical studies to separate distinct crustal blocks, whereas mapping shows that it lies entirely within a Silurian turbidite package. These conflicts are resolved if the two fault zones represent boundaries between Ordovician or older crustal blocks that had accreted to form a composite terrane prior to deposition of the cover sequences. The faults now mapped within these younger rocks formed by reactivation of the pre-Silurian boundaries during late Acadian time; movement continued until the late Carboniferous. Most of the accretionary history of Maine had thus ended before the Silurian. A complex composite terrane may have formed during Cambrian-Ordovician time that (1) interacted with cratonic North America during the Taconian orogeny and (2) became the “basement” upon which the Silurian and Lower Devonian strata of eastern Maine were deposited.

A novel method for a multi-level hierarchical composite with brick-and-mortar structure

PubMed Central

Brandt, Kristina; Wolff, Michael F. H.; Salikov, Vitalij; Heinrich, Stefan; Schneider, Gerold A.

2013-01-01

The fascination for hierarchically structured hard tissues such as enamel or nacre arises from their unique structure-properties-relationship. During the last decades this numerously motivated the synthesis of composites, mimicking the brick-and-mortar structure of nacre. However, there is still a lack in synthetic engineering materials displaying a true hierarchical structure. Here, we present a novel multi-step processing route for anisotropic 2-level hierarchical composites by combining different coating techniques on different length scales. It comprises polymer-encapsulated ceramic particles as building blocks for the first level, followed by spouted bed spray granulation for a second level, and finally directional hot pressing to anisotropically consolidate the composite. The microstructure achieved reveals a brick-and-mortar hierarchical structure with distinct, however not yet optimized mechanical properties on each level. It opens up a completely new processing route for the synthesis of multi-level hierarchically structured composites, giving prospects to multi-functional structure-properties relationships. PMID:23900554

A novel method for a multi-level hierarchical composite with brick-and-mortar structure.

PubMed

Brandt, Kristina; Wolff, Michael F H; Salikov, Vitalij; Heinrich, Stefan; Schneider, Gerold A

2013-01-01

The fascination for hierarchically structured hard tissues such as enamel or nacre arises from their unique structure-properties-relationship. During the last decades this numerously motivated the synthesis of composites, mimicking the brick-and-mortar structure of nacre. However, there is still a lack in synthetic engineering materials displaying a true hierarchical structure. Here, we present a novel multi-step processing route for anisotropic 2-level hierarchical composites by combining different coating techniques on different length scales. It comprises polymer-encapsulated ceramic particles as building blocks for the first level, followed by spouted bed spray granulation for a second level, and finally directional hot pressing to anisotropically consolidate the composite. The microstructure achieved reveals a brick-and-mortar hierarchical structure with distinct, however not yet optimized mechanical properties on each level. It opens up a completely new processing route for the synthesis of multi-level hierarchically structured composites, giving prospects to multi-functional structure-properties relationships.

A novel method for a multi-level hierarchical composite with brick-and-mortar structure

NASA Astrophysics Data System (ADS)

Brandt, Kristina; Wolff, Michael F. H.; Salikov, Vitalij; Heinrich, Stefan; Schneider, Gerold A.

2013-07-01

The fascination for hierarchically structured hard tissues such as enamel or nacre arises from their unique structure-properties-relationship. During the last decades this numerously motivated the synthesis of composites, mimicking the brick-and-mortar structure of nacre. However, there is still a lack in synthetic engineering materials displaying a true hierarchical structure. Here, we present a novel multi-step processing route for anisotropic 2-level hierarchical composites by combining different coating techniques on different length scales. It comprises polymer-encapsulated ceramic particles as building blocks for the first level, followed by spouted bed spray granulation for a second level, and finally directional hot pressing to anisotropically consolidate the composite. The microstructure achieved reveals a brick-and-mortar hierarchical structure with distinct, however not yet optimized mechanical properties on each level. It opens up a completely new processing route for the synthesis of multi-level hierarchically structured composites, giving prospects to multi-functional structure-properties relationships.

Finite-frequency P-wave tomography of the Western Canada Sedimentary Basin: Implications for the lithospheric evolution in Western Laurentia

NASA Astrophysics Data System (ADS)

Chen, Yunfeng; Gu, Yu Jeffrey; Hung, Shu-Huei

2017-02-01

The lithosphere beneath the Western Canada Sedimentary Basin has potentially undergone Precambrian subduction and collisional orogenesis, resulting in a complex network of crustal domains. To improve the understanding of its evolutionary history, we combine data from the USArray and three regional networks to invert for P-wave velocities of the upper mantle using finite-frequency tomography. Our model reveals distinct, vertically continuous high (> 1%) velocity perturbations at depths above 200 km beneath the Precambrian Buffalo Head Terrane, Hearne craton and Medicine Hat Block, which sharply contrasts with those beneath the Canadian Rockies (<- 1%) at comparable depths. The P velocity increases from - 0.5% above 70 km depth to 1.5% at 330 km depth beneath southern Alberta, which provides compelling evidence for a deep, structurally complex Hearne craton. In comparison, the lithosphere is substantially thinner beneath the adjacent Buffalo Head Terrane (160 km) and Medicine Hat Block (200 km). These findings are consistent with earlier theories of tectonic assembly in this region, which featured distinct Archean and Proterozoic plate convergences between the Hearne craton and its neighboring domains. The highly variable, bimodally distributed craton thicknesses may also reflect different lithospheric destruction processes beneath the western margin of Laurentia.

General and Direct Method for Preparing Oligonucleotide-Functionalized Metal-Organic Framework Nanoparticles.

PubMed

Wang, Shunzhi; McGuirk, C Michael; Ross, Michael B; Wang, Shuya; Chen, Pengcheng; Xing, Hang; Liu, Yuan; Mirkin, Chad A

2017-07-26

Metal-organic frameworks (MOFs) are a class of modular, crystalline, and porous materials that hold promise for storage and transport of chemical cargoes. Though MOFs have been studied in bulk forms, ways of deliberately manipulating the external surface functionality of MOF nanoparticles are less developed. A generalizable approach to modify their surfaces would allow one to impart chemical functionality onto the particle surface that is independent of the bulk MOF structure. Moreover, the use of a chemically programmable ligand, such as DNA, would allow for the manipulation of interparticle interactions. Herein, we report a coordination chemistry-based strategy for the surface functionalization of the external metal nodes of MOF nanoparticles with terminal phosphate-modified oligonucleotides. The external surfaces of nine distinct archetypical MOF particles containing four different metal species (Zr, Cr, Fe, and Al) were successfully functionalized with oligonucleotides, illustrating the generality of this strategy. By taking advantage of the programmable and specific interactions of DNA, 11 distinct MOF particle-inorganic particle core-satellite clusters were synthesized. In these hybrid nanoclusters, the relative stoichiometry, size, shape, and composition of the building blocks can all be independently controlled. This work provides access to a new set of nucleic acid-nanoparticle conjugates, which may be useful as programmable material building blocks and as probes for measuring and manipulating intracellular processes.

Asymmetric organic-inorganic hybrid membrane formation via block copolymer-nanoparticle co-assembly.

PubMed

Gu, Yibei; Dorin, Rachel M; Wiesner, Ulrich

2013-01-01

A facile method for forming asymmetric organic-inorganic hybrid membranes for selective separation applications is developed. This approach combines co-assembly of block copolymer (BCP) and inorganic nanoparticles (NPs) with non-solvent induced phase separation. The method is successfully applied to two distinct molar mass BCPs with different fractions of titanium dioxide (TiO2) NPs. The resulting hybrid membranes exhibit structural asymmetry with a thin nanoporous surface layer on top of a macroporous fingerlike support layer. Key parameters that dictate membrane surface morphology include the fraction of inorganics used and the length of time allowed for surface layer development. The resulting membranes exhibit both good selectivity and high permeability (3200 ± 500 Lm(-2) h(-1) bar(-1)). This fast and straightforward synthesis method for asymmetric hybrid membranes provides a new self-assembly platform upon which multifunctional and high-performance organic-inorganic hybrid membranes can be formed.

A combinatorial code for pattern formation in Drosophila oogenesis.

PubMed

Yakoby, Nir; Bristow, Christopher A; Gong, Danielle; Schafer, Xenia; Lembong, Jessica; Zartman, Jeremiah J; Halfon, Marc S; Schüpbach, Trudi; Shvartsman, Stanislav Y

2008-11-01

Two-dimensional patterning of the follicular epithelium in Drosophila oogenesis is required for the formation of three-dimensional eggshell structures. Our analysis of a large number of published gene expression patterns in the follicle cells suggests that they follow a simple combinatorial code based on six spatial building blocks and the operations of union, difference, intersection, and addition. The building blocks are related to the distribution of inductive signals, provided by the highly conserved epidermal growth factor receptor and bone morphogenetic protein signaling pathways. We demonstrate the validity of the code by testing it against a set of patterns obtained in a large-scale transcriptional profiling experiment. Using the proposed code, we distinguish 36 distinct patterns for 81 genes expressed in the follicular epithelium and characterize their joint dynamics over four stages of oogenesis. The proposed combinatorial framework allows systematic analysis of the diversity and dynamics of two-dimensional transcriptional patterns and guides future studies of gene regulation.

Tailored hierarchical micelle architectures using living crystallization-driven self-assembly in two dimensions

NASA Astrophysics Data System (ADS)

Hudson, Zachary M.; Boott, Charlotte E.; Robinson, Matthew E.; Rupar, Paul A.; Winnik, Mitchell A.; Manners, Ian

2014-10-01

Recent advances in the self-assembly of block copolymers have enabled the precise fabrication of hierarchical nanostructures using low-cost solution-phase protocols. However, the preparation of well-defined and complex planar nanostructures in which the size is controlled in two dimensions (2D) has remained a challenge. Using a series of platelet-forming block copolymers, we have demonstrated through quantitative experiments that the living crystallization-driven self-assembly (CDSA) approach can be extended to growth in 2D. We used 2D CDSA to prepare uniform lenticular platelet micelles of controlled size and to construct precisely concentric lenticular micelles composed of spatially distinct functional regions, as well as complex structures analogous to nanoscale single- and double-headed arrows and spears. These methods represent a route to hierarchical nanostructures that can be tailored in 2D, with potential applications as diverse as liquid crystals, diagnostic technology and composite reinforcement.

Eastern rim of the Chesapeake Bay impact crater: Morphology, stratigraphy, and structure

USGS Publications Warehouse

Poag, C.W.

2005-01-01

This study reexamines seven reprocessed (increased vertical exaggeration) seismic reflection profiles that cross the eastern rim of the Chesapeake Bay impact crater. The eastern rim is expressed as an arcuate ridge that borders the crater in a fashion typical of the "raised" rim documented in many well preserved complex impact craters. The inner boundary of the eastern rim (rim wall) is formed by a series of raterfacing, steep scarps, 15-60 m high. In combination, these rim-wall scarps represent the footwalls of a system of crater-encircling normal faults, which are downthrown toward the crater. Outboard of the rim wall are several additional normal-fault blocks, whose bounding faults trend approximately parallel to the rim wall. The tops of the outboard fault blocks form two distinct, parallel, flat or gently sloping, terraces. The innermost terrace (Terrace 1) can be identified on each profile, but Terrace 2 is only sporadically present. The terraced fault blocks are composed mainly of nonmarine, poorly to moderately consolidated, siliciclastic sediments, belonging to the Lower Cretaceous Potomac Formation. Though the ridge-forming geometry of the eastern rim gives the appearance of a raised compressional feature, no compelling evidence of compressive forces is evident in the profiles studied. The structural mode, instead, is that of extension, with the clear dominance of normal faulting as the extensional mechanism. 

Antibody VH and VL recombination using phage and ribosome display technologies reveals distinct structural routes to affinity improvements with VH-VL interface residues providing important structural diversity

PubMed Central

Groves, Maria AT; Amanuel, Lily; Campbell, Jamie I; Rees, D Gareth; Sridharan, Sudharsan; Finch, Donna K; Lowe, David C; Vaughan, Tristan J

2014-01-01

In vitro selection technologies are an important means of affinity maturing antibodies to generate the optimal therapeutic profile for a particular disease target. Here, we describe the isolation of a parent antibody, KENB061 using phage display and solution phase selections with soluble biotinylated human IL-1R1. KENB061 was affinity matured using phage display and targeted mutagenesis of VH and VL CDR3 using NNS randomization. Affinity matured VHCDR3 and VLCDR3 library blocks were recombined and selected using phage and ribosome display protocol. A direct comparison of the phage and ribosome display antibodies generated was made to determine their functional characteristics. PMID:24256948

Extensional tectonics and collapse structures in the Suez Rift (Egypt)

NASA Technical Reports Server (NTRS)

Chenet, P. Y.; Colletta, B.; Desforges, G.; Ousset, E.; Zaghloul, E. A.

1985-01-01

The Suez Rift is a 300 km long and 50 to 80 km wide basin which cuts a granitic and metamorphic shield of Precambrian age, covered by sediments of Paleozoic to Paleogene age. The rift structure is dominated by tilted blocks bounded by NW-SE normal faults. The reconstruction of the paleostresses indicates a N 050 extension during the whole stage of rifting. Rifting began 24 My ago with dikes intrusions; main faulting and subsidence occurred during Early Miocene producing a 80 km wide basin (Clysmic Gulf). During Pliocene and Quaternary times, faulting is still active but subsidence is restricted to a narrower area (Present Gulf). On the Eastern margin of the gulf, two sets of fault trends are predominant: (1) N 140 to 150 E faults parallel to the gulf trend with pure dip-slip displacement; and (2) cross faults, oriented NOO to N 30 E that have a strike-slip component consistent with the N 050 E distensive stress regime. The mean dip cross fault is steeper (70 to 80 deg) than the dip of the faults parallel to the Gulf (30 to 70 deg). These two sets of fault define diamond shaped tilted block. The difference of mechanical behavior between the basement rocks and the overlying sedimentary cover caused structural disharmony and distinct fault geometries.

Trophic structure of a coastal fish community determined with diet and stable isotope analyses.

PubMed

Malek, A J; Collie, J S; Taylor, D L

2016-09-01

A combination of dietary guild analysis and nitrogen (δ(15) N) and carbon (δ(13) C) stable-isotope analysis was used to assess the trophic structure of the fish community in Rhode Island and Block Island Sounds, an area off southern New England identified for offshore wind energy development. In the autumn of 2009, 2010 and 2011, stomach and tissue samples were taken from 20 fish and invertebrate species for analysis of diet composition and δ(15) N and δ(13) C signatures. The food chain in Rhode Island and Block Island Sounds comprises approximately four trophic levels within which the fish community is divided into distinct dietary guilds, including planktivores, benthivores, crustacivores and piscivores. Within these guilds, inter-species isotopic and dietary overlap is high, suggesting that resource partitioning or competitive interactions play a major role in structuring the fish community. Carbon isotopes indicate that most fishes are supported by pelagic phytoplankton, although there is evidence that benthic production also plays a role, particularly for obligate benthivores such as skates Leucoraja spp. This type of analysis is useful for developing an ecosystem-based approach to management, as it identifies species that act as direct links to basal resources as well as species groups that share trophic roles. © 2016 The Fisheries Society of the British Isles.

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

PubMed Central

Kang, Yanyong; Zhou, X. Edward; Gao, Xiang; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; Barty, Anton; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Ke, Jiyuan; Eileen Tan, M. H.; Zhang, Chenghai; Moeller, Arne; West, Graham M.; Pascal, Bruce; Van Eps, Ned; Caro, Lydia N.; Vishnivetskiy, Sergey A.; Lee, Regina J.; Suino-Powell, Kelly M.; Gu, Xin; Pal, Kuntal; Ma, Jinming; Zhi, Xiaoyong; Boutet, Sébastien; Williams, Garth J.; Messerschmidt, Marc; Gati, Cornelius; Zatsepin, Nadia A.; Wang, Dingjie; James, Daniel; Basu, Shibom; Roy-Chowdhury, Shatabdi; Conrad, Chelsie; Coe, Jesse; Liu, Haiguang; Lisova, Stella; Kupitz, Christopher; Grotjohann, Ingo; Fromme, Raimund; Jiang, Yi; Tan, Minjia; Yang, Huaiyu; Li, Jun; Wang, Meitian; Zheng, Zhong; Li, Dianfan; Howe, Nicole; Zhao, Yingming; Standfuss, Jörg; Diederichs, Kay; Dong, Yuhui; Potter, Clinton S; Carragher, Bridget; Caffrey, Martin; Jiang, Hualiang; Chapman, Henry N.; Spence, John C. H.; Fromme, Petra; Weierstall, Uwe; Ernst, Oliver P.; Katritch, Vsevolod; Gurevich, Vsevolod V.; Griffin, Patrick R.; Hubbell, Wayne L.; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2015-01-01

G protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signaling to numerous G protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly, in which rhodopsin uses distinct structural elements, including TM7 and Helix 8 to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ~20° rotation between the N- and C- domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signaling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology. PMID:26200343

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

DOE PAGES

Kang, Yanyong; Zhou, X. Edward; Gao, Xiang; ...

2015-07-22

G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ~20° rotationmore » between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. In conclusion, this structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.« less

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser.

PubMed

Kang, Yanyong; Zhou, X Edward; Gao, Xiang; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; Barty, Anton; White, Thomas A; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W; Ke, Jiyuan; Tan, M H Eileen; Zhang, Chenghai; Moeller, Arne; West, Graham M; Pascal, Bruce D; Van Eps, Ned; Caro, Lydia N; Vishnivetskiy, Sergey A; Lee, Regina J; Suino-Powell, Kelly M; Gu, Xin; Pal, Kuntal; Ma, Jinming; Zhi, Xiaoyong; Boutet, Sébastien; Williams, Garth J; Messerschmidt, Marc; Gati, Cornelius; Zatsepin, Nadia A; Wang, Dingjie; James, Daniel; Basu, Shibom; Roy-Chowdhury, Shatabdi; Conrad, Chelsie E; Coe, Jesse; Liu, Haiguang; Lisova, Stella; Kupitz, Christopher; Grotjohann, Ingo; Fromme, Raimund; Jiang, Yi; Tan, Minjia; Yang, Huaiyu; Li, Jun; Wang, Meitian; Zheng, Zhong; Li, Dianfan; Howe, Nicole; Zhao, Yingming; Standfuss, Jörg; Diederichs, Kay; Dong, Yuhui; Potter, Clinton S; Carragher, Bridget; Caffrey, Martin; Jiang, Hualiang; Chapman, Henry N; Spence, John C H; Fromme, Petra; Weierstall, Uwe; Ernst, Oliver P; Katritch, Vsevolod; Gurevich, Vsevolod V; Griffin, Patrick R; Hubbell, Wayne L; Stevens, Raymond C; Cherezov, Vadim; Melcher, Karsten; Xu, H Eric

2015-07-30

G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ∼20° rotation between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

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

Kang, Yanyong; Zhou, X. Edward; Gao, Xiang

G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ~20° rotationmore » between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. In conclusion, this structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.« less

Definition of Two Angiogenic Pathways by Distinct α_v Integrins

NASA Astrophysics Data System (ADS)

Friedlander, Martin; Brooks, Peter C.; Shaffer, Robert W.; Kincaid, Christine M.; Varner, Judith A.; Cheresh, David A.

1995-12-01

Angiogenesis depends on cytokines and vascular cell adhesion events. Two cytokine-dependent pathways of angiogenesis were shown to exist and were defined by their dependency on distinct vascular cell integrins. In vivo angiogenesis in corneal or chorioallantoic membrane models induced by basic fibroblast growth factor or by tumor necrosis factor-α depended on α_vβ_3, whereas angiogenesis initiated by vascular endothelial growth factor, transforming growth factor-α, or phorbol ester depended on α_vβ_5. Antibody to each integrin selectively blocked one of these pathways, and a cyclic peptide antagonist of both integrins blocked angiogenesis stimulated by each cytokine tested. These pathways are further distinguished by their sensitivity to calphostin C, an inhibitor of protein kinase C that blocked angiogenesis potentiated by α_vβ_5 but not by α_vβ_3.

The sensitivity of GNSS measurements in Fennoscandia to distinct three-dimensional upper-mantle structures

NASA Astrophysics Data System (ADS)

Steffen, Holger; Wu, Patrick

2015-04-01

This poster will present the results of Steffen & Wu (2014). The sensitivity of GNSS measurements in Fennoscandia to nearby viscosity variations in the upper mantle is investigated using a three-dimensional finite element model of glacial isostatic adjustment (GIA). Based on the lateral viscosity structure inferred from seismic tomography and the location of the ice margin at the last glacial maximum (LGM), the GIA earth model is subdivided into four layers, where each of them contains an amalgamation of about 20 blocks of different shapes in the central area. The sensitivity kernels of the three velocity components at 10 selected GNSS stations are then computed for all the blocks. We find that GNSS stations within the formerly glaciated area are most sensitive to mantle viscosities below and in its near proximity, i.e., within about 250 km in general. However, this can be as large as 1000 km if the stations lie near the center of uplift. The sensitivity of all stations to regions outside the ice margin during the LGM is generally negligible. In addition, it is shown that prominent structures in the second (250-450 km depth) and third layers (450-550 km depth) of the upper mantle may be readily detected by GNSS measurements, while the viscosity in the first mantle layer below the lithosphere (70-250 km depth) along the Norwegian coast, which is related to lateral lithospheric thickness variation there, can also be detected but with limited sensitivity. For future investigations on the lateral viscosity structure, preference should be on GNSS stations within the LGM ice margin. But these stations can be grouped into clusters to improve the inference of viscosity in a specific area. However, the GNSS measurements used in such inversion should be weighted according to their sensitivity. Such weighting should also be applied when they are used in combination with other GIA data (e.g., relative sea-level and gravity data) for the inference of mantle viscosity. Reference: Steffen, H. and Wu, P.: The sensitivity of GNSS measurements in Fennoscandia to distinct three-dimensional upper-mantle structures, Solid Earth, 5, 557-567, doi:10.5194/se-5-557-2014, 2014.

Structural inheritance and coastal geomorphology in SW Brittany, France: An onshore/offshore integrated approach

NASA Astrophysics Data System (ADS)

Raimbault, Céline; Duperret, Anne; Le Gall, Bernard; Authemayou, Christine

2018-04-01

The Variscan crystalline basement exposed along the SW Brittany coast recorded extensive long-term planation processes during Mesozoic times. Detailed onshore-offshore mapping (600 km2) in the Penmarc'h-Concarneau granitic coastal area reveals a km-scale, deeply fractured submarine rocky shelf. High-resolution offshore imagery (bathymetry and seismic reflection dataset), combined to structural field investigations, on these surfaces allow us to identify a preserved network of both ductile and brittle structures. The inherited fault pattern is dominated by the N160°E-trending and long-lived Concarneau-Toulven fault zone (CTFS) that separates two distinct morphostructural blocks, and strongly influences the seaward limit of the Concarneau submarine rocky shelf, as well as the linear coastline of the Concarneau embayment. The structural imprint of the CTFS decreases progressively westwards with respect to a composite network of large-scale N50°E- and N140°E-oriented faults bounding the seaward edge of the Penmarc'h rocky shelf. The latter in turn splits into three large-scale blocks along N50°E- (La Torche Fault - LTF), N140°E- (Saint Guénolé Fault - SGF) and N160°E-trending normal faults. The morphostructural evolutionary model applied here to the Penmarc'h-Concarneau granitic coastal area resulted from the combined effects of structural Variscan inheritance and post-Variscan tectonics. Paleo-stress analysis of striated fault planes indicates three main Cenozoic tectonic events, inferred to have operated from Eocene to post-Oligocene times. The 3D-architecture of the Concarneau embayment, as a rocky shelf partially sealed with quaternary sediments, chiefly resulted from the reactivation of the CTFS during Eocene and Oligocene times. Further west, the surface of the Penmarc'h rocky shelf was tilted southeastward by the brittle reactivation of the LTF, and dissected by a horst-graben network post-Oligocene in age. The present-day morphology of the Penmarc'h and Concarneau domains depends on distinct driving processes: the Concarneau N160°E coastline is clearly controlled by tectonic processes via the CTFS, while the Penmarc'h headland land-sea contact appears to have been shaped by post-Cenozoic eustatism.

Integrating geology and geomorphology; the key to unlocking Quaternary tectonic framework of the San Andreas Fault zone in the San Gorgonio Pass region, southern California

NASA Astrophysics Data System (ADS)

Kendrick, K. J.; Matti, J. C.

2012-12-01

The San Gorgonio Pass (SGP) region of southern California is a locus of long-continued Quaternary deformation and landscape evolution within a structural complexity, colloquially referred to as a knot in the San Andreas Fault (SAF) zone. The geomorphology of the SGP region reflects the complex history of geologic events involved in the formation and resolution of this structural knot. We recognize five morphologically distinct terrains in and around SGP; the San Gorgonio Block (SGB), Yucaipa Ridge (YRB), Pisgah Peak (PPB), Kitching Peak (KPB), and Devil's Garden blocks (DGB). Morphometric analyses, including drainage density, hypsometry, topographic profiles, and stream-power measurements and discontinuities, consistently demonstrate distinctions between the blocks. Our focus in this study is on the KPB and PPB terrains, both developed in crystalline rocks of San Gabriel Mountains type. KPB is bounded on the north by the Mission Creek strand of the SAF and on the east by the Whitewater Fault; PPB is bounded on the north by the San Bernardino strand of the SAF, which continues southeastward into the core of SGP and there separates PPB from KPB. KPB has significantly greater topographic relief than PPB, and the two blocks have internal morphometric and geologic characteristics that differ significantly. Canyons in KPB lack thick Quaternary alluvial fills, and hillslopes have shed numerous bedrock landslides. Canyons in PPB contain large volumes of Middle-Pleistocene through Holocene alluvium, associated with areally extensive relict geomorphic surfaces. We use the geomorphic differences, along with geologic factors, to reconstruct tectonically driven landscape evolution over the last 100-200 Ka years. The KPB and PPB both are bounded southward by contractional structures of the San Gorgonio Pass Fault zone (SGPFZ), but geologic complexity within this zone differs markedly south of each block. South of KPB, the SGPFZ consists of multiple thrust-fault strands, some older than 500 ka, has a wide spatial footprint along a N-S axis, and Holocene alluvium is disrupted by numerous fault scarps. By contrast, south of PPB the SGPFZ consists of fewer thrust-fault strands, has a relatively narrow footprint, and faults breaking Holocene deposits are uncommon. The San Bernardino strand of the SAF intersects the SGPFZ at about the boundary between these two domains. Morphometric data indicate that the KPB has undergone significantly greater uplift than the PPB since inception of the San Bernardino strand, proposed by Matti and Morton (1993) to have occurred at ~125ka. Age estimates associated with the PPB and DGB allow us to broadly estimate relative uplift rates. Drainage reconstruction of the Whitewater River and its tributaries across the YRB likewise allow us to validate and refine the uplift estimated by Spotila and others (2001). YRB has been uplifted relative to SGB since the inception of the Mill Creek Strand of the SAF.

Preservation of adobe buildings. Study of materials

NASA Astrophysics Data System (ADS)

Velosa, A.; Rocha, F.; Costa, C.; Varum, H.

2012-04-01

Adobe buildings are common in the central region of Portugal due to the lack of natural stone in the surrounding area. This type of construction technique lasted until the 20th Century, at which time cementitious materials, with faster hardening and greater structural capacity substituted traditional materials and techniques. Currently, a significant percentage of these buildings is vacant and many are degraded and in need of conservation actions. Adobes from central Portugal are distinctive as they are lightly coloured and made from air lime and quarry sand. Although some adobes were manufactured locally, most were produced almost 'industrially' and sold to nearby regions. In order to preserve this heritage, conservation actions must be undertaken. So as to ensure the adequacy of these actions and compatibility between original materials and new ones, a thorough study of adobe compostion is mandatory. The current study is an initial step in the characterization of earth based construction materials from central Portugal. Adobe samples were collected from residential buildings in two different locations. The determination of the composition of adobe blocks encompassed the determination of the binder fraction and of their chemical composition and also the particle size analysis of the aggregate. For this purpose FRX analysis, acid dissolution and dry sieving were performed. Methylene blue test was also executed in order to determine the clay fraction. Additionally, the mineral composition of powder samples and oriented samples was performed using XRD analysis in order to determine the clay minerals present in the blocks. As adobe blocks are extremely prone to the action of water the Geelong test was undertaken in order to provide information in terms of durability. It was concluded that air lime was generally used in adobe compositions. However, the clay content varies in adobes from different regions, providing distinct durability characteristics to these materials.

Design and synthesis of diverse functional kinked nanowire structures for nanoelectronic bioprobes.

PubMed

Xu, Lin; Jiang, Zhe; Qing, Quan; Mai, Liqiang; Zhang, Qingjie; Lieber, Charles M

2013-02-13

Functional kinked nanowires (KNWs) represent a new class of nanowire building blocks, in which functional devices, for example, nanoscale field-effect transistors (nanoFETs), are encoded in geometrically controlled nanowire superstructures during synthesis. The bottom-up control of both structure and function of KNWs enables construction of spatially isolated point-like nanoelectronic probes that are especially useful for monitoring biological systems where finely tuned feature size and structure are highly desired. Here we present three new types of functional KNWs including (1) the zero-degree KNW structures with two parallel heavily doped arms of U-shaped structures with a nanoFET at the tip of the "U", (2) series multiplexed functional KNW integrating multi-nanoFETs along the arm and at the tips of V-shaped structures, and (3) parallel multiplexed KNWs integrating nanoFETs at the two tips of W-shaped structures. First, U-shaped KNWs were synthesized with separations as small as 650 nm between the parallel arms and used to fabricate three-dimensional nanoFET probes at least 3 times smaller than previous V-shaped designs. In addition, multiple nanoFETs were encoded during synthesis in one of the arms/tip of V-shaped and distinct arms/tips of W-shaped KNWs. These new multiplexed KNW structures were structurally verified by optical and electron microscopy of dopant-selective etched samples and electrically characterized using scanning gate microscopy and transport measurements. The facile design and bottom-up synthesis of these diverse functional KNWs provides a growing toolbox of building blocks for fabricating highly compact and multiplexed three-dimensional nanoprobes for applications in life sciences, including intracellular and deep tissue/cell recordings.

The nature of Archean terrane boundaries: an example from the northern Wyoming Province

USGS Publications Warehouse

Mogk, D.W.; Mueller, P.A.; Wooden, J.L.

1992-01-01

The Archean northern Wyoming Province can be subdivided into two geologically distinct terranes, the Beartooth-Bighorn magmatic terrane (BBMT) and the Montana metasedimentary terrane (MMT). The BBMT is characterized by voluminous Late Archean (2.90-2.74 Ga) magmatic rocks (primarily tonalite, trondhjemite, and granite); metasedimentary rocks are preserved only as small, rare enclaves in this magmatic terrane. The magmatic rocks typically have geochemical and isotopic signatures that suggest petrogenesis in a continental magmatic arc environment. The MMT, as exposed in the northern Gallatin and Madison Ranges, is dominated by Middle Archean trondhjemitic gneisses (3.2-3.0 Ga); metasedimentary rocks, however, are significantly more abundant than in the BBMT. Each terrane has experienced a separate and distinct geologic history since at least 3.6 Ga ago based on differences in metamorphic and structural styles, composition of magmatic and metasupracrustal rocks, and isotopic ages; consequently, these may be described as discrete terranes in the Cordilleran sense. Nonetheless, highly radiogenic and distinctive Pb-Pb isotopic signatures in rocks of all ages in both terranes indicate that the two terranes share a significant aspect of their history. This suggests that these two Early to Middle Archean crustal blocks, that initially evolved as part of a larger crustal province, experienced different geologic histories from at least 3.6 Ga until their juxtaposition in the Late Archean (between 2.75 to 2.55 Ga ago). Consequently, the boundary between the BBMT and MMT appears to separate terranes that are not likely to be exotic in the sense of their Phanerozoic counterparts. Other Archean provinces do appear to contain crustal blocks with different isotopic signatures (e.g. West Greenland, India, South Africa). The use of the term exotic, therefore, must be cautious in situations where geographic indicators such as paleontologic and/or paleomagnetic data are not available. In these cases, isotopic signatures are one of the most useful features for assessing overall genetic relations amongst geologically distinct terranes. ?? 1992.

Middle Jurassic Radiolaria from a siliceous argillite block in a structural melange zone near Viqueque, Timor Leste: Paleogeographic implications

NASA Astrophysics Data System (ADS)

Haig, David W.; Bandini, Alexandre Nicolas

2013-10-01

Thin-bedded siliceous argillite forming a large block within a structural melange zone at Viqueque, Timor Leste, has yielded a Middle Jurassic (late Bathonian-early Callovian) radiolarian assemblage belonging to Unitary Association Zone 7. Fifty-five species are recognized and illustrated, forming the most diverse radiolarian fauna yet documented from the Jurassic of Timor. The fauna shows little similarity in species content to the few other assemblages previously listed from the Middle or Late Jurassic of Timor, and also has few species in common with faunas known elsewhere in the region from Rotti, Sumatra, South Kalimantan, and Sula. Based on lithofacies similarities and age, the siliceous argillite succession in the melange block at Viqueque is included in the Noni Group originally described as the lower part of the Palelo Series in West Timor. In terms of lithofacies, the Noni Group is distinct from other stratigraphic units known in Timor. It may be associated with volcanic rocks but age relationships are uncertain, although some of the radiolarian cherts in the Noni Group in West Timor have been reported to include tuffaceous sediment. The deep-water character of the siliceous hemipelagite-pelagite facies, the probable volcanic association, and an age close to that of continental breakup in the region suggest deposition in a newly rifted Indian Ocean. In Timor's tectonostratigraphic classification scheme, the Noni Group is here placed in the "Indian Ocean Megasequence".

Leukemia inhibitory factor: a novel bone-active cytokine.

PubMed

Reid, L R; Lowe, C; Cornish, J; Skinner, S J; Hilton, D J; Willson, T A; Gearing, D P; Martin, T J

1990-03-01

A number of cytokines have been found to be potent regulators of bone resorption and to share the properties originally attributed to osteoclast-activating factor. One such activity, differentiation-inducing factor (DIF, D-factor) from mouse spleen cells, shares a number of biological and biochemical properties with the recently characterized and cloned leukemia inhibitory factor (LIF). We have assessed the effects of recombinant LIF on bone resorption and other parameters in neonatal mouse calvaria. Both recombinant murine and human (h) LIFs stimulated 45Ca release from prelabeled calvaria in a dose-dependent manner. The increase in bone resorption was associated with an increase in the number of osteoclasts per mm2 bone. The osteolytic effect of hLIF were blocked by 10(-7) M indomethacin. hLIF also stimulated incorporation of [3H] thymidine into calvaria, but the dose-response relationship was distinct from that for bone resorption, and this effect was not blocked by indomethacin. Similarly, hLIF increased [3H]phenylalanine incorporation into calvaria, and this was also not inhibited by indomethacin. It is concluded that LIF stimulates bone resorption by a mechanism involving prostaglandin production, but that a distinct mechanism is responsible for its stimulation of DNA and protein synthesis. The primary structure of LIF differs from that of other fully characterized, bone-active cytokines, and it, thus, represents a novel factor which may be involved in the normal regulation of bone cell function.

General and Direct Method for Preparing Oligonucleotide-Functionalized Metal–Organic Framework Nanoparticles

PubMed Central

2017-01-01

Metal–organic frameworks (MOFs) are a class of modular, crystalline, and porous materials that hold promise for storage and transport of chemical cargoes. Though MOFs have been studied in bulk forms, ways of deliberately manipulating the external surface functionality of MOF nanoparticles are less developed. A generalizable approach to modify their surfaces would allow one to impart chemical functionality onto the particle surface that is independent of the bulk MOF structure. Moreover, the use of a chemically programmable ligand, such as DNA, would allow for the manipulation of interparticle interactions. Herein, we report a coordination chemistry-based strategy for the surface functionalization of the external metal nodes of MOF nanoparticles with terminal phosphate-modified oligonucleotides. The external surfaces of nine distinct archetypical MOF particles containing four different metal species (Zr, Cr, Fe, and Al) were successfully functionalized with oligonucleotides, illustrating the generality of this strategy. By taking advantage of the programmable and specific interactions of DNA, 11 distinct MOF particle–inorganic particle core–satellite clusters were synthesized. In these hybrid nanoclusters, the relative stoichiometry, size, shape, and composition of the building blocks can all be independently controlled. This work provides access to a new set of nucleic acid–nanoparticle conjugates, which may be useful as programmable material building blocks and as probes for measuring and manipulating intracellular processes. PMID:28718644

Structural basis of the therapeutic anti-PD-L1 antibody atezolizumab.

PubMed

Zhang, Fei; Qi, Xiaoqiang; Wang, Xiaoxiao; Wei, Diyang; Wu, Jiawei; Feng, Lingling; Cai, Haiyan; Wang, Yugang; Zeng, Naiyan; Xu, Ting; Zhou, Aiwu; Zheng, Ying

2017-10-27

Monoclonal antibodies targeting PD-1/PD-L1 signaling pathway have achieved unprecedented success in cancer treatment over the last few years. Atezolizumab is the first PD-L1 monoclonal antibody approved by US FDA for cancer therapy; however the molecular basis of atezolizumab in blocking PD-1/PD-L1 interaction is not fully understood. Here we have solved the crystal structure of PD-L1/atezolizumab complex at 2.9 angstrom resolution. The structure shows that atezolizumab binds the front beta-sheet of PD-L1 through three CDR loops from the heavy chain and one CDR loop from the light chain. The binding involves extensive hydrogen-bonding and hydrophobic interactions. Notably there are multiple aromatic residues from the CDR loops forming Pi-Pi stacking or cation-Pi interactions within the center of the binding interface and the buried surface area is more than 2000 Å 2 , which is the largest amongst all the known PD-L1/antibody structures. Mutagenesis study revealed that two hot-spot residues (E58, R113) of PD-L1 contribute significantly to the binding of atezolizumab. The structure also shows that atezolizumab binds PD-L1 with a distinct heavy and light chain orientation and it blocks PD-1/PD-L1 interaction through competing with PD-1 for the same PD-L1 surface area. Taken together, the complex structure of PD-L1/atezolizumab solved here revealed the molecular mechanism of atezolizumab in immunotherapy and provides basis for future monoclonal antibody optimization and rational design of small chemical compounds targeting PD-L1 surface.

Structural basis of the therapeutic anti-PD-L1 antibody atezolizumab

PubMed Central

Wei, Diyang; Wu, Jiawei; Feng, Lingling; Cai, Haiyan; Wang, Yugang; Zeng, Naiyan; Xu, Ting; Zhou, Aiwu; Zheng, Ying

2017-01-01

Monoclonal antibodies targeting PD-1/PD-L1 signaling pathway have achieved unprecedented success in cancer treatment over the last few years. Atezolizumab is the first PD-L1 monoclonal antibody approved by US FDA for cancer therapy; however the molecular basis of atezolizumab in blocking PD-1/PD-L1 interaction is not fully understood. Here we have solved the crystal structure of PD-L1/atezolizumab complex at 2.9 angstrom resolution. The structure shows that atezolizumab binds the front beta-sheet of PD-L1 through three CDR loops from the heavy chain and one CDR loop from the light chain. The binding involves extensive hydrogen-bonding and hydrophobic interactions. Notably there are multiple aromatic residues from the CDR loops forming Pi-Pi stacking or cation-Pi interactions within the center of the binding interface and the buried surface area is more than 2000 Å2, which is the largest amongst all the known PD-L1/antibody structures. Mutagenesis study revealed that two hot-spot residues (E58, R113) of PD-L1 contribute significantly to the binding of atezolizumab. The structure also shows that atezolizumab binds PD-L1 with a distinct heavy and light chain orientation and it blocks PD-1/PD-L1 interaction through competing with PD-1 for the same PD-L1 surface area. Taken together, the complex structure of PD-L1/atezolizumab solved here revealed the molecular mechanism of atezolizumab in immunotherapy and provides basis for future monoclonal antibody optimization and rational design of small chemical compounds targeting PD-L1 surface. PMID:29163822

Evidence of Blocking with Geometric Cues in a Virtual Watermaze

ERIC Educational Resources Information Center

Redhead, Edward S.; Hamilton, Derek A.

2009-01-01

Three computer based experiments, testing human participants in a non-immersive virtual watermaze task, used a blocking design to assess whether two sets of geometric cues would compete in a manner described by associative models of learning. In stage 1, participants were required to discriminate between visually distinct platforms. In stage 2,…

Control of hierarchical polymer mechanics with bioinspired metal-coordination dynamics

PubMed Central

Grindy, Scott C.; Learsch, Robert; Mozhdehi, Davoud; Cheng, Jing; Barrett, Devin G.; Guan, Zhibin; Messersmith, Phillip B.; Holten-Andersen, Niels

2015-01-01

In conventional polymer materials, mechanical performance is traditionally engineered via material structure, using motifs such as polymer molecular weight, polymer branching, or copolymer-block design1. Here, by means of a model system of 4-arm poly(ethylene glycol) hydrogels crosslinked with multiple, kinetically distinct dynamic metal-ligand coordinate complexes, we show that polymer materials with decoupled spatial structure and mechanical performance can be designed. By tuning the relative concentration of two types of metal-ligand crosslinks, we demonstrate control over the material’s mechanical hierarchy of energy-dissipating modes under dynamic mechanical loading, and therefore the ability to engineer a priori the viscoelastic properties of these materials by controlling the types of crosslinks rather than by modifying the polymer itself. This strategy to decouple material mechanics from structure may inform the design of soft materials for use in complex mechanical environments. PMID:26322715

Differential inhibition of Ca2+ channels in mature rat cerebellar Purkinje cells by sFTX-3.3 and FTX-3.3.

PubMed

Dupere, J R; Moya, E; Blagbrough, I S; Usowicz, M M

1996-01-01

Synthetic funnel web spider toxin (sFTX-3.3) is a polyamine amide analogue of FTX, a toxin fraction isolated from the venom of the funnel web spider, Agelenopsis aperta, that blocks P-type Ca2+ channels. The structures of these polyamine containing compounds are not identical: sFTX-3.3 contains an amide carbonyl oxygen that is absent from the predicted structure of native FTX. Recently, a compound called FTX-3.3 was synthesized with the structure predicted for native FTX. We have compared the effects of polyamine amide sFTX-3.3 and polyamine FTX-3.3, on Ca2+ channel currents in the soma of mature rat cerebellar Purkinje neurons, in which the predominant Ca2+ channels are defined as P-type. Differential inhibition by sFTX-3.3 and FTX-3.3 revealed three populations of Ca2+ channels. One group, mediating approximately 66% of the current, was blocked by sFTX-3.3 with an IC50 (concentration producing half maximal inhibition) of 33 nM or by FTX-3.3 with an IC50 of 55 pM. A second population (5-25% of the total current) was inhibited by sFTX-3.3 with an IC50 of 33 nM, but was insensitive to FTX-3.3, while a third (10-30%) was blocked by FTX-3.3 with an IC50 of 125 nM and was resistant to sFTX-3.3. These channels also showed distinctive current-voltage relationships. Our results suggest that P-type Ca2+ channels in mature rat cerebellar Purkinje cells may be subdivided according to pharmacological and biophysical properties.

Overlapping Ballistic Ejecta Fields: Separating Distinct Blasts at Kings Bowl, Idaho

NASA Astrophysics Data System (ADS)

Borg, C.; Kobs-Nawotniak, S. E.; Hughes, S. S.; Sears, D. W. G.; Heldmann, J. L.; Lim, D. S. S.; Haberle, C. W.; Sears, H.; Elphic, R. C.; Kobayashi, L.; Garry, W. B.; Neish, C.; Karunatillake, S.; Button, N.; Purcell, S.; Mallonee, H.; Ostler, B.

2015-12-01

Kings Bowl is a ~2200ka pit crater created by a phreatic blast along a volcanic fissure in the eastern Snake River Plain (ESRP), Idaho. The main crater measures approximately 80m in length, 30m in width, and 30m in depth, with smaller pits located nearby on the Great Rift fissure, and has been targeted by the FINESSE team as a possible analogue for Cyane Fossae, Mars. The phreatic eruption is believed to have occurred due to the interaction of groundwater with lava draining back into the fissure following a lava lake high stand, erupting already solidified basalt from this and previous ERSP lava flows. The contemporaneous draw back of the lava with the explosions may conceal some smaller possible blast pits as more lava drained into the newly formed pits. Ballistic ejecta from the blasts occur on both sides of the fissure. To the east, the ballistic blocks are mantled by fine tephra mixed with eolian dust, the result of a westerly wind during the explosions. We use differential GPS to map the distribution of ballistic blocks on the west side of the fissure, recording position, percent vesiculation, and the length of 3 mutually perpendicular axes for each block >20cm along multiple transects parallel to the fissure. From the several hundred blocks recorded, we have been able to separate the ballistic field into several distinct blast deposits on the basis of size distributions and block concentration. The smaller pits identified from the ballistic fields correspond broadly to the northern and southern limits of the tephra/dust field east of the fissure. Soil formation and bioturbation of the tephra by sagebrush have obliterated any tephrostratigraphy that could have been linked to individual blasts. The ballistic block patterns at Kings Bowl may be used to identify distinct ejecta groups in high-resolution imagery of Mars or other planetary bodies.

Formation and Decay of the Arrestin·Rhodopsin Complex in Native Disc Membranes*

PubMed Central

Beyrière, Florent; Sommer, Martha E.; Szczepek, Michal; Bartl, Franz J.; Hofmann, Klaus Peter; Heck, Martin; Ritter, Eglof

2015-01-01

In the G protein-coupled receptor rhodopsin, light-induced cis/trans isomerization of the retinal ligand triggers a series of distinct receptor states culminating in the active Metarhodopsin II (Meta II) state, which binds and activates the G protein transducin (Gt). Long before Meta II decays into the aporeceptor opsin and free all-trans-retinal, its signaling is quenched by receptor phosphorylation and binding of the protein arrestin-1, which blocks further access of Gt to Meta II. Although recent crystal structures of arrestin indicate how it might look in a precomplex with the phosphorylated receptor, the transition into the high affinity complex is not understood. Here we applied Fourier transform infrared spectroscopy to monitor the interaction of arrestin-1 and phosphorylated rhodopsin in native disc membranes. By isolating the unique infrared signature of arrestin binding, we directly observed the structural alterations in both reaction partners. In the high affinity complex, rhodopsin adopts a structure similar to Gt-bound Meta II. In arrestin, a modest loss of β-sheet structure indicates an increase in flexibility but is inconsistent with a large scale structural change. During Meta II decay, the arrestin-rhodopsin stoichiometry shifts from 1:1 to 1:2. Arrestin stabilizes half of the receptor population in a specific Meta II protein conformation, whereas the other half decays to inactive opsin. Altogether these results illustrate the distinct binding modes used by arrestin to interact with different functional forms of the receptor. PMID:25847250

The emotional memory effect: differential processing or item distinctiveness?

PubMed

Schmidt, Stephen R; Saari, Bonnie

2007-12-01

A color-naming task was followed by incidental free recall to investigate how emotional words affect attention and memory. We compared taboo, nonthreatening negative-affect, and neutral words across three experiments. As compared with neutral words, taboo words led to longer color-naming times and better memory in both within- and between-subjects designs. Color naming of negative-emotion nontaboo words was slower than color naming of neutral words only during block presentation and at relatively short interstimulus intervals (ISIs). The nontaboo emotion words were remembered better than neutral words following blocked and random presentation and at both long and short ISIs, but only in mixed-list designs. Our results support multifactor theories of the effects of emotion on attention and memory. As compared with neutral words, threatening stimuli received increased attention, poststimulus elaboration, and benefit from item distinctiveness, whereas nonthreatening emotional stimuli benefited only from increased item distinctiveness.

A comparison of helicopter-borne electromagnetic systems for hydrogeologic studies

USGS Publications Warehouse

Bedrosian, Paul A.; Schamper, Cyril; Auken, Esben

2016-01-01

The increased application of airborne electromagnetic surveys to hydrogeological studies is driving a demand for data that can consistently be inverted for accurate subsurface resistivity structure from the near surface to depths of several hundred metres. We present an evaluation of three commercial airborne electromagnetic systems over two test blocks in western Nebraska, USA. The selected test blocks are representative of shallow and deep alluvial aquifer systems with low groundwater salinity and an electrically conductive base of aquifer. The aquifer units show significant lithologic heterogeneity and include both modern and ancient river systems. We compared the various data sets to one another and inverted resistivity models to borehole lithology and to ground geophysical models. We find distinct differences among the airborne electromagnetic systems as regards the spatial resolution of models, the depth of investigation, and the ability to recover near-surface resistivity variations. We further identify systematic biases in some data sets, which we attribute to incomplete or inexact calibration or compensation procedures.

Nonreciprocal lasing in topological cavities of arbitrary geometries

NASA Astrophysics Data System (ADS)

Bahari, Babak; Ndao, Abdoulaye; Vallini, Felipe; El Amili, Abdelkrim; Fainman, Yeshaiahu; Kanté, Boubacar

2017-11-01

Resonant cavities are essential building blocks governing many wave-based phenomena, but their geometry and reciprocity fundamentally limit the integration of optical devices. We report, at telecommunication wavelengths, geometry-independent and integrated nonreciprocal topological cavities that couple stimulated emission from one-way photonic edge states to a selected waveguide output with an isolation ratio in excess of 10 decibels. Nonreciprocity originates from unidirectional edge states at the boundary between photonic structures with distinct topological invariants. Our experimental demonstration of lasing from topological cavities provides the opportunity to develop complex topological circuitry of arbitrary geometries for the integrated and robust generation and transport of photons in classical and quantum regimes.

Structure of malaria invasion protein RH5 with erythrocyte basigin and blocking antibodies.

PubMed

Wright, Katherine E; Hjerrild, Kathryn A; Bartlett, Jonathan; Douglas, Alexander D; Jin, Jing; Brown, Rebecca E; Illingworth, Joseph J; Ashfield, Rebecca; Clemmensen, Stine B; de Jongh, Willem A; Draper, Simon J; Higgins, Matthew K

2014-11-20

Invasion of host erythrocytes is essential to the life cycle of Plasmodium parasites and development of the pathology of malaria. The stages of erythrocyte invasion, including initial contact, apical reorientation, junction formation, and active invagination, are directed by coordinated release of specialized apical organelles and their parasite protein contents. Among these proteins, and central to invasion by all species, are two parasite protein families, the reticulocyte-binding protein homologue (RH) and erythrocyte-binding like proteins, which mediate host-parasite interactions. RH5 from Plasmodium falciparum (PfRH5) is the only member of either family demonstrated to be necessary for erythrocyte invasion in all tested strains, through its interaction with the erythrocyte surface protein basigin (also known as CD147 and EMMPRIN). Antibodies targeting PfRH5 or basigin efficiently block parasite invasion in vitro, making PfRH5 an excellent vaccine candidate. Here we present crystal structures of PfRH5 in complex with basigin and two distinct inhibitory antibodies. PfRH5 adopts a novel fold in which two three-helical bundles come together in a kite-like architecture, presenting binding sites for basigin and inhibitory antibodies at one tip. This provides the first structural insight into erythrocyte binding by the Plasmodium RH protein family and identifies novel inhibitory epitopes to guide design of a new generation of vaccines against the blood-stage parasite.

Layer-by-layer strippable Ag multilayer films fabricated by modular assembly.

PubMed

Li, Yan; Chen, Xiaoyan; Li, Qianqian; Song, Kai; Wang, Shihui; Chen, Xiaoyan; Zhang, Kai; Fu, Yu; Jiao, Yong-Hua; Sun, Ting; Liu, Fu-Chun; Han, En-Hou

2014-01-21

We have developed a new method to fabricate multilayer films, which uses prepared thin films as modular blocks and transfer as operation mode to build up multilayer structures. In order to distinguish it from the in situ fabrication manner, this method is called modular assembly in this study. On the basis of such concept, we have fabricated a multilayer film using the silver mirror film as the modular block and poly(lactic acid) as the transfer tool. Due to the special double-layer structure of the silver mirror film, the resulting multilayer film had a well-defined stratified architecture with alternate porous/compact layers. As a consequence of the distinct structure, the interaction between the adjacent layers was so weak that the multilayer film could be layer-by-layer stripped. In addition, the top layer in the film could provide an effective protection on the morphology and surface property of the underlying layers. This suggests that if the surface of the film was deteriorated, the top layer could be peeled off and the freshly exposed surface would still maintain the original function. The successful preparation of the layer-by-layer strippable silver multilayer demonstrates that modular assembly is a feasible and effective method to build up multilayer films capable of creating novel and attractive micro/nanostructures, having great potential in the fabrication of nanodevices and coatings.

Structural Polymorphism in a Self-Assembled Tri-Aromatic Peptide System.

PubMed

Brown, Noam; Lei, Jiangtao; Zhan, Chendi; Shimon, Linda J W; Adler-Abramovich, Lihi; Wei, Guanghong; Gazit, Ehud

2018-04-24

Self-assembly is a process of key importance in natural systems and in nanotechnology. Peptides are attractive building blocks due to their relative facile synthesis, biocompatibility, and other unique properties. Diphenylalanine (FF) and its derivatives are known to form nanostructures of various architectures and interesting and varied characteristics. The larger triphenylalanine peptide (FFF) was found to self-assemble as efficiently as FF, forming related but distinct architectures of plate-like and spherical nanostructures. Here, to understand the effect of triaromatic systems on the self-assembly process, we examined carboxybenzyl-protected diphenylalanine (z-FF) as a minimal model for such an arrangement. We explored different self-assembly conditions by changing solvent compositions and peptide concentrations, generating a phase diagram for the assemblies. We discovered that z-FF can form a variety of structures, including nanowires, fibers, nanospheres, and nanotoroids, the latter were previously observed only in considerably larger or co-assembly systems. Secondary structure analysis revealed that all assemblies possessed a β-sheet conformation. Additionally, in solvent combinations with high water ratios, z-FF formed rigid and self-healing hydrogels. X-ray crystallography revealed a "wishbone" structure, in which z-FF dimers are linked by hydrogen bonds mediated by methanol molecules, with a 2-fold screw symmetry along the c-axis. All-atom molecular dynamics (MD) simulations revealed conformations similar to the crystal structure. Coarse-grained MD simulated the assembly of the peptide into either fibers or spheres in different solvent systems, consistent with the experimental results. This work thus expands the building block library for the fabrication of nanostructures by peptide self-assembly.

Hierarchical Nanostructures Self-Assembled from a Mixture System Containing Rod-Coil Block Copolymers and Rigid Homopolymers

PubMed Central

Li, Yongliang; Jiang, Tao; Lin, Shaoliang; Lin, Jiaping; Cai, Chunhua; Zhu, Xingyu

2015-01-01

Self-assembly behavior of a mixture system containing rod-coil block copolymers and rigid homopolymers was investigated by using Brownian dynamics simulations. The morphologies of formed hierarchical self-assemblies were found to be dependent on the Lennard-Jones (LJ) interaction εRR between rod blocks, lengths of rod and coil blocks in copolymer, and mixture ratio of block copolymers to homopolymers. As the εRR value decreases, the self-assembled structures of mixtures are transformed from an abacus-like structure to a helical structure, to a plain fiber, and finally are broken into unimers. The order parameter of rod blocks was calculated to confirm the structure transition. Through varying the length of rod and coil blocks, the regions of thermodynamic stability of abacus, helix, plain fiber, and unimers were mapped. Moreover, it was discovered that two levels of rod block ordering exist in the helices. The block copolymers are helically wrapped on the homopolymer bundles to form helical string, while the rod blocks are twistingly packed inside the string. In addition, the simulation results are in good agreement with experimental observations. The present work reveals the mechanism behind the formation of helical (experimentally super-helical) structures and may provide useful information for design and preparation of the complex structures. PMID:25965726

Characterizing the inverses of block tridiagonal, block Toeplitz matrices

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

Boffi, Nicholas M.; Hill, Judith C.; Reuter, Matthew G.

2014-12-04

We consider the inversion of block tridiagonal, block Toeplitz matrices and comment on the behaviour of these inverses as one moves away from the diagonal. Using matrix M bius transformations, we first present an O(1) representation (with respect to the number of block rows and block columns) for the inverse matrix and subsequently use this representation to characterize the inverse matrix. There are four symmetry-distinct cases where the blocks of the inverse matrix (i) decay to zero on both sides of the diagonal, (ii) oscillate on both sides, (iii) decay on one side and oscillate on the other and (iv)more » decay on one side and grow on the other. This characterization exposes the necessary conditions for the inverse matrix to be numerically banded and may also aid in the design of preconditioners and fast algorithms. Finally, we present numerical examples of these matrix types.« less

A protein block based fold recognition method for the annotation of twilight zone sequences.

PubMed

Suresh, V; Ganesan, K; Parthasarathy, S

2013-03-01

The description of protein backbone was recently improved with a group of structural fragments called Structural Alphabets instead of the regular three states (Helix, Sheet and Coil) secondary structure description. Protein Blocks is one of the Structural Alphabets used to describe each and every region of protein backbone including the coil. According to de Brevern (2000) the Protein Blocks has 16 structural fragments and each one has 5 residues in length. Protein Blocks fragments are highly informative among the available Structural Alphabets and it has been used for many applications. Here, we present a protein fold recognition method based on Protein Blocks for the annotation of twilight zone sequences. In our method, we align the predicted Protein Blocks of a query amino acid sequence with a library of assigned Protein Blocks of 953 known folds using the local pair-wise alignment. The alignment results with z-value ≥ 2.5 and P-value ≤ 0.08 are predicted as possible folds. Our method is able to recognize the possible folds for nearly 35.5% of the twilight zone sequences with their predicted Protein Block sequence obtained by pb_prediction, which is available at Protein Block Export server.

Tunable Encapsulation Structure of Block Copolymer Coated Single-Walled Carbon Nanotubes in Aqueous Solution

DOE PAGES

Han, Youngkyu; Ahn, Suk-Kyun; Zhang, Zhe; ...

2015-05-15

The nano-sized and shape-tunable molecular building blocks can provide great opportunities for the fabrication of precisely controlled nanostructures. In this work, we have fabricated a molecular building block of single-walled carbon nanotubes (SWNTs) coated by PPO-PEO-PPO block copolymers whose encapsulation structure can be controlled via temperature or addition of small molecules. The structure and optical properties of SWNT-block copolymers have been investigated by small angle neutron scattering (SANS), ultraviolet-visible (UV-vis) spectroscopy, atomic force microscopy (AFM), and molecular dynamics (MD) simulation. The structure of the hydrated block copolymer layer surrounding SWNT can be controlled reversibly by varying temperature as well asmore » by irreversibly adding 5-methylsalicylic acid (5MS). Increasing hydrophobicity of the polymers with temperature and strong tendency of 5MS to interact with both block copolymers and orbitals of the SWNTs are likely to be responsible for the significant structural change of the block copolymer encapsulation layer, from loose corona shell to tightly encapsulating compact shell. These result shows an efficient and simple way to fabricate and manipulate carbon-based nano building blocks in aqueous systems with tunable structure.« less

77 FR 27269 - Access to Aircraft Situation Display to Industry (ASDI) and National Airspace System Status...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-09

... members for this purpose. To assist the FAA in accurately and efficiently processing the number of... information. The receipt of this information could influence whether the FAA can add or delete aircraft from... blocking at the FAA source or at the industry level. The distinction between blocking ASDI data at the FAA...

Structure and Dynamics of Ionic Block Copolymer Melts: Computational Study

DOE PAGES

Aryal, Dipak; Agrawal, Anupriya; Perahia, Dvora; ...

2017-09-06

Structure and dynamics of melts of copolymers with an ABCBA topology, where C is an ionizable block, have been studied by fully atomistic molecular dynamics (MD) simulations. Introducing an ionizable block for functionality adds a significant element to the coupled set of interactions that determine the structure and dynamics of the macromolecule. The polymer consists of a randomly sulfonated polystyrene C block tethered to a flexible poly(ethylene-r-propylene) bridge B and end-capped with poly(tert-butylstyrene) A. The chemical structure and topology of these polymers constitute a model for incorporation of ionic blocks within a framework that provides tactility and mechanical stability. Heremore » in this paper we resolve the structure and dynamics of a structured polymer on the nanoscale constrained by ionic clusters. We find that the melts form intertwined networks of the A and C blocks independent of the degree of sulfonation of the C block with no long-range order. The cluster cohesiveness and morphology affect both macroscopic translational motion and segmental dynamics of all the blocks.« less

Structure and Dynamics of Ionic Block Copolymer Melts: Computational Study

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

Aryal, Dipak; Agrawal, Anupriya; Perahia, Dvora

Structure and dynamics of melts of copolymers with an ABCBA topology, where C is an ionizable block, have been studied by fully atomistic molecular dynamics (MD) simulations. Introducing an ionizable block for functionality adds a significant element to the coupled set of interactions that determine the structure and dynamics of the macromolecule. The polymer consists of a randomly sulfonated polystyrene C block tethered to a flexible poly(ethylene-r-propylene) bridge B and end-capped with poly(tert-butylstyrene) A. The chemical structure and topology of these polymers constitute a model for incorporation of ionic blocks within a framework that provides tactility and mechanical stability. Heremore » in this paper we resolve the structure and dynamics of a structured polymer on the nanoscale constrained by ionic clusters. We find that the melts form intertwined networks of the A and C blocks independent of the degree of sulfonation of the C block with no long-range order. The cluster cohesiveness and morphology affect both macroscopic translational motion and segmental dynamics of all the blocks.« less

Divergent Coordination Chemistry: Parallel Synthesis of [2×2] Iron(II) Grid-Complex Tauto-Conformers.

PubMed

Schäfer, Bernhard; Greisch, Jean-François; Faus, Isabelle; Bodenstein, Tilmann; Šalitroš, Ivan; Fuhr, Olaf; Fink, Karin; Schünemann, Volker; Kappes, Manfred M; Ruben, Mario

2016-08-26

The coordination of iron(II) ions by a homoditopic ligand L with two tridentate chelates leads to the tautomerism-driven emergence of complexity, with isomeric tetramers and trimers as the coordination products. The structures of the two dominant [Fe(II) 4 L4 ](8+) complexes were determined by X-ray diffraction, and the distinctness of the products was confirmed by ion-mobility mass spectrometry. Moreover, these two isomers display contrasting magnetic properties (Fe(II) spin crossover vs. a blocked Fe(II) high-spin state). These results demonstrate how the coordination of a metal ion to a ligand that can undergo tautomerization can increase, at a higher hierarchical level, complexity, here expressed by the formation of isomeric molecular assemblies with distinct physical properties. Such results are of importance for improving our understanding of the emergence of complexity in chemistry and biology. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.

PubMed

Hawkins, R David; Hon, Gary C; Lee, Leonard K; Ngo, Queminh; Lister, Ryan; Pelizzola, Mattia; Edsall, Lee E; Kuan, Samantha; Luu, Ying; Klugman, Sarit; Antosiewicz-Bourget, Jessica; Ye, Zhen; Espinoza, Celso; Agarwahl, Saurabh; Shen, Li; Ruotti, Victor; Wang, Wei; Stewart, Ron; Thomson, James A; Ecker, Joseph R; Ren, Bing

2010-05-07

Human embryonic stem cells (hESCs) share an identical genome with lineage-committed cells, yet possess the remarkable properties of self-renewal and pluripotency. The diverse cellular properties in different cells have been attributed to their distinct epigenomes, but how much epigenomes differ remains unclear. Here, we report that epigenomic landscapes in hESCs and lineage-committed cells are drastically different. By comparing the chromatin-modification profiles and DNA methylomes in hESCs and primary fibroblasts, we find that nearly one-third of the genome differs in chromatin structure. Most changes arise from dramatic redistributions of repressive H3K9me3 and H3K27me3 marks, which form blocks that significantly expand in fibroblasts. A large number of potential regulatory sequences also exhibit a high degree of dynamics in chromatin modifications and DNA methylation. Additionally, we observe novel, context-dependent relationships between DNA methylation and chromatin modifications. Our results provide new insights into epigenetic mechanisms underlying properties of pluripotency and cell fate commitment.

Self-assembly of thin, triangular prisms into open networks at a flat air-water interface

NASA Astrophysics Data System (ADS)

Solomon, Michael; Ferrar, Joseph; Bedi, Deshpreet; Zhou, Shangnan; Mao, Xiaoming

We observe capillary-driven binding between thin, equilateral triangle microprisms at a flat air-water interface. The triangles are fabricated from epoxy resin via SU-8 photolithography. For small thickness to length (T/L) ratios, two distinct pairwise particle-particle binding events occur with roughly equal frequency, and optical and environmental scanning electron microscopy (eSEM) demonstrate that these two distinct binding events are driven by the specific manner in which the interface is pinned to the particle surface. Additionally, particle bending is observed for the lowest T/L ratios, which leads to enhanced interface curvature and thus enhanced strength of capillary-driven attractions, and may also play a pivotal role in the dichotomy in particle-particle binding. Dichotomy in particle-particle binding is not observed at thicker T/L ratios, although capillary-driven binding still occurs. Ultimately, the particles self-assemble into space-spanning open networks, and the results suggest design parameters for the fabrication of building blocks of ordered open structures, such as the Kagome lattice.

An Adaptive Mesh Algorithm: Mesh Structure and Generation

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

Scannapieco, Anthony J.

2016-06-21

The purpose of Adaptive Mesh Refinement is to minimize spatial errors over the computational space not to minimize the number of computational elements. The additional result of the technique is that it may reduce the number of computational elements needed to retain a given level of spatial accuracy. Adaptive mesh refinement is a computational technique used to dynamically select, over a region of space, a set of computational elements designed to minimize spatial error in the computational model of a physical process. The fundamental idea is to increase the mesh resolution in regions where the physical variables are represented bymore » a broad spectrum of modes in k-space, hence increasing the effective global spectral coverage of those physical variables. In addition, the selection of the spatially distributed elements is done dynamically by cyclically adjusting the mesh to follow the spectral evolution of the system. Over the years three types of AMR schemes have evolved; block, patch and locally refined AMR. In block and patch AMR logical blocks of various grid sizes are overlaid to span the physical space of interest, whereas in locally refined AMR no logical blocks are employed but locally nested mesh levels are used to span the physical space. The distinction between block and patch AMR is that in block AMR the original blocks refine and coarsen entirely in time, whereas in patch AMR the patches change location and zone size with time. The type of AMR described herein is a locally refi ned AMR. In the algorithm described, at any point in physical space only one zone exists at whatever level of mesh that is appropriate for that physical location. The dynamic creation of a locally refi ned computational mesh is made practical by a judicious selection of mesh rules. With these rules the mesh is evolved via a mesh potential designed to concentrate the nest mesh in regions where the physics is modally dense, and coarsen zones in regions where the physics is modally sparse.« less

The prehistoric Vajont rockslide: An updated geological model

NASA Astrophysics Data System (ADS)

Paronuzzi, Paolo; Bolla, Alberto

2012-10-01

This study presents the detailed reconstruction of the entire structure of the prehistoric Vajont rockslide (about 270-300 million m3 of rocks and debris) for the first time, describing the complex geometry and the characteristic superimposition of distinct rigid blocks on a very thick shear zone. The prehistoric Vajont rockslide was characterized by an enormous 'en masse' motion of a rigid overlying rock mass (100-130 m thick) that moved downslope, sliding onto a very thick shear zone (40-50 m thick, on average) made up of a chaotic assemblage of blocks, limestone angular gravel, and high plasticity clays (montmorillonitic clays). Coarse loose sediments, still exposed on the 9 October 1963 detachment surface, are always associated with large blocks made of strongly fractured rock masses (Fonzaso Formation: middle-upper Jurassic) preserving the stratification. The blocks of stratified and folded limestone sequences appear to be 'sheared off' from the underlying bedrock and can be considered as displaced rock masses planed off by the motion of the overlying rigid rock mass ('rock mass shavings'). The prehistoric Vajont rockslide was characterized by a multistage failure with a marked retrogressive evolution. The first rupture (Pian del Toc block) rapidly destabilized the upper slope, mobilizing a second rock mass block (Pian della Pozza block) that, in turn, determined the multiple rupture of the revealed shear zone material (Massalezza lobe). Even if the exact timing of the different phases is not known, the entire multistaged failure process was very rapid. At the end of the multistage retrogressive failure, the slope morphology of the northern toe of Mt. Toc was drastically changed and the large failed rock mass settled into the preexisting Vajont Valley assuming the unusual chair-like geometry. The Vajont rockslide represents a very significant example on how a complex geological situation, if not adequately analyzed and reconstructed, can lead to dangerous misinterpretations or even to erroneous engineering-geological and geotechnical models. Accurate fieldwork and modern technologies can be fundamental in solving such a very intriguing 'geological puzzle.'

Opal-like Multicolor Appearance of Self-Assembled Photonic Array.

PubMed

Arnon, Zohar A; Pinotsi, Dorothea; Schmidt, Matthias; Gilead, Sharon; Guterman, Tom; Sadhanala, Aditya; Ahmad, Shahab; Levin, Aviad; Walther, Paul; Kaminski, Clemens F; Fändrich, Marcus; Kaminski Schierle, Gabriele S; Adler-Abramovich, Lihi; Shimon, Linda J W; Gazit, Ehud

2018-06-20

Molecular self-assembly of short peptide building blocks leads to the formation of various material architectures that may possess unique physical properties. Recent studies had confirmed the key role of biaromaticity in peptide self-assembly, with the diphenylalanine (FF) structural family as an archetypal model. Another significant direction in the molecular engineering of peptide building blocks is the use of fluorenylmethoxycarbonyl (Fmoc) modification, which promotes the assembly process and may result in nanostructures with distinctive features and macroscopic hydrogel with supramolecular features and nanoscale order. Here, we explored the self-assembly of the protected, noncoded fluorenylmethoxycarbonyl-β,β-diphenyl-Ala-OH (Fmoc-Dip) amino acid. This process results in the formation of elongated needle-like crystals with notable aromatic continuity. By altering the assembly conditions, arrays of spherical particles were formed that exhibit strong light scattering. These arrays display vivid coloration, strongly resembling the appearance of opal gemstones. However, unlike the Rayleigh scattering effect produced by the arrangement of opal, the described optical phenomenon is attributed to Mie scattering. Moreover, by controlling the solution evaporation rate, i.e., the assembly kinetics, we were able to manipulate the resulting coloration. This work demonstrates a bottom-up approach, utilizing self-assembly of a protected amino acid minimal building block, to create arrays of organic, light-scattering colorful surfaces.

Joint Inversion for Lithospheric Structures: Implications for the Growth and Deformation in Northeastern Tibetan Plateau

NASA Astrophysics Data System (ADS)

Deng, Yangfan; Li, Jiangtao; Song, Xiaodong; Zhu, Lupei

2018-05-01

Several geodynamic models have been proposed for the deformation mechanism of Tibetan Plateau (TP), but it remains controversial. Here we applied a method of joint inversion of receiver functions and surface wave dispersions with P wave velocity constraint to a dense linear array in the NE Tibet. The results show that the geological blocks, separated by major faults at the surface, are characterized by distinct features in the crust, the Moho, and the uppermost mantle. The main features include crustal low-velocity zones (LVZs) with variable strengths, anomalous Vp/Vs ratios that are correlated with LVZs, a large Moho jump, and other abrupt changes near major faults, strong mantle lithosphere anomalies, and correlation of crustal and mantle velocities. The results suggest a lithospheric-scale deformation of continuous shortening as well as localized faulting, which is affected by the strength of the lithosphere blocks. The thickened mantle lithosphere can be removed, which facilitates the formation of middle-lower crustal LVZ and flow. However, such flow is likely a consequence of the deformation rather than a driving force for the outward growth of the TP. The proposed model of TP deformation and growth can reconcile the continuous deformation within the blocks and major faults at the surface.

Structure-property-glass transition relationships in non-isocyanate polyurethanes investigated by dynamic nanoindentation

NASA Astrophysics Data System (ADS)

Weyand, Stephan; Blattmann, Hannes; Schimpf, Vitalij; Mülhaupt, Rolf; Schwaiger, Ruth

2016-07-01

Newly developed green-chemistry approaches towards the synthesis of non-isocyanate polyurethane (NIPU) systems represent a promising alternative to polyurethanes (PU) eliminating the need for harmful ingredients. A series of NIPU systems were studied using different nanoindentation techniques in order to understand the influence of molecular parameters on the mechanical behavior. Nanoindentation revealed a unique characteristic feature of those materials, i.e. stiffening with increasing deformation. It is argued that the origin of this observed stiffening is a consequence of the thermodynamic state of the polymer network, the molecular characteristics of the chemical building blocks and resulting anisotropic elastic response of the network structure. Flat-punch nanoindentation was applied in order to characterize the constitutive viscoelastic nature of the materials. The complex modulus shows distinct changes as a function of the NIPU network topology illustrating the influence of the chemical building blocks. The reproducibility of the data indicates that the materials are homogeneous over the volumes sampled by nanoindentation. Our study demonstrates that nanoindentation is very well-suited to investigate the molecular characteristics of NIPU materials that cannot be quantified in conventional experiments. Moreover, the technique provides insight into the functional significance of complex molecular architectures thereby supporting the development of NIPU materials with tailored properties.

Earth Observations taken by the Expedition 14 crew

NASA Image and Video Library

2007-12-30

ISS014-E-10547 (30 Dec. 2006) --- Barcelona, Spain is featured in this image photographed by an Expedition 14 crewmember on the International Space Station. Barcelona occupies a low plateau along the Mediterranean coastal plain. The city is the second largest in Spain (after the capital of Madrid), and hosts the country's largest seaport (portions of which are visible at lower right). This detailed view captures several notable features of the Barcelona urban landscape. The architectural design of the Eixample district (center) displays a grid pattern distinctive for Barcelona. Built during the 19th and 20th centuries, the district was built with octagonal city blocks -- originally intended to be open structures of only two or three sides surrounding gardens and open space. While the original street grid pattern remains, today many of the octagonal blocks are completely built up. The adjacent Cuitat Vella, or old city, presents a much denser building pattern which dates from Roman times. Also visible at lower right is the 173-meter high Montjuic Mountain -- historically the location of fortresses due to its strategic position overlooking the city's harbor. Light tan and orange structures visible at the crest of the mountain include the stadium and other buildings used in the 1992 Summer Olympic Games at Barcelona.

para-Azaquinodimethane: A Compact Quinodimethane Variant as an Ambient Stable Building Block for High-Performance Low Band Gap Polymers

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

Liu, Xuncheng; He, Bo; Anderson, Christopher L.

Quinoidal structures incorporating expanded para-quinodimethane (p-QM) units have garnered great interest as functional organic electronic, optical, and magnetic materials. The direct use of the compact p-QM unit as an electronic building block, however, has been inhibited by the high reactivity conveyed by its biradical character. Herein, we introduce a stable p-QM variant, namely p-azaquinodimethane (p-AQM), that incorporates nitrogen atoms in the central ring and alkoxy substituents on the periphery to increase the stability of the quinoidal structure. The succinct synthesis from readily available precursors leads to regio- and stereospecific p-AQMs that can be readily integrated into the backbone of conjugatedmore » polymers. The quinoidal character of the p-AQM unit endows the resulting polymers with narrow band gaps and high carrier transport mobilities. The study of a series of copolymers employing different numbers of thiophene units revealed an unconventional trend in band gaps, which is distinct from the widely adopted donor-acceptor approach to tuning the band gaps of conjugated polymers. Theoretical calculations have shed light on the nature of this trend, which may provide a unique class of conjugated polymers with promising optical and electronic properties.« less

para-Azaquinodimethane: A Compact Quinodimethane Variant as an Ambient Stable Building Block for High-Performance Low Band Gap Polymers

DOE PAGES

Liu, Xuncheng; He, Bo; Anderson, Christopher L.; ...

2017-05-24

Quinoidal structures incorporating expanded para-quinodimethane (p-QM) units have garnered great interest as functional organic electronic, optical, and magnetic materials. The direct use of the compact p-QM unit as an electronic building block, however, has been inhibited by the high reactivity conveyed by its biradical character. Herein, we introduce a stable p-QM variant, namely p-azaquinodimethane (p-AQM), that incorporates nitrogen atoms in the central ring and alkoxy substituents on the periphery to increase the stability of the quinoidal structure. The succinct synthesis from readily available precursors leads to regio- and stereospecific p-AQMs that can be readily integrated into the backbone of conjugatedmore » polymers. The quinoidal character of the p-AQM unit endows the resulting polymers with narrow band gaps and high carrier transport mobilities. The study of a series of copolymers employing different numbers of thiophene units revealed an unconventional trend in band gaps, which is distinct from the widely adopted donor-acceptor approach to tuning the band gaps of conjugated polymers. Theoretical calculations have shed light on the nature of this trend, which may provide a unique class of conjugated polymers with promising optical and electronic properties.« less

Functional diversification of cerato-platanins in Moniliophthora perniciosa as seen by differential expression and protein function specialization.

PubMed

de O Barsottini, Mario R; de Oliveira, Juliana F; Adamoski, Douglas; Teixeira, Paulo J P L; do Prado, Paula F V; Tiezzi, Henrique O; Sforça, Mauricio L; Cassago, Alexandre; Portugal, Rodrigo V; de Oliveira, Paulo S L; de M Zeri, Ana C; Dias, Sandra M G; Pereira, Gonçalo A G; Ambrosio, Andre L B

2013-11-01

Cerato-platanins (CP) are small, cysteine-rich fungal-secreted proteins involved in the various stages of the host-fungus interaction process, acting as phytotoxins, elicitors, and allergens. We identified 12 CP genes (MpCP1 to MpCP12) in the genome of Moniliophthora perniciosa, the causal agent of witches' broom disease in cacao, and showed that they present distinct expression profiles throughout fungal development and infection. We determined the X-ray crystal structures of MpCP1, MpCP2, MpCP3, and MpCP5, representative of different branches of a phylogenetic tree and expressed at different stages of the disease. Structure-based biochemistry, in combination with nuclear magnetic resonance and mass spectrometry, allowed us to define specialized capabilities regarding self-assembling and the direct binding to chitin and N-acetylglucosamine (NAG) tetramers, a fungal cell wall building block, and to map a previously unknown binding region in MpCP5. Moreover, fibers of MpCP2 were shown to act as expansin and facilitate basidiospore germination whereas soluble MpCP5 blocked NAG6-induced defense response. The correlation between these roles, the fungus life cycle, and its tug-of-war interaction with cacao plants is discussed.

CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN SEROTYPE B.

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

SWAMINATHAN,S.; ESWARAMOORTHY,S.

2001-11-19

The toxigenic strains of Clostridium botulinum produce seven serologically distinct types of neurotoxins labeled A - G (EC 3.4.24.69), while Clostridium tetani produces tetanus neurotoxin (EC 3.4.24.68). Botulinum and tetanus neurotoxins (BoNTs and TeNT) are produced as single inactive chains of molecular mass of approximately 150 kDa. Most of these neurotoxins are released after being cleaved into two chains, a heavy chain (HI) of 100 kDa and a light chain (L) of 50 kDa held together by an interchain disulfide bond, by tissue proteinases. BoNT/E is released as a single chain but cleaved by host proteinases [1]. Clostvidium botulinum neurotoxinsmore » are extremely poisonous proteins with their LD{sub 50} for humans in the range of 0.1 - 1 ng kg{sup -1} [2]. Botulinum neurotoxins are responsible for neuroparalytic syndromes of botulism characterized by serious neurological disorders and flaccid paralysis. BoNTs block the release of acetylcholine at the neuromuscular junction causing flaccid paralysis while TeNT blocks the release of neurotransmitters like glycine and {gamma}-aminobutyric acid (GABA) in the inhibitory interneurons of the spinal cord resulting in spastic paralysis. In spite of different clinical symptoms, their aetiological agents intoxicate neuronal cells in the same way and these toxins have similar structural organization [3].« less

Stereoselective Inhibition of the hERG1 Potassium Channel

PubMed Central

Grilo, Liliana Sintra; Carrupt, Pierre-Alain; Abriel, Hugues

2010-01-01

A growing number of drugs have been shown to prolong cardiac repolarization, predisposing individuals to life-threatening ventricular arrhythmias known as Torsades de Pointes. Most of these drugs are known to interfere with the human ether à-gogo related gene 1 (hERG1) channel, whose current is one of the main determinants of action potential duration. Prolonged repolarization is reflected by lengthening of the QT interval of the electrocardiogram, as seen in the suitably named drug-induced long QT syndrome. Chirality (presence of an asymmetric atom) is a common feature of marketed drugs, which can therefore exist in at least two enantiomers with distinct three-dimensional structures and possibly distinct biological fates. Both the pharmacokinetic and pharmacodynamic properties can differ between enantiomers, as well as also between individuals who take the drug due to metabolic polymorphisms. Despite the large number of reports about drugs reducing the hERG1 current, potential stereoselective contributions have only been scarcely investigated. In this review, we present a non-exhaustive list of clinically important molecules which display chiral toxicity that may be related to hERG1-blocking properties. We particularly focus on methadone cardiotoxicity, which illustrates the importance of the stereoselective effect of drug chirality as well as individual variations resulting from pharmacogenetics. Furthermore, it seems likely that, during drug development, consideration of chirality in lead optimization and systematic assessment of the hERG1 current block with all enantiomers could contribute to the reduction of the risk of drug-induced LQTS. PMID:21833176

Effect of Rho family GTP-binding proteins on Amoeba proteus.

PubMed

Kłopocka, W; Redowicz, M J

2003-03-01

While there is a number of studies on the effects of Rho GTPases on the actin-based cytoskeleton in higher eukaryotes, studies in protozoans are rather limited. The problem seems to be intriguing since the structure of protozoan cytoskeletons is distinct from most vertebrate cells. By blocking endogenous Rho family proteins of highly motile Amoeba proteus with C3 transferase and antibodies against human RhoA and Rac1, we tried to assess the in vivo role of these proteins in amoebae. In migrating amoebae, both proteins are concentrated in the cortical layer and seem to colocalize with filamentous actin. Endogenous Rac1, but not RhoA, is accumulated in the perinuclear cytoskeleton. Blocking Rac- or Rho-like proteins caused distinct and irreversible changes in the locomotive shape of the examined amoebae and significant inhibition of their migration. Amoebae microinjected with anti-Rac1 antibodies were contracted, shortened, and developed only few wide pseudopodia. More pronounced changes were observed in cells treated with anti-RhoA antibodies. They exhibited an atypical locomotion not leading to their effective displacement. After treatment with 50 microg of C3 transferase per ml, cells rapidly contracted and almost completely rounded up, became refractile with the granules beaten into a dense mass, detached from the surface and died. Ten times lower concentration of the enzyme caused similar changes as the inhibition of endogenous RhoA-like protein. These results indicate that Rho family-based regulation plays a key role in amoebic migration.

Modular and Orthogonal Synthesis of Hybrid Polymers and Networks

PubMed Central

Liu, Shuang; Dicker, Kevin T.; Jia, Xinqiao

2015-01-01

Biomaterials scientists strive to develop polymeric materials with distinct chemical make-up, complex molecular architectures, robust mechanical properties and defined biological functions by drawing inspirations from biological systems. Salient features of biological designs include (1) repetitive presentation of basic motifs; and (2) efficient integration of diverse building blocks. Thus, an appealing approach to biomaterials synthesis is to combine synthetic and natural building blocks in a modular fashion employing novel chemical methods. Over the past decade, orthogonal chemistries have become powerful enabling tools for the modular synthesis of advanced biomaterials. These reactions require building blocks with complementary functionalities, occur under mild conditions in the presence of biological molecules and living cells and proceed with high yield and exceptional selectivity. These chemistries have facilitated the construction of complex polymers and networks in a step-growth fashion, allowing facile modulation of materials properties by simple variations of the building blocks. In this review, we first summarize features of several types of orthogonal chemistries. We then discuss recent progress in the synthesis of step growth linear polymers, dendrimers and networks that find application in drug delivery, 3D cell culture and tissue engineering. Overall, orthogonal reactions and modulular synthesis have not only minimized the steps needed for the desired chemical transformations but also maximized the diversity and functionality of the final products. The modular nature of the design, combined with the potential synergistic effect of the hybrid system, will likely result in novel hydrogel matrices with robust structures and defined functions. PMID:25572255

Formation and decay of the arrestin·rhodopsin complex in native disc membranes.

PubMed

Beyrière, Florent; Sommer, Martha E; Szczepek, Michal; Bartl, Franz J; Hofmann, Klaus Peter; Heck, Martin; Ritter, Eglof

2015-05-15

In the G protein-coupled receptor rhodopsin, light-induced cis/trans isomerization of the retinal ligand triggers a series of distinct receptor states culminating in the active Metarhodopsin II (Meta II) state, which binds and activates the G protein transducin (Gt). Long before Meta II decays into the aporeceptor opsin and free all-trans-retinal, its signaling is quenched by receptor phosphorylation and binding of the protein arrestin-1, which blocks further access of Gt to Meta II. Although recent crystal structures of arrestin indicate how it might look in a precomplex with the phosphorylated receptor, the transition into the high affinity complex is not understood. Here we applied Fourier transform infrared spectroscopy to monitor the interaction of arrestin-1 and phosphorylated rhodopsin in native disc membranes. By isolating the unique infrared signature of arrestin binding, we directly observed the structural alterations in both reaction partners. In the high affinity complex, rhodopsin adopts a structure similar to Gt-bound Meta II. In arrestin, a modest loss of β-sheet structure indicates an increase in flexibility but is inconsistent with a large scale structural change. During Meta II decay, the arrestin-rhodopsin stoichiometry shifts from 1:1 to 1:2. Arrestin stabilizes half of the receptor population in a specific Meta II protein conformation, whereas the other half decays to inactive opsin. Altogether these results illustrate the distinct binding modes used by arrestin to interact with different functional forms of the receptor. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Phase response curves for models of earthquake fault dynamics

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

Franović, Igor, E-mail: franovic@ipb.ac.rs; Kostić, Srdjan; Perc, Matjaž

We systematically study effects of external perturbations on models describing earthquake fault dynamics. The latter are based on the framework of the Burridge-Knopoff spring-block system, including the cases of a simple mono-block fault, as well as the paradigmatic complex faults made up of two identical or distinct blocks. The blocks exhibit relaxation oscillations, which are representative for the stick-slip behavior typical for earthquake dynamics. Our analysis is carried out by determining the phase response curves of first and second order. For a mono-block fault, we consider the impact of a single and two successive pulse perturbations, further demonstrating how themore » profile of phase response curves depends on the fault parameters. For a homogeneous two-block fault, our focus is on the scenario where each of the blocks is influenced by a single pulse, whereas for heterogeneous faults, we analyze how the response of the system depends on whether the stimulus is applied to the block having a shorter or a longer oscillation period.« less

Block of Brain Sodium Channels by Peptide Mimetics of the Isoleucine, Phenylalanine, and Methionine (IFM) Motif from the Inactivation Gate

PubMed Central

Eaholtz, Galen; Colvin, Anita; Leonard, Daniele; Taylor, Charles; Catterall, William A.

1999-01-01

Inactivation of sodium channels is thought to be mediated by an inactivation gate formed by the intracellular loop connecting domains III and IV. A hydrophobic motif containing the amino acid sequence isoleucine, phenylalanine, and methionine (IFM) is required for the inactivation process. Peptides containing the IFM motif, when applied to the cytoplasmic side of these channels, produce two types of block: fast block, which resembles the inactivation process, and slow, use-dependent block stimulated by strong depolarizing pulses. Fast block by the peptide ac-KIFMK-NH2, measured on sodium channels whose inactivation was slowed by the α-scorpion toxin from Leiurus quinquestriatus (LqTx), was reversed with a time constant of 0.9 ms upon repolarization. In contrast, control and LqTx-modified sodium channels were slower to recover from use-dependent block. For fast block, linear peptides of three to six amino acid residues containing the IFM motif and two positive charges were more effective than peptides with one positive charge, whereas uncharged IFM peptides were ineffective. Substitution of the IFM residues in the peptide ac-KIFMK-NH2 with smaller, less hydrophobic residues prevented fast block. The positively charged tripeptide IFM-NH2 did not cause appreciable fast block, but the divalent cation IFM-NH(CH2)2NH2 was as effective as the pentapeptide ac-KIFMK-NH2. The constrained peptide cyclic KIFMK containing two positive charges did not cause fast block. These results indicate that the position of the positive charges is unimportant, but flexibility or conformation of the IFM-containing peptide is important to allow fast block. Slow, use-dependent block was observed with IFM-containing peptides of three to six residues having one or two positive charges, but not with dipeptides or phenylalanine-amide. In contrast to its lack of fast block, cyclic KIFMK was an effective use-dependent blocker. Substitutions of amino acid residues in the tripeptide IFM-NH2 showed that large hydrophobic residues are preferred in all three positions for slow, use-dependent block. However, substitution of the large hydrophobic residue diphenylalanine or the constrained residues phenylglycine or tetrahydroisoquinoline for phe decreased potency, suggesting that this phe residue must be able to enter a restricted hydrophobic pocket during the binding of IFM peptides. Together, the results on fast block and slow, use-dependent block indicate that IFM peptides form two distinct complexes of different stability and structural specificity with receptor site(s) on the sodium channel. It is proposed that fast block represents binding of these peptides to the inactivation gate receptor, while slow, use-dependent block represents deeper binding of the IFM peptides in the pore. PMID:9925825

Lead-isotopic evidence for distinct source of granite and for distinct basement in the northern Appalachians, Maine.

USGS Publications Warehouse

Ayuso, R.A.

1986-01-01

Lead-isotopic compositions of feldspars in high-level Devonian granitic plutons across the northern Appalachians were measured. The presence of three fundamentally different sources of granites was indicated by three distinct lead-isotope groups. Plutons in the coastal lithotectonic block are the most radiogenic (206Pb/204Pb) 18.25-19.25; 207Pb/204Pb 15.59-15.67; 208Pb/204Pb 38.00-38.60); plutons in northern Maine are the least radiogenic (206Pb/204Pb 18.00-18.50; 207Pb/204Pb 15.51-15.55; 208Pb/204Pb 37.80-38.38). Intermediate lead-isotope values characterize the plutons in central Maine. All plutons show relatively radiogenic lead values for their ages and suggest the imprint of continental crustal sources, particularly in the coastal block. These plutons were formed in different crustal fragments in a continental environment, that were juxtaposed after emplacement of the granites.-L.C.H.

Defining Hsp70 Subnetworks in Dengue Virus Replication Reveals Key Vulnerability in Flavivirus Infection

PubMed Central

Taguwa, Shuhei; Maringer, Kevin; Li, Xiaokai; Bernal-Rubio, Dabeiba; Rauch, Jennifer N.; Gestwicki, Jason E.; Andino, Raul; Fernandez-Sesma, Ana; Frydman, Judith

2015-01-01

Summary Viral protein homeostasis depends entirely on the machinery of the infected cell. Accordingly, viruses can illuminate the interplay between cellular proteostasis components and their distinct substrates. Here we define how the Hsp70 chaperone network mediates the dengue virus life cycle. Cytosolic Hsp70 isoforms are required at distinct steps of the viral cycle, including entry, RNA replication and virion biogenesis. Hsp70 function at each step is specified by nine distinct DNAJ cofactors. Of these, DnaJB11 relocalizes to virus-induced replication complexes to promote RNA synthesis, while DnaJB6 associates with capsid protein and facilitates virion biogenesis. Importantly, an allosteric Hsp70 inhibitor, JG40, potently blocks infection of different dengue serotypes in human primary blood cells without eliciting viral resistance or exerting toxicity to the host cells. JG40 also blocks replication of other medically-important flaviviruses including yellow fever, West Nile and Japanese encephalitis viruses. Thus, targeting host Hsp70 subnetworks provides a path for broad-spectrum antivirals. PMID:26582131

The Mobile Margin of (Far) North America: GPS Constraints on Active Deformation in Alaska and the Role of the Yakutat Block

NASA Astrophysics Data System (ADS)

Elliott, J.; Freymueller, J. T.; Larsen, C. F.; Motyka, R. J.

2010-12-01

GPS data from southern Alaska and the northern Canadian Cordillera have helped redefine the region’s tectonic landscape. Instead of a comparatively simple interaction between the Pacific and North American plates, with relative motion accommodated on a single boundary fault, we find a margin made up of a number of small blocks and deformation zones with relative motion distributed across a variety of structures. Much of this complexity can be attributed to the Yakutat block, an allochthonous terrane that has been colliding with southern Alaska since the Miocene. We present a GPS-derived tectonic model for the Yakutat block collision and its effects on southern Alaska and eastern Canada. The Yakutat block moves NNW at a rate of 50 mm/a, resulting in ~ 45 mm/a of NW-directed convergence with southern Alaska. Along its eastern edge, the Yakutat block is deforming, represented in our model by two small northwesterly moving blocks outboard of the Fairweather fault. Part of the strain from the collision is transferred east of the Fairweather - Queen Charlotte fault system, causing the region inboard of the Fairweather fault to undergo a distinct clockwise rotation into the northern Canadian Cordillera. Further south, the region directly east of the Queen Charlotte fault displays a much slower clockwise rotation, suggesting that it is at least partially pulled along by the northern block motion. About 5% of the relative motion is transferred even further east, causing small northeasterly motions well into the northern Cordillera. The northwestern edge of the Yakutat block marks the main deformation front between that block and southern Alaska. Multiple narrow, northwesterly moving blocks bounded by N- to NW-dipping thrust faults are required to explain the GPS data between the Malaspina Glacier and the Bagley Ice Valley. These “blocks” may be more aptly termed crustal slivers or deformation zones due to their size and because their bounding faults may sole out into a main thrust instead of cutting through the lithosphere. In contrast with the region to the east, relative convergence is accommodated over a fairly short distance across the St. Elias Mountains. West of the deformation front, the en echelon blocks and faults continue until the vicinity of the Bering Glacier, where the GPS data reveal a rotation towards the north as the tectonic regime transitions from the collision and accretion of the Yakutat block to subduction along the Aleutian Megathrust. North of the Chugach and St. Elias Ranges, the Southern Alaska block rotates counterclockwise.

Targeted Lymphoma Cell Death by Novel Signal Transduction Modifications

DTIC Science & Technology

2007-07-01

monoclonal antibodies (mAbs) that bind the two NH2-terminal immunoglobulin domains of CD22 and specifically block the interaction of CD22 with its...ligand blocking mAbs that effectively crosslink CD22 have distinct functional properties and facilitate assembly of an effector protein complex. These...immune mechanisms such as antibody and complement dependent cellular cytotoxicity. We hypothesize that enhancing the intrinsic pro-apoptotic

Geochronological and lead-isotope evidences for rapid crust formation in middle-proterozoic time: The Labrador example

NASA Technical Reports Server (NTRS)

Schaerer, Urs

1988-01-01

Extensive U-Pb geochronological studies in the Grenville and Makkovik provinces have shown that eastern Labrador is underlain by two distinct crustal blocks. In order to substantiate the juvenile character of the middle-Proterozoic crustal block, the isotopic compositon of lead in leached k-feldspars from the same rocks were analyzed. The results of the analysis are briefly discussed.

O and H Isotope Ratios of Syenite Blocks in the El Abrigo Ignimbrite, Tenerife, Canary Islands: A Hydrothermal Fingerprint for Assimilation

NASA Astrophysics Data System (ADS)

Larson, P. B.; Nichols, H. J.; Wolff, J. A.; Marti, J.

2001-12-01

As part of an ongoing project investigating assimilation in ocean island magmas, we are measuring stable isotope ratios of hydrothermally altered lithic fragments in phonolitic pyroclastic deposits from Tenerife, Canary Islands. Nepheline syenite blocks occur in the 0.196 Ma El Abrigo ignimbrite of the Diego Hernandez Formation (DHF). The DHF is the most recent of at least three caldera-forming magmatic cycles on Tenerife. The blocks are fragments of evolved plutons that are chemically similar to phonolites but extend to more strongly differentiated compositions. Distinct major and trace element concentrations suggest that the blocks derive from two intrusions, here referred to as A and B. The B syenites have chemical affinities with the El Abrigo phonolite, and some blocks contain small pockets of residual glass, suggesting that the B pluton may have been coeval with the El Abrigo magma. O isotope ratios of the B syenites lie within the range 4.8 to 7.0 per mil. The B samples are mostly fresh, and their higher O isotope ratios are near pristine magmatic values. Lower values occur in rocks with mild hydrothermal mineralogic alteration, and their values reflect limited high-temperature water-rock isotope exchange. O isotope ratios for A blocks are lower (0.1 to 6.3 per mil, most less than 2.0 per mil), and some samples show extensive mineral alteration. Near-ubiquitous alteration among the A samples, distinct major and trace element compositions, and lack of glass show that this syenite was older than, and unrelated to, the El Abrigo magma. Syenite D/H ratios range from -90 to -120 per mil. O vs H isotope relations indicate that an 18O-depleted meteoric water was the most important reservoir for the high-temperature hydrothermal fluid. Assimilation of altered syenite should provide a distinct stable isotope fingerprint that would be inherited by the product magma. DHF phonolites yield O ratios in the range 5.5 to 7.0 per mil, which may be this fingerprint. Assimilation of variably altered syenites, with accompanying fractionation, is a viable mechanism for producing this stable isotope variability in the magmas.

Exploring the influence of encoding format on subsequent memory.

PubMed

Turney, Indira C; Dennis, Nancy A; Maillet, David; Rajah, M Natasha

2017-05-01

Distinctive encoding is greatly influenced by gist-based processes and has been shown to suffer when highly similar items are presented in close succession. Thus, elucidating the mechanisms underlying how presentation format affects gist processing is essential in determining the factors that influence these encoding processes. The current study utilised multivariate partial least squares (PLS) analysis to identify encoding networks directly associated with retrieval performance in a blocked and intermixed presentation condition. Subsequent memory analysis for successfully encoded items indicated no significant differences between reaction time and retrieval performance and presentation format. Despite no significant behavioural differences, behaviour PLS revealed differences in brain-behaviour correlations and mean condition activity in brain regions associated with gist-based vs. distinctive encoding. Specifically, the intermixed format encouraged more distinctive encoding, showing increased activation of regions associated with strategy use and visual processing (e.g., frontal and visual cortices, respectively). Alternatively, the blocked format exhibited increased gist-based processes, accompanied by increased activity in the right inferior frontal gyrus. Together, results suggest that the sequence that information is presented during encoding affects the degree to which distinctive encoding is engaged. These findings extend our understanding of the Fuzzy Trace Theory and the role of presentation format on encoding processes.

A guide to analysis and reconstruction of serial block face scanning electron microscopy data

PubMed Central

TAGGART, M.; RIND, F.C.; WHITE, K.

2018-01-01

Summary Serial block face scanning electron microscopy (SBF‐SEM) is a relatively new technique that allows the acquisition of serially sectioned, imaged and digitally aligned ultrastructural data. There is a wealth of information that can be obtained from the resulting image stacks but this presents a new challenge for researchers – how to computationally analyse and make best use of the large datasets produced. One approach is to reconstruct structures and features of interest in 3D. However, the software programmes can appear overwhelming, time‐consuming and not intuitive for those new to image analysis. There are a limited number of published articles that provide sufficient detail on how to do this type of reconstruction. Therefore, the aim of this paper is to provide a detailed step‐by‐step protocol, accompanied by tutorial videos, for several types of analysis programmes that can be used on raw SBF‐SEM data, although there are more options available than can be covered here. To showcase the programmes, datasets of skeletal muscle from foetal and adult guinea pigs are initially used with procedures subsequently applied to guinea pig cardiac tissue and locust brain. The tissue is processed using the heavy metal protocol developed specifically for SBF‐SEM. Trimmed resin blocks are placed into a Zeiss Sigma SEM incorporating the Gatan 3View and the resulting image stacks are analysed in three different programmes, Fiji, Amira and MIB, using a range of tools available for segmentation. The results from the image analysis comparison show that the analysis tools are often more suited to a particular type of structure. For example, larger structures, such as nuclei and cells, can be segmented using interpolation, which speeds up analysis; single contrast structures, such as the nucleolus, can be segmented using the contrast‐based thresholding tools. Knowing the nature of the tissue and its specific structures (complexity, contrast, if there are distinct membranes, size) will help to determine the best method for reconstruction and thus maximize informative output from valuable tissue. PMID:29333754

A guide to analysis and reconstruction of serial block face scanning electron microscopy data.

PubMed

Cocks, E; Taggart, M; Rind, F C; White, K

2018-05-01

Serial block face scanning electron microscopy (SBF-SEM) is a relatively new technique that allows the acquisition of serially sectioned, imaged and digitally aligned ultrastructural data. There is a wealth of information that can be obtained from the resulting image stacks but this presents a new challenge for researchers - how to computationally analyse and make best use of the large datasets produced. One approach is to reconstruct structures and features of interest in 3D. However, the software programmes can appear overwhelming, time-consuming and not intuitive for those new to image analysis. There are a limited number of published articles that provide sufficient detail on how to do this type of reconstruction. Therefore, the aim of this paper is to provide a detailed step-by-step protocol, accompanied by tutorial videos, for several types of analysis programmes that can be used on raw SBF-SEM data, although there are more options available than can be covered here. To showcase the programmes, datasets of skeletal muscle from foetal and adult guinea pigs are initially used with procedures subsequently applied to guinea pig cardiac tissue and locust brain. The tissue is processed using the heavy metal protocol developed specifically for SBF-SEM. Trimmed resin blocks are placed into a Zeiss Sigma SEM incorporating the Gatan 3View and the resulting image stacks are analysed in three different programmes, Fiji, Amira and MIB, using a range of tools available for segmentation. The results from the image analysis comparison show that the analysis tools are often more suited to a particular type of structure. For example, larger structures, such as nuclei and cells, can be segmented using interpolation, which speeds up analysis; single contrast structures, such as the nucleolus, can be segmented using the contrast-based thresholding tools. Knowing the nature of the tissue and its specific structures (complexity, contrast, if there are distinct membranes, size) will help to determine the best method for reconstruction and thus maximize informative output from valuable tissue. © 2018 The Authors. Journal of Microscopy published by John Wiley & Sons Ltd on behalf of Royal Microscopical Society.

Rayleigh Wave Phase Velocities Beneath the Central and Southern East African Rift System

NASA Astrophysics Data System (ADS)

Adams, A. N.; Miller, J. C.

2017-12-01

This study uses the Automated Generalized Seismological Data Function (AGSDF) method to develop a model of Rayleigh wave phase velocities in the central and southern portions of the East African Rift System (EARS). These phase velocity models at periods of 20-100s lend insight into the lithospheric structures associated with surficial rifting and volcanism, as well as basement structures that pre-date and affect the course of rifting. A large dataset of >700 earthquakes is used, comprised of Mw=6.0+ events that occurred between the years 1995 and 2016. These events were recorded by a composite array of 176 stations from twelve non-contemporaneous seismic networks, each with a distinctive array geometry and station spacing. Several first-order features are resolved in this phase velocity model, confirming findings from previous studies. (1) Low velocities are observed in isolated regions along the Western Rift Branch and across the Eastern Rift Branch, corresponding to areas of active volcanism. (2) Two linear low velocity zones are imaged trending southeast and southwest from the Eastern Rift Branch in Tanzania, corresponding with areas of seismic activity and indicating possible incipient rifting. (3) High velocity regions are observed beneath both the Tanzania Craton and the Bangweulu Block. Furthermore, this model indicates several new findings. (1) High velocities beneath the Bangweulu Block extend to longer periods than those found beneath the Tanzania Craton, perhaps indicating that rifting processes have not altered the Bangweulu Block as extensively as the Tanzania Craton. (2) At long periods, the fast velocities beneath the Bangweulu Block extend eastwards beyond the surficial boundaries, to and possibly across the Malawi Rift. This may suggest the presence of older, thick blocks of lithosphere in regions where they are not exposed at the surface. (3) Finally, while the findings of this study correspond well with previous studies in regions of overlapping data, the greatest deviations, as well as the highest standard deviation in measurements, are found in volcanically active regions characterized by high anisotropy, suggesting that the influence of seismic anisotropy may have vary significantly between tomography methods.

Tectonic slicing and mixing processes along the subduction interface: The Sistan example (Eastern Iran)

NASA Astrophysics Data System (ADS)

Bonnet, G.; Agard, P.; Angiboust, S.; Monié, P.; Jentzer, M.; Omrani, J.; Whitechurch, H.; Fournier, M.

2018-06-01

Suture zones preserve metamorphosed relicts of subducted ocean floor later exhumed along the plate interface that can provide critical insights on subduction zone processes. Mélange-like units are exceptionally well-exposed in the Sistan suture (Eastern Iran), which results from the closure of a branch of the Neotethys between the Lut and Afghan continental blocks. High pressure rocks found in the inner part of the suture zone (i.e., Ratuk complex) around Gazik are herein compared to previously studied outcrops along the belt. Detailed field investigations and mapping allow the distinction of two kinds of subduction-related block-in-matrix units: a siliciclastic-matrix complex and a serpentinite-matrix complex. The siliciclastic-matrix complex includes barely metamorphosed blocks of serpentinized peridotite, radiolarite and basalt of maximum greenschist-facies grade (i.e., maximum temperature of 340 °C). The serpentinite-matrix complex includes blocks of various grades and lithologies: mafic eclogites, amphibolitized blueschists, blue-amphibole-bearing metacherts and aegirine-augite-albite rocks. Eclogites reached peak pressure conditions around 530 °C and 2.3 GPa and isothermal retrogression down to 530 °C and 0.9 GPa. Estimation of peak PT conditions for the other rocks are less-well constrained but suggest equilibration at P < 1 GPa. Strikingly similar Ar-Ar ages of 86 ± 3 Ma, along 70 km, are obtained for phengite and amphibole from fourteen eclogite and amphibolitized blueschist blocks. Ages in Gazik are usually younger than further south (e.g., Sulabest), but there is little age difference between the various kinds of rocks. These results (radiometric ages, observed structures and rock types) support a tectonic origin of the serpentinite-matrix mélange and shed light on subduction zone dynamics, particularly on coeval detachment and exhumation mechanisms of slab-derived rocks.

Intradomain phase transitions in flexible block copolymers with self-aligning segments.

PubMed

Burke, Christopher J; Grason, Gregory M

2018-05-07

We study a model of flexible block copolymers (BCPs) in which there is an enlthalpic preference for orientational order, or local alignment, among like-block segments. We describe a generalization of the self-consistent field theory of flexible BCPs to include inter-segment orientational interactions via a Landau-de Gennes free energy associated with a polar or nematic order parameter for segments of one component of a diblock copolymer. We study the equilibrium states of this model numerically, using a pseudo-spectral approach to solve for chain conformation statistics in the presence of a self-consistent torque generated by inter-segment alignment forces. Applying this theory to the structure of lamellar domains composed of symmetric diblocks possessing a single block of "self-aligning" polar segments, we show the emergence of spatially complex segment order parameters (segment director fields) within a given lamellar domain. Because BCP phase separation gives rise to spatially inhomogeneous orientation order of segments even in the absence of explicit intra-segment aligning forces, the director fields of BCPs, as well as thermodynamics of lamellar domain formation, exhibit a highly non-linear dependence on both the inter-block segregation (χN) and the enthalpy of alignment (ε). Specifically, we predict the stability of new phases of lamellar order in which distinct regions of alignment coexist within the single mesodomain and spontaneously break the symmetries of the lamella (or smectic) pattern of composition in the melt via in-plane tilt of the director in the centers of the like-composition domains. We further show that, in analogy to Freedericksz transition confined nematics, the elastic costs to reorient segments within the domain, as described by the Frank elasticity of the director, increase the threshold value ε needed to induce this intra-domain phase transition.

Intradomain phase transitions in flexible block copolymers with self-aligning segments

NASA Astrophysics Data System (ADS)

Burke, Christopher J.; Grason, Gregory M.

2018-05-01

We study a model of flexible block copolymers (BCPs) in which there is an enlthalpic preference for orientational order, or local alignment, among like-block segments. We describe a generalization of the self-consistent field theory of flexible BCPs to include inter-segment orientational interactions via a Landau-de Gennes free energy associated with a polar or nematic order parameter for segments of one component of a diblock copolymer. We study the equilibrium states of this model numerically, using a pseudo-spectral approach to solve for chain conformation statistics in the presence of a self-consistent torque generated by inter-segment alignment forces. Applying this theory to the structure of lamellar domains composed of symmetric diblocks possessing a single block of "self-aligning" polar segments, we show the emergence of spatially complex segment order parameters (segment director fields) within a given lamellar domain. Because BCP phase separation gives rise to spatially inhomogeneous orientation order of segments even in the absence of explicit intra-segment aligning forces, the director fields of BCPs, as well as thermodynamics of lamellar domain formation, exhibit a highly non-linear dependence on both the inter-block segregation (χN) and the enthalpy of alignment (ɛ). Specifically, we predict the stability of new phases of lamellar order in which distinct regions of alignment coexist within the single mesodomain and spontaneously break the symmetries of the lamella (or smectic) pattern of composition in the melt via in-plane tilt of the director in the centers of the like-composition domains. We further show that, in analogy to Freedericksz transition confined nematics, the elastic costs to reorient segments within the domain, as described by the Frank elasticity of the director, increase the threshold value ɛ needed to induce this intra-domain phase transition.

A new oxytelluride: Perovskite and CsCl intergrowth in Ba 3Yb 2O 5Te

DOE PAGES

Whalen, J. B.; Besara, T.; Vasquez, R.; ...

2013-04-27

The new oxytelluride Ba 3Yb 2O 5Te was obtained from an alkaline earth flux. Ba3Yb2O5Te crystallizes in the tetragonal space group P4/ mmm (#123), with a=4.3615(3) Å and c=11.7596(11) angstrom, Z=1. The structure combines two distinct building blocks, a Ba 2Yb 2O 5 perovskite-like double layer with square bipyramidal coordination of the ytterbium ions, and a CsCl-type BaTe layer. Short range magnetic order is apparent at below 5 K, with the magnetic behavior above this temperature dominated by crystal field effects. The structure may be considered as an analog to the Ruddlesden-Popper phases, where the NaCl-type layer has been replacedmore » by the CsCl-type layer. Finally, the two-dimensional magnetic behavior is expected based on the highly anisotropic nature of the structure.« less

Cardiac myocyte diversity and a fibroblast network in the junctional region of the zebrafish heart revealed by transmission and serial block-face scanning electron microscopy.

PubMed

Lafontant, Pascal J; Behzad, Ali R; Brown, Evelyn; Landry, Paul; Hu, Norman; Burns, Alan R

2013-01-01

The zebrafish has emerged as an important model of heart development and regeneration. While the structural characteristics of the developing and adult zebrafish ventricle have been previously studied, little attention has been paid to the nature of the interface between the compact and spongy myocardium. Here we describe how these two distinct layers are structurally and functionally integrated. We demonstrate by transmission electron microscopy that this interface is complex and composed primarily of a junctional region occupied by collagen, as well as a population of fibroblasts that form a highly complex network. We also describe a continuum of uniquely flattened transitional cardiac myocytes that form a circumferential plate upon which the radially-oriented luminal trabeculae are anchored. In addition, we have uncovered within the transitional ring a subpopulation of markedly electron dense cardiac myocytes. At discrete intervals the transitional cardiac myocytes form contact bridges across the junctional space that are stabilized through localized desmosomes and fascia adherentes junctions with adjacent compact cardiac myocytes. Finally using serial block-face scanning electron microscopy, segmentation and volume reconstruction, we confirm the three-dimensional nature of the junctional region as well as the presence of the sheet-like fibroblast network. These ultrastructural studies demonstrate the previously unrecognized complexity with which the compact and spongy layers are structurally integrated, and provide a new basis for understanding development and regeneration in the zebrafish heart.

Diazole-based powdered cocrystal featuring a helical hydrogen-bonded network: structure determination from PXRD, solid-state NMR and computer modeling.

PubMed

Sardo, Mariana; Santos, Sérgio M; Babaryk, Artem A; López, Concepción; Alkorta, Ibon; Elguero, José; Claramunt, Rosa M; Mafra, Luís

2015-02-01

We present the structure of a new equimolar 1:1 cocrystal formed by 3,5-dimethyl-1H-pyrazole (dmpz) and 4,5-dimethyl-1H-imidazole (dmim), determined by means of powder X-ray diffraction data combined with solid-state NMR that provided insight into topological details of hydrogen bonding connectivities and weak interactions such as CH···π contacts. The use of various 1D/2D (13)C, (15)N and (1)H high-resolution solid-state NMR techniques provided structural insight on local length scales revealing internuclear proximities and relative orientations between the dmim and dmpz molecular building blocks of the studied cocrystal. Molecular modeling and DFT calculations were also employed to generate meaningful structures. DFT refinement was able to decrease the figure of merit R(F(2)) from ~11% (PXRD only) to 5.4%. An attempt was made to rationalize the role of NH···N and CH···π contacts in stabilizing the reported cocrystal. For this purpose four imidazole derivatives with distinct placement of methyl substituents were reacted with dmpz to understand the effect of methylation in blocking or enabling certain intermolecular contacts. Only one imidazole derivative (dmim) was able to incorporate into the dmpz trimeric motif thus resulting in a cocrystal, which contains both hydrophobic (methyl groups) and hydrophilic components that self-assemble to form an atypical 1D network of helicoidal hydrogen bonded pattern, featuring structural similarities with alpha-helix arrangements in proteins. The 1:1 dmpz···dmim compound I is the first example of a cocrystal formed by two different azoles. Copyright © 2014 Elsevier Inc. All rights reserved.

Comparative analysis of native and permethylated human milk oligosaccharides by liquid chromatography coupled to high resolution mass spectrometry.

PubMed

Oursel, Stéphanie; Cholet, Sophie; Junot, Christophe; Fenaille, François

2017-12-15

Human milk oligosaccharides (HMOs) represent the third most abundant components of milk after lactose and lipids. HMOs are indigestible by the suckling infant but can act as prebiotics and have significant biological functions regarding the organism defense against pathogens (such as bacteria or viruses) by preventing interactions with their receptors. Although constituted of only five distinct monosaccharide building blocks, HMOs are highly structurally diverse compounds with many co-existing structural isomers. Here we report the development and comparison of two distinct glycomic platforms based on liquid chromatography coupled to high resolution mass spectrometry (LC-MS) for analyzing HMOs. We have implemented and thoroughly compared the LC-MS of permethylated and native HMOs on reversed phase (RP) and porous graphitic carbon (PGC) columns for their ability to resolve the natural heterogeneity of milk oligosaccharides at the highest sensitivity. Our data essentially underlines the usefulness of analyzing HMOs as permethylated derivatives especially for getting more precise structural information at high sensitivity. For instance, permethylation annihilates gas-phase fucose migration during MS/MS experiments, thus facilitating spectra interpretation and giving access to relevant information regarding oligosaccharide branching and isomer distinction. At the opposite, LC-MS profiling of native HMOs (using PGC) in milk performed best in terms of detected species, while also being much faster in terms of sample preparation. Although less efficient than PGC chromatography, RPLC proved successful for separating pairs of permethylated isomeric HMOs. A key advantage of RP over PGC liquid chromatography is that retention times can be correlated to molecular weights, which can greatly facilitate further HMO identification using retention time prediction. Altogether these data lead us to think that LC-MS analysis of native HMOs (using PGC) can be used as first-line profiling approach while permethylation can be performed afterwards for facilitating structural characterization. Copyright © 2017 Elsevier B.V. All rights reserved.

Block copolymers for alkaline fuel cell membrane materials

NASA Astrophysics Data System (ADS)

Li, Yifan

Alkaline fuel cells (AFCs) using anion exchange membranes (AEMs) as electrolyte have recently received considerable attention. AFCs offer some advantages over proton exchange membrane fuel cells, including the potential of non-noble metal (e.g. nickel, silver) catalyst on the cathode, which can dramatically lower the fuel cell cost. The main drawback of traditional AFCs is the use of liquid electrolyte (e.g. aqueous potassium hydroxide), which can result in the formation of carbonate precipitates by reaction with carbon dioxide. AEMs with tethered cations can overcome the precipitates formed in traditional AFCs. Our current research focuses on developing different polymer systems (blend, block, grafted, and crosslinked polymers) in order to understand alkaline fuel cell membrane in many aspects and design optimized anion exchange membranes with better alkaline stability, mechanical integrity and ionic conductivity. A number of distinct materials have been produced and characterized. A polymer blend system comprised of poly(vinylbenzyl chloride)-b-polystyrene (PVBC-b-PS) diblock copolymer, prepared by nitroxide mediated polymerization (NMP), with poly(2,6-dimethyl-1,4-phenylene oxide) (PPO) or brominated PPO was studied for conversion into a blend membrane for AEM. The formation of a miscible blend matrix improved mechanical properties while maintaining high ionic conductivity through formation of phase separated ionic domains. Using anionic polymerization, a polyethylene based block copolymer was designed where the polyethylene-based block copolymer formed bicontinuous morphological structures to enhance the hydroxide conductivity (up to 94 mS/cm at 80 °C) while excellent mechanical properties (strain up to 205%) of the polyethylene block copolymer membrane was observed. A polymer system was designed and characterized with monomethoxy polyethylene glycol (mPEG) as a hydrophilic polymer grafted through substitution of pendent benzyl chloride groups of a PVBC-b-PS. The incorporation of the hydrophilic polymer allows for an investigation of the effect of hydration on ionic conductivity, resulting in the increase in membrane water affinity, enhancement of conductivity and reduced dependence of conductivity on relative humidity. A study of crosslinking of block copolymers was done wherein the crosslinking occurs in the non-matrix phase in order to maintain mechanical properties. The formation of a cationic crosslinked structure improves the mechanical integrity of the membrane in water while showing little deleterious effect on ionic conductivity and mechanical properties.

Implicit and explicit processing in deep dyslexia: Semantic blocking as a test for failure of inhibition in the phonological output lexicon.

PubMed

Colangelo, Annette; Buchanan, Lori

2006-12-01

The failure of inhibition hypothesis posits a theoretical distinction between implicit and explicit access in deep dyslexia. Specifically, the effects of failure of inhibition are assumed only in conditions that have an explicit selection requirement in the context of production (i.e., aloud reading). In contrast, the failure of inhibition hypothesis proposes that implicit processing and explicit access to semantic information without production demands are intact in deep dyslexia. Evidence for intact implicit and explicit access requires that performance in deep dyslexia parallels that observed in neurologically intact participants on tasks based on implicit and explicit processes. In other words, deep dyslexics should produce normal effects in conditions with implicit task demands (i.e., lexical decision) and on tasks based on explicit access without production (i.e., forced choice semantic decisions) because failure of inhibition does not impact the availability of lexical information, only explicit retrieval in the context of production. This research examined the distinction between implicit and explicit processes in deep dyslexia using semantic blocking in lexical decision and forced choice semantic decisions as a test for the failure of inhibition hypothesis. The results of the semantic blocking paradigm support the distinction between implicit and explicit processing and provide evidence for failure of inhibition as an explanation for semantic errors in deep dyslexia.

Materials by Design—A Perspective From Atoms to Structures

PubMed Central

Buehler, Markus J.

2013-01-01

Biological materials are effectively synthesized, controlled, and used for a variety of purposes—in spite of limitations in energy, quality, and quantity of their building blocks. Whereas the chemical composition of materials in the living world plays a some role in achieving functional properties, the way components are connected at different length scales defines what material properties can be achieved, how they can be altered to meet functional requirements, and how they fail in disease states and other extreme conditions. Recent work has demonstrated this by using large-scale computer simulations to predict materials properties from fundamental molecular principles, combined with experimental work and new mathematical techniques to categorize complex structure-property relationships into a systematic framework. Enabled by such categorization, we discuss opportunities based on the exploitation of concepts from distinct hierarchical systems that share common principles in how function is created, linking music to materials science. PMID:24163499

Sidescan backscatter variations of cold seeps on the Hikurangi Margin (New Zealand): indications for different stages in seep development

NASA Astrophysics Data System (ADS)

Dumke, Ines; Klaucke, Ingo; Berndt, Christian; Bialas, Jörg

2014-06-01

Cold seeps on the Hikurangi Margin off New Zealand exhibit various seabed morphologies producing different intensity patterns in sidescan backscatter images. Acoustic backscatter characteristics of 25 investigated seep sites fall into four distinct types characterised by variations in backscatter intensity, distribution and inferred structural heights. The types reflect different carbonate morphologies including up to 20-m-high structures (type 1), low-relief crusts (type 2), scattered blocks (type 3) and carbonate-free sites (type 4). Each seep corresponds to a single type; intermediates were not observed. This correlates well with published data on seep fauna at each site, with the four types representing three different faunal habitats of successive stages of seep development. Backscatter signatures in sidescan sonar images of cold seeps may therefore serve as a convenient proxy for variations in faunal habitats.

Giant landslide deposits in northwest Argentina

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

Fauque, L.; Strecker, M.R.; Bloom, A.L.

1985-01-01

Giant Quaternary landslide deposits occur along mountain fronts in the structural transition zone between the high-angle reverse-fault-bounded Sierras Pampeanas and the low-angle thrust belt of the Sierras Subandinas. There are two modes of occurrence: (1) chaotic masses without distinct geometry, and (2) masses with distinct lobate geometry similar to glacial moraines. Type (1) deposits occur where the moving rock mass followed a narrow valley and blocked the drainage. Many of these caused subsequent formation of lakes and changed the sedimentation processes on pediments at the mountain fronts. In type (2) deposits, lateral and frontal ridges are up to 10 mmore » higher than the interior parts; in some places pressure ridges within the lobes are well preserved. Type (2) deposits show reverse grading and were deposited on relatively smooth pediments or alluvial fans. The lobate geometry strongly suggests that type (2) deposits are a product of flowage and are debris stream or sturzstrom deposits (sense of Heim, 1932 and Hsu, 1975). All investigated deposits occur in areas of demonstrated Quaternary faulting and are interpreted as the result of tectonic movements, although structural inhomogeneities in the source area may have been a significant factor for some of the landslides. No datable materials have yet been found associated with the deposits.« less

Metal ions may suppress or enhance cellular differentiation in Candida albicans and Candida tropicalis biofilms.

PubMed

Harrison, Joe J; Ceri, Howard; Yerly, Jerome; Rabiei, Maryam; Hu, Yaoping; Martinuzzi, Robert; Turner, Raymond J

2007-08-01

Candida albicans and Candida tropicalis are polymorphic fungi that develop antimicrobial-resistant biofilm communities that are characterized by multiple cell morphotypes. This study investigated cell type interconversion and drug and metal resistance as well as community organization in biofilms of these microorganisms that were exposed to metal ions. To study this, Candida biofilms were grown either in microtiter plates containing gradient arrays of metal ions or in the Calgary Biofilm Device for high-throughput susceptibility testing. Biofilm formation and antifungal resistance were evaluated by viable cell counts, tetrazolium salt reduction, light microscopy, and confocal laser scanning microscopy in conjunction with three-dimensional visualization. We discovered that subinhibitory concentrations of certain metal ions (CrO(4)(2-), Co(2+), Cu(2+), Ag(+), Zn(2+), Cd(2+), Hg(2+), Pb(2+), AsO(2)(-), and SeO(3)(2-)) caused changes in biofilm structure by blocking or eliciting the transition between yeast and hyphal cell types. Four distinct biofilm community structure types were discerned from these data, which were designated "domed," "layer cake," "flat," and "mycelial." This study suggests that Candida biofilm populations may respond to metal ions to form cell-cell and solid-surface-attached assemblages with distinct patterns of cellular differentiation.

Using Intact Iron Microbial Mats to Gain Insights Into Mat Ecology and Geochemical Niche at the Microbial Scale

NASA Astrophysics Data System (ADS)

Glazer, B. T.; Chan, C. S. Y.; Mcallister, S.; Leavitt, A.; Emerson, D.

2015-12-01

Microbial mats are formed by microorganisms working in coordinated symbiosis, often benefitting the community by controlling the local geochemical or physical environment. Thus, the ecology of the mat depends on the individual roles of microbes organized into niches within a larger architecture. Chemolithotrophic Fe-oxidizing bacteria (FeOB) form distinctive Fe oxyhydroxide biominerals which constitute the building blocks of the mat. However, the majority of our progress has been in understanding the overall community structure. Understanding the physical mat structure on the microbial scale is important to unraveling FeOB evolution, the biogeochemistry and ecology of Fe-rich habitats, and ultimately interpreting FeOB biosignatures in the rock record. Mats in freshwater and marine environments contain strikingly similar biomineral morphologies, yet they are formed by phylogenetically distinct microorganisms. This suggests that the overall architecture and underlying genetics of freshwater and marine mats has evolved to serve particular roles specific to Fe oxidation. Thus, we conducted a comparative study of Fe seep freshwater mats and marine hydrothermal mats. We have developed a new approach to sampling Fe mats in order to preserve the delicate structure for analysis by confocal and scanning electron microscopy. Our analyses of these intact mats show that freshwater and marine mats are similarly initiated by a single type of structure-former. These ecosystem engineers form either a hollow sheath or a twisted stalk biomineral during mat formation, with a highly directional structure. These microbes appear to be the vanguard organisms that anchor the community within oxygen/Fe(II) gradients, further allowing for community succession in the mat interior as evidenced by other mineralized morphologies. Patterns in biomineral thickness and directionality were indicative of redox gradients and temporal changes in the geochemical environment. These observations show that the FeOB create the structure of the environment for the entire microbial community, acting as environmental engineers. Furthermore, they leave behind distinctive signatures of environmental conditions (e.g. presence of oxygen, hydrothermal pulsing), which can be recorded in the rock record.

Determining the Mechanical Properties of Lattice Block Structures

NASA Technical Reports Server (NTRS)

Wilmoth, Nathan

2013-01-01

Lattice block structures and shape memory alloys possess several traits ideal for solving intriguing new engineering problems in industries such as aerospace, military, and transportation. Recent testing at the NASA Glenn Research Center has investigated the material properties of lattice block structures cast from a conventional aerospace titanium alloy as well as lattice block structures cast from nickel-titanium shape memory alloy. The lattice block structures for both materials were sectioned into smaller subelements for tension and compression testing. The results from the cast conventional titanium material showed that the expected mechanical properties were maintained. The shape memory alloy material was found to be extremely brittle from the casting process and only compression testing was completed. Future shape memory alloy lattice block structures will utilize an adjusted material composition that will provide a better quality casting. The testing effort resulted in baseline mechanical property data from the conventional titanium material for comparison to shape memory alloy materials once suitable castings are available.

Metabauxite horizons containing remobilized-origin gem diaspore and related mineralization, Milas-Muğla province, SW Turkey

NASA Astrophysics Data System (ADS)

Hatipoğlu, Murat; Türk, Necdet; Chamberlain, Steven C.; Murat Akgün, A.

2010-10-01

Remobilized-origin gem diaspore and related minerals occur as infill within structurally controlled voids that developed in the upper of two distinct karst unconformity-type metabauxite (diasporite) horizons in the İlbir Mountains area of the Milas-Muğla province, SW Turkey. Colour-change diaspore (trademarked as zultanite) and associated mineral specimens (greenish muscovite, chloritoid, donbassite, specular hematite, ilmenite, goethite, and younger calcite) occur in fracture zones (veins and open structures) that cross-cut the metabauxite horizons. The mineralized fracture zones do not extend into the enclosing marbles, probably because of the ductility contrast between the brittle bauxite and relatively plastic carbonate beds. Thick, white to light gray and dark gray limestone beds were deposited in the İlbir Mountains area during the Cretaceous (146-65 Ma), and contain two stratigraphically distinct karst-fill bauxite horizons. Al-, Fe-, Si- and Ti-rich solutions that infiltrated the karstified limestone probably originated from altered schist and gneiss that surround the basin. The limestone beds (>2000 m thick) were subjected to burial metamorphism, forming marble. Subsequently, the marble block was folded during nappe emplacement toward the SSW as part of late Alpine contractional deformation during the Paleogene (65-23.8 Ma). The upper bauxite horizons within the folded block were cross-cut by fracture zones because of their relatively brittle rheology. At this time, increased pressure and temperature in the bauxite horizons resulted in remobilization of the primary constituents of the bauxite within an aqueous complex, resulting in the crystallization of coarse-grained assemblages in the cross-cutting structures. Ultimately, erosion and mineral exploration revealed the steeply dipping bauxite outcrops and mine workings evident today. This paper focuses on the mine geology of surface outcrops of diasporic bauxite, the upper bauxite horizon within underground mine galleries at elevations of 600, 632, 637, 642, 652, 657, and 702 m, and in open pits at sites in the Küçükçamlık and Büyükçamlık hills, Milas-Muğla province, SW Turkey.

DNA packaging and the pathway of bacteriophage T4 head assembly.

PubMed Central

Hsiao, C L; Black, L W

1977-01-01

A cold-sensitive mutation in the structural gene for a minor phage T4 capsid protein (p20) leads to formation of heads containing p20 and cleaved head proteins and empty of DNA. Such heads can be filled with DNA and converted to active phages in vivo uponshift to high temperature. It appears that p20 has two distinct roles in head assembly: first, in construction of the prehead shell (blocked by ts and am mutation) and, second,in DNA packaging (blocked by cs mutation). The latter function is closely associated with gene 17 product, previously known to be required for DNA packagaing. Temperature shift studies of cs-ts double mutants and other observations allow determination of phage function required for DNA packaging. Contrary to previous proposals, we find that T4 DNA packaging is not directly coupled to and can follow DNA synthesis, protein cleavage, prehead core removal, and gene 21-mediated cleavage-induced increase in head volume. Our evidence suggests that an altered head assembly pathway exists and that DNA packaging is probably initiated by DNA-capsid (p20) interaction. Images PMID:269421

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

Roy, D.W.; Schmitt, L.; Woussen, G.

Airborne SAR images provided essential clues to the tectonic setting of (1) the MbLg 6.5 Saguenay earthquake of 25 November 1988, (2) the Charlevoix-Kamouraska seismic source zone, and (3) some of the low *eve* seismic activity in the Eastern seismic background zone of Canada. The event occurred in the southeastern part of the Canadian Shield in an area where the boundary between the Saguenay graben and the Jacques Cartier horst is not well defined. These two tectonic blocks are both associated with the Iapetan St-Lawrence rift. These blocks exhibit several important structural breaks and distinct domains defined by the lineamentmore » orientations, densities, and habits. Outcrop observations confirm that several lineament sets correspond to Precambrian ductile shear zones reactivated as brittle faults during the Phanerozoic. In addition, the northeast and southwest limits of recent seismic activity in the Charlevoix-Kamouraska zone correspond to major elements of the fracture pattern identified on the SAR images. These fractures appear to be related to the interaction of the Charlevoix astrobleme with the tectonic features of the area. 20 refs.« less

Block coals from Indiana: Inferences on changing depositional environment

USGS Publications Warehouse

Mastalerz, Maria; Padgett, P.L.; Eble, C.F.

2000-01-01

Significant differences in coal petrography, palynology and coal quality were found between the Lower Block and Upper Block Coal Members (Brazil Formation, Pennsylvanian) in Daviess County, Indiana. The Lower Block Coal Member ranges in thickness from 51 to 74 cm and the Upper Block Coal Member ranges from 20 to 65 cm. Average sulfur content and ash yield of the Lower Block coal (0.98%, 7.65%) are lower than in the Upper Block coal. Megascopically, the coals show distinct differences. The Lower Block is a banded coal with numerous thin fusain horizons and a thin clay parting in the lower third of the seam. The Upper Block coal has a dulling-upward trend, with a bright clarain found at the base that grades into a clarain and then into a durain in the upper portion of the seam. Vitrinite content of the Lower Block coal ranges from 63% to 78%, with the highest vitrinite content found in the middle portion of the seam. In the Upper Block coal, vitrinite content ranges from 40% to 83%, with the highest values found in the lower part of the seam. Ash yield is higher in the upper part of the Upper Block coal, reaching up to 40%. The Lower Block coal is dominated by lycopod trees and tree ferns. The Upper Block coal shows marked differences in spore assemblages between lower and upper parts of the seam. The lower half is dominated by large lycopod trees and tree ferns, similar to the Lower Block coal. The upper half is dominated by small lycopods, mainly Densosporites and Radiizonates. These differences between the Lower Block and Upper Block Coal Members are significant correlation tools applicable to mining exploration and chronostratigraphy. (C) 2000 Elsevier Science B.V. All rights reserved.Significant differences in coal petrography, palynology and coal quality were found between the Lower Block and Upper Block Coal Members (Brazil Formation, Pennsylvanian) in Daviess County, Indiana. The Lower Block Coal Member ranges in thickness from 51 to 74 cm and the Upper Block Coal Member ranges from 20 to 65 cm. Average sulfur content and ash yield of the Lower Block coal (0.98%, 7.65%) are lower than in the Upper Block coal. Megascopically, the coals show distinct differences. The Lower Block is a banded coal with numerous thin fusain horizons and a thin clay parting in the lower third of the seam. The Upper Block coal has a dulling-upward trend, with a bright clarain found at the base that grades into a clarain and then into a durain in the upper portion of the seam. Vitrinite content of the Lower Block coal ranges from 63% to 78%, with the highest vitrinite content found in the middle portion of the seam. In the Upper Block coal, vitrinite content ranges from 40% to 83%, with the highest values found in the lower part of the seam. Ash yield is higher in the upper part of the Upper Block coal, reaching up to 40%. The Lower Block coal is dominated by lycopod trees and tree ferns. The Upper Block coal shows marked differences in spore assemblages between lower and upper parts of the seam. The lower half is dominated by large lycopod trees and tree ferns, similar to the Lower Block coal. The upper half is dominated by small lycopods, mainly Densosporites and Radiizonates. These differences between the Lower Block and Upper Block Coal members are significant correlation tools applicable to mining exploration and chronostratigraphy.

Pattern interpolation in thin films of lamellar, symmetric copolymers on nano-patterned substrates

NASA Astrophysics Data System (ADS)

Detcheverry, Francois; Nagpal, Umang; Liu, Guoliang; Nealey, Paul; de Pablo, Juan

2009-03-01

A molecular model of block copolymer systems is used to conduct a systematic study of the morphologies that arise when thin films of symmetric, lamellar forming block copolymer materials are deposited on nanopatterned surfaces. Over 500 distinct cases are considered. It is found that, in general, three distinct morphologies can arise depending on the strength of the substrate-polymer interactions, the film thickness, and the period of the substrate pattern. The relative stability of those morphologies is determined by direct calculation of the free energy differences. The dynamic propensity of those morphologies to emerge is examined by careful analysis of simulated trajectories. The results of this systematic study are used to interpret recent experimental data for films of polystyrene-PMMA copolymers on chemically nanopatterned surfaces.

A combination of new screening assays for prioritization of transmission-blocking antimalarials reveals distinct dynamics of marketed and experimental drugs.

PubMed

Bolscher, J M; Koolen, K M J; van Gemert, G J; van de Vegte-Bolmer, M G; Bousema, T; Leroy, D; Sauerwein, R W; Dechering, K J

2015-05-01

The development of drugs to reduce malaria transmission is an important part of malaria eradication plans. We set out to develop and validate a combination of new screening assays for prioritization of transmission-blocking molecules. We developed high-throughput assays for screening compounds against gametocytes, the parasite stages responsible for onward transmission to mosquitoes. An existing gametocyte parasitic lactate dehydrogenase (pLDH) assay was adapted for use in 384-well plates, and a novel homogeneous immunoassay to monitor the functional transition of female gametocytes into gametes was developed. A collection of 48 marketed and experimental antimalarials was screened and subsequently tested for impact on sporogony in Anopheles mosquitoes, to directly quantify the transmission-blocking properties of antimalarials in relation to their effects on gametocyte pLDH activity or gametogenesis. The novel screening assays revealed distinct stage-specific kinetics and dynamics of drug effects. Peroxides showed the most potent transmission-blocking effects, with an intermediate speed of action and IC50 values that were 20-40-fold higher than the IC50s against the asexual stages causing clinical malaria. Finally, the novel synthetic peroxide OZ439 appeared to be a promising drug candidate as it exerted gametocytocidal and transmission-blocking effects at clinically relevant concentrations. © The Author 2015. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Structure of the transporter associated with antigen processing trapped by herpes simplex virus

PubMed Central

Oldham, Michael L; Grigorieff, Nikolaus; Chen, Jue

2016-01-01

The transporter associated with antigen processing (TAP) is an ATP-binding cassette (ABC) transporter essential to cellular immunity against viral infection. Some persistent viruses have evolved strategies to inhibit TAP so that they may go undetected by the immune system. The herpes simplex virus for example evades immune surveillance by blocking peptide transport with a small viral protein ICP47. In this study, we determined the structure of human TAP bound to ICP47 by electron cryo-microscopy (cryo-EM) to 4.0 Å. The structure shows that ICP47 traps TAP in an inactive conformation distinct from the normal transport cycle. The specificity and potency of ICP47 inhibition result from contacts between the tip of the helical hairpin and the apex of the transmembrane cavity. This work provides a clear molecular description of immune evasion by a persistent virus. It also establishes the molecular structure of TAP to facilitate mechanistic studies of the antigen presentation process. DOI: http://dx.doi.org/10.7554/eLife.21829.001 PMID:27935481

Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV

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

Zheng, Yi; Han, Gye Won; Abagyan, Ruben

CCR5 is the primary chemokine receptor utilized by HIV to infect leukocytes, whereas CCR5 ligands inhibit infection by blocking CCR5 engagement with HIV gp120. To guide the design of improved therapeutics, we solved the structure of CCR5 in complex with chemokine antagonist [5P7]CCL5. Several structural features appeared to contribute to the anti-HIV potency of [5P7]CCL5, including the distinct chemokine orientation relative to the receptor, the near-complete occupancy of the receptor binding pocket, the dense network of intermolecular hydrogen bonds, and the similarity of binding determinants with the FDA-approved HIV inhibitor Maraviroc. Molecular modeling indicated that HIV gp120 mimicked the chemokinemore » interaction with CCR5, providing an explanation for the ability of CCR5 to recognize diverse ligands and gp120 variants. Our findings reveal that structural plasticity facilitates receptor-chemokine specificity and enables exploitation by HIV, and provide insight into the design of small molecule and protein inhibitors for HIV and other CCR5-mediated diseases.« less

Naming Block Structures: A Multimodal Approach

ERIC Educational Resources Information Center

Cohen, Lynn; Uhry, Joanna

2011-01-01

This study describes symbolic representation in block play in a culturally diverse suburban preschool classroom. Block play is "multimodal" and can allow children to experiment with materials to represent the world in many forms of literacy. Combined qualitative and quantitative data from seventy-seven block structures were collected and analyzed.…

Significant role of structural fractures in Ren-Qiu buried-block oil field, eastern China

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

Fei, Q.; Xie-Pei, W.

1983-03-01

Ren-qui oil field is in a buried block of Sinian (upper Proterozoic) rocks located in the Ji-zhong depression of the western Bohai Bay basin in eastern China. The main reservoir consists of Sinian dolomite rocks. It is a fault block with a large growth fault on the west side which trends north-northeast with throws of up to 1 km (0.6 mi) or more. The source rocks for the oil are Paleogene age and overlie the Sinian dolomite rocks. The structural fractures are the main factor forming the reservoir of the buried-block oil field. Three structural lines, trending northeast, north-northeast, andmore » northwest, form the regional netted fracture system. The north-northeast growth fault controlled the structural development of the buried block. The block was raised and eroded before the Tertiary sediments were deposited. In the Eocene Epoch, the Ji-zhong depression subsided, but the deposition, faulting, and related uplift of the block happened synchronously as the block was gradually submerged. At the same time, several horizontal and vertical karst zones were formed by the karst water along the netted structural fractures. The Eocene oil source rocks lapped onto the block and so the buried block, with many developed karst fractures, was surrounded by a great thickness of source rocks. As the growth fault developed, the height of the block was increased from 400 m (1300 ft) before the Oligocene to 1300 m (4250 ft) after. As the petroleum was generated, it migrated immediately into the karst fractures of the buried block along the growth fault. The karst-fractured block reservoir has an 800-m (2600-ft) high oil-bearing closure and good connections developed between the karst fractures.« less

Structural Genomics: Correlation Blocks, Population Structure, and Genome Architecture

PubMed Central

Hu, Xin-Sheng; Yeh, Francis C.; Wang, Zhiquan

2011-01-01

An integration of the pattern of genome-wide inter-site associations with evolutionary forces is important for gaining insights into the genomic evolution in natural or artificial populations. Here, we assess the inter-site correlation blocks and their distributions along chromosomes. A correlation block is broadly termed as the DNA segment within which strong correlations exist between genetic diversities at any two sites. We bring together the population genetic structure and the genomic diversity structure that have been independently built on different scales and synthesize the existing theories and methods for characterizing genomic structure at the population level. We discuss how population structure could shape correlation blocks and their patterns within and between populations. Effects of evolutionary forces (selection, migration, genetic drift, and mutation) on the pattern of genome-wide correlation blocks are discussed. In eukaryote organisms, we briefly discuss the associations between the pattern of correlation blocks and genome assembly features in eukaryote organisms, including the impacts of multigene family, the perturbation of transposable elements, and the repetitive nongenic sequences and GC-rich isochores. Our reviews suggest that the observable pattern of correlation blocks can refine our understanding of the ecological and evolutionary processes underlying the genomic evolution at the population level. PMID:21886455

Adolescent Boys' and Girls' Block Constructions Differ in Structural Balance: A Block-Building Characteristic Related to Math Achievement

ERIC Educational Resources Information Center

Casey, Beth M.; Pezaris, Elizabeth E.; Bassi, Julie

2012-01-01

Two studies were conducted on block building in adolescents, assessing middle school (Study 1) and high school students (Study 2). Students were asked to build something interesting with blocks. In both samples, the same pattern of gender differences were found; boys built taller structures than girls, and balanced a larger number of blocks on a…

Paleomagnetic constraints on deformation of superfast-spread oceanic crust exposed at Pito Deep Rift

NASA Astrophysics Data System (ADS)

Horst, A. J.; Varga, R. J.; Gee, J. S.; Karson, J. A.

2011-12-01

The uppermost oceanic crust produced at the superfast spreading (˜142 km Ma-1, full-spreading rate) southern East Pacific Rise (EPR) during the Gauss Chron is exposed in a tectonic window along the northeastern wall of the Pito Deep Rift. Paleomagnetic analysis of fully oriented dike (62) and gabbro (5) samples from two adjacent study areas yield bootstrapped mean remanence directions of 38.9° ± 8.1°, -16.7° ± 15.6°, n = 23 (Area A) and 30.4° ± 8.0°, -25.1° ± 12.9°, n = 44 (Area B), both are significantly distinct from the Geocentric Axial Dipole expected direction at 23° S. Regional tectonics and outcrop-scale structural data combined with bootstrapped remanence directions constrain models that involve a sequence of three rotations that result in dikes restored to subvertical orientations related to (1) inward-tilting of crustal blocks during spreading (Area A = 11°, Area B = 22°), (2) clockwise, vertical-axis rotation of the Easter Microplate (A = 46°, B = 44°), and (3) block tilting at Pito Deep Rift (A = 21°, B = 10°). These data support a structural model for accretion at the southern EPR in which outcrop-scale faulting and block rotation accommodates spreading-related subaxial subsidence that is generally less than that observed in crust generated at a fast spreading rate exposed at Hess Deep Rift. These data also support previous estimates for the clockwise rotation of crust adjacent to the Easter Microplate. Dike sample natural remanent magnetization (NRM) has an arithmetic mean of 5.96 A/m ± 3.76, which suggests that they significantly contribute to observed magnetic anomalies from fast- to superfast-spread crust.

Impact of cycling cells and cell cycle regulation on Hydra regeneration.

PubMed

Buzgariu, Wanda; Wenger, Yvan; Tcaciuc, Nina; Catunda-Lemos, Ana-Paula; Galliot, Brigitte

2018-01-15

Hydra tissues are made from three distinct populations of stem cells that continuously cycle and pause in G2 instead of G1. To characterize the role of cell proliferation after mid-gastric bisection, we have (i) used flow cytometry and classical markers to monitor cell cycle modulations, (ii) quantified the transcriptomic regulations of 202 genes associated with cell proliferation during head and foot regeneration, and (iii) compared the impact of anti-proliferative treatments on regeneration efficiency. We confirm two previously reported events: an early mitotic wave in head-regenerating tips, when few cell cycle genes are up-regulated, and an early-late wave of proliferation on the second day, preceded by the up-regulation of 17 cell cycle genes. These regulations appear more intense after mid-gastric bisection than after decapitation, suggesting a position-dependent regulation of cell proliferation during head regeneration. Hydroxyurea, which blocks S-phase progression, delays head regeneration when applied before but not after bisection. This result is consistent with the fact that the Hydra central region is enriched in G2-paused adult stem cells, poised to divide upon injury, thus forming a necessary constitutive pro-blastema. However a prolonged exposure to hydroxyurea does not block regeneration as cells can differentiate apical structures without traversing S-phase, and also escape in few days the hydroxyurea-induced S-phase blockade. Thus Hydra head regeneration, which is a fast event, is highly plastic, relying on large stocks of adult stem cells paused in G2 at amputation time, which immediately divide to proliferate and/or differentiate apical structures even when S-phase is blocked. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Blocking of conditioned taste avoidance induced by wheel running.

PubMed

Pierce, W David; Heth, C Donald

2010-01-01

In Experiment 1, compared to non-reinforced presentation of a food stimulus (A-->no US), the association of a food stimulus with wheel running (A-->US) blocked subsequent avoidance of a distinctive flavor (X), when both the food and flavor were followed by wheel running (AX-->US). Experiment 2 replicated and extended the blocking effect, demonstrating that the amount of avoidance of X after AX-->wheel training depended on the correlation between A-alone trials and wheel running-the predictiveness of the A stimulus. The present study is the first to demonstrate associative blocking of conditioned taste avoidance (CTA) induced by wheel running and strongly implicates associative learning as the basis for this kind of avoidance. 2009 Elsevier B.V. All rights reserved.

Three acidic residues are at the active site of a beta-propeller architecture in glycoside hydrolase families 32, 43, 62, and 68.

PubMed

Pons, Tirso; Naumoff, Daniil G; Martínez-Fleites, Carlos; Hernández, Lázaro

2004-02-15

Multiple-sequence alignment of glycoside hydrolase (GH) families 32, 43, 62, and 68 revealed three conserved blocks, each containing an acidic residue at an equivalent position in all the enzymes. A detailed analysis of the site-directed mutations so far performed on invertases (GH32), arabinanases (GH43), and bacterial fructosyltransferases (GH68) indicated a direct implication of the conserved residues Asp/Glu (block I), Asp (block II), and Glu (block III) in substrate binding and hydrolysis. These residues are close in space in the 5-bladed beta-propeller fold determined for Cellvibrio japonicus alpha-L-arabinanase Arb43A [Nurizzo et al., Nat Struct Biol 2002;9:665-668] and Bacillus subtilis endo-1,5-alpha-L-arabinanase. A sequence-structure compatibility search using 3D-PSSM, mGenTHREADER, INBGU, and SAM-T02 programs predicted indistinctly the 5-bladed beta-propeller fold of Arb43A and the 6-bladed beta-propeller fold of sialidase/neuraminidase (GH33, GH34, and GH83) as the most reliable topologies for GH families 32, 62, and 68. We conclude that the identified acidic residues are located at the active site of a beta-propeller architecture in GH32, GH43, GH62, and GH68, operating with a canonical reaction mechanism of either inversion (GH43 and likely GH62) or retention (GH32 and GH68) of the anomeric configuration. Also, we propose that the beta-propeller architecture accommodates distinct binding sites for the acceptor saccharide in glycosyl transfer reaction. Copyright 2003 Wiley-Liss, Inc.

Program structure-based blocking

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

Bertolli, Carlo; Eichenberger, Alexandre E.; O'Brien, John K.

2017-09-26

Embodiments relate to program structure-based blocking. An aspect includes receiving source code corresponding to a computer program by a compiler of a computer system. Another aspect includes determining a prefetching section in the source code by a marking module of the compiler. Yet another aspect includes performing, by a blocking module of the compiler, blocking of instructions located in the prefetching section into instruction blocks, such that the instruction blocks of the prefetching section only contain instructions that are located in the prefetching section.

Digital Alchemy for Materials Design: Colloids and Beyond

NASA Astrophysics Data System (ADS)

van Anders, Greg; Klotsa, Daphne; Karas, Andrew; Dodd, Paul; Glotzer, Sharon

Starting with the early alchemists, a holy grail of science has been to make desired materials by manipulating basic building blocks. Building blocks that show promise for assembling new complex materials can be synthesized at the nanoscale with attributes that would astonish the ancient alchemists in their versatility. However, this versatility means that connecting building-block attributes to bulk structure is both necessary for rationally engineering materials and difficult because building block attributes can be altered in many ways. We show how to exploit the malleability of colloidal nanoparticle ``elements'' to quantitatively link building-block attributes to bulk structure through a statistical thermodynamic framework we term ``digital alchemy''. We use this framework to optimize building blocks for a given target structure and to determine which building-block attributes are most important to control for self-assembly, through a set of novel thermodynamic response functions. We thereby establish direct links between the attributes of colloidal building blocks and the bulk structures they form. Moreover, our results give concrete solutions to the more general conceptual challenge of optimizing emergent behaviors in nature and can be applied to other types of matter.

Two-dimensional phase separated structures of block copolymers on solids

NASA Astrophysics Data System (ADS)

Sen, Mani; Jiang, Naisheng; Endoh, Maya; Koga, Tadanori; Ribbe, Alexander

The fundamental, yet unsolved question in block copolymer (BCP) thin films is the self-organization process of BCPs at the solid-polymer melt interface. We here focus on the self-organization processes of cylinder-forming polystyrene-block-poly (4-vinylpyridine) diblock copolymer and lamellar-forming poly (styrene-block-butadiene-block-styrene) triblock copolymer on Si substrates as model systems. In order to reveal the buried interfacial structures, the following experimental protocols were utilized: the BCP monolayer films were annealed under vacuum at T>Tg of the blocks (to equilibrate the melts); vitrification of the annealed BCP films via rapid quench to room temperature; subsequent intensive solvent leaching (to remove unadsorbed chains) with chloroform, a non-selective good solvent for the blocks. The strongly bound BCP layers were then characterized by using atomic force microscopy, scanning electron microscopy, grazing incidence small angle X-ray scattering, and X-ray reflectivity. The results showed that both blocks lie flat on the substrate, forming the two-dimensional, randomly phase-separated structure irrespective of their microdomain structures and interfacial energetics. Acknowledgement of financial support from NSF Grant (CMMI -1332499).

A diversity-oriented synthesis strategy enabling the combinatorial-type variation of macrocyclic peptidomimetic scaffolds.

PubMed

Isidro-Llobet, Albert; Hadje Georgiou, Kathy; Galloway, Warren R J D; Giacomini, Elisa; Hansen, Mette R; Méndez-Abt, Gabriela; Tan, Yaw Sing; Carro, Laura; Sore, Hannah F; Spring, David R

2015-04-21

Macrocyclic peptidomimetics are associated with a broad range of biological activities. However, despite such potentially valuable properties, the macrocyclic peptidomimetic structural class is generally considered as being poorly explored within drug discovery. This has been attributed to the lack of general methods for producing collections of macrocyclic peptidomimetics with high levels of structural, and thus shape, diversity. In particular, there is a lack of scaffold diversity in current macrocyclic peptidomimetic libraries; indeed, the efficient construction of diverse molecular scaffolds presents a formidable general challenge to the synthetic chemist. Herein we describe a new, advanced strategy for the diversity-oriented synthesis (DOS) of macrocyclic peptidomimetics that enables the combinatorial variation of molecular scaffolds (core macrocyclic ring architectures). The generality and robustness of this DOS strategy is demonstrated by the step-efficient synthesis of a structurally diverse library of over 200 macrocyclic peptidomimetic compounds, each based around a distinct molecular scaffold and isolated in milligram quantities, from readily available building-blocks. To the best of our knowledge this represents an unprecedented level of scaffold diversity in a synthetically derived library of macrocyclic peptidomimetics. Cheminformatic analysis indicated that the library compounds access regions of chemical space that are distinct from those addressed by top-selling brand-name drugs and macrocyclic natural products, illustrating the value of our DOS approach to sample regions of chemical space underexploited in current drug discovery efforts. An analysis of three-dimensional molecular shapes illustrated that the DOS library has a relatively high level of shape diversity.

Isotopic, geochemical, and temporal characterization of Proterozoic basement rocks in the Quitovac region, northwestern Sonora, Mexico: Implications for the reconstruction of the southwestern margin of Laurentia

USGS Publications Warehouse

Iriondo, A.; Premo, W.R.; Martínez-Torres, Luis M.; Budahn, J.R.; Atkinson, William W.; Siems, D.F.; Guaras-Gonzalez, B.

2004-01-01

A detailed geochemical characterization of 19 representative Proterozoic basement rocks in the Quitovac region in northwestern Sonora, Mexico, has identified two distinct Paleoproterozoic basement blocks that coincide spatially with the previously proposed Caborca and "North America" blocks. New U-Pb zircon geochronology revises their age ranges, the Caborca (1.78-1.69 Ga) and "North America" (1.71-1.66 Ga) blocks at Quitovac, and precludes a simple age differentiation between them. In addition, Grenvillian-age granitoids (ca. 1.1 Ga), spatially associated with the Caborca block have been identified at Quitovac. Nd isotopes and major- and trace-element geochemistry support the distinction of these Paleoproterozoic blocks. Granitoids of the "North America" block are characterized by depleted ??Nd values (3.4-3.9) and younger Nd model ages (1800-1740 Ma) and have lower K2O, Y, Rb, Ba, Th, REE, and Fe/Mg values than coeval rocks of the Caborca block. The Caborca block granitoids are likewise characterized by slightly less depleted ??Nd (0.6-2.6) and older Nd model ages (2070-1880 Ma). Despite the subtle differences, granitoids from both the Caborca and "North America" blocks exhibit island arc-like affinities. We propose that the Proterozoic basement rocks from the Quitovac region are an extension of the Proterozoic crustal provinces in the southwestern United States. Specifically, rocks of the Caborca block exhibit an affinity to rocks of either the Yavapai province or the Mojave-Yavapai transition zone, whereas rocks of the "North America" block have signatures similar to those of the Mazatzal province or possibly the Yavapai province of Arizona. The new isotopic ages and geochemical data do not support the existence of the Late Jurassic Mojave-Sonora megashear at Quitovac, as originally proposed. However, the Quitovac region accounts only for a small fraction of the Proterozoic basement in Sonora, so these findings do not eliminate the possibility of a megashear elsewhere in northern Sonora. Our new data create the possibility of alternative hypotheses for the distribution of Paleoproterozoic crustal provinces in southwestern North America that affect reconstructions of the original southwestern margin of Laurentia, and reduce uncertainties in the configuration, timing, and existence of the Proterozoic supercontinent, Rodinia.

Dynamic DNA-controlled "stop-and-go" assembly of well-defined protein domains on RNA-scaffolded TMV-like nanotubes.

PubMed

Schneider, Angela; Eber, Fabian J; Wenz, Nana L; Altintoprak, Klara; Jeske, Holger; Eiben, Sabine; Wege, Christina

2016-12-01

A DNA-based approach allows external control over the self-assembly process of tobacco mosaic virus (TMV)-like ribonucleoprotein nanotubes: their growth from viral coat protein (CP) subunits on five distinct RNA scaffolds containing the TMV origin of assembly (OAs) could be temporarily blocked by a stopper DNA oligomer hybridized downstream (3') of the OAs. At two upstream (5') sites tested, simple hybridization was not sufficient for stable stalling, which correlates with previous findings on a non-symmetric assembly of TMV. The growth of DNA-arrested particles could be restarted efficiently by displacement of the stopper via its toehold by using a release DNA oligomer, even after storage for twelve days. This novel strategy for growing proteinaceous tubes under tight kinetic and spatial control combines RNA guidance and its site-specific but reversible interruption by DNA blocking elements. As three of the RNA scaffolds contained long heterologous non-TMV sequence portions that included the stopping sites, this method is applicable to all RNAs amenable to TMV CP encapsidation, albeit with variable efficiency most likely depending on the scaffolds' secondary structures. The use of two distinct, selectively addressable CP variants during the serial assembly stages finally enabled an externally configured fabrication of nanotubes with highly defined subdomains. The "stop-and-go" strategy thus might pave the way towards production routines of TMV-like particles with variable aspect ratios from a single RNA scaffold, and of nanotubes with two or even more adjacent protein domains of tightly pre-defined lengths.

An electrostatic Particle-In-Cell code on multi-block structured meshes

NASA Astrophysics Data System (ADS)

Meierbachtol, Collin S.; Svyatskiy, Daniil; Delzanno, Gian Luca; Vernon, Louis J.; Moulton, J. David

2017-12-01

We present an electrostatic Particle-In-Cell (PIC) code on multi-block, locally structured, curvilinear meshes called Curvilinear PIC (CPIC). Multi-block meshes are essential to capture complex geometries accurately and with good mesh quality, something that would not be possible with single-block structured meshes that are often used in PIC and for which CPIC was initially developed. Despite the structured nature of the individual blocks, multi-block meshes resemble unstructured meshes in a global sense and introduce several new challenges, such as the presence of discontinuities in the mesh properties and coordinate orientation changes across adjacent blocks, and polyjunction points where an arbitrary number of blocks meet. In CPIC, these challenges have been met by an approach that features: (1) a curvilinear formulation of the PIC method: each mesh block is mapped from the physical space, where the mesh is curvilinear and arbitrarily distorted, to the logical space, where the mesh is uniform and Cartesian on the unit cube; (2) a mimetic discretization of Poisson's equation suitable for multi-block meshes; and (3) a hybrid (logical-space position/physical-space velocity), asynchronous particle mover that mitigates the performance degradation created by the necessity to track particles as they move across blocks. The numerical accuracy of CPIC was verified using two standard plasma-material interaction tests, which demonstrate good agreement with the corresponding analytic solutions. Compared to PIC codes on unstructured meshes, which have also been used for their flexibility in handling complex geometries but whose performance suffers from issues associated with data locality and indirect data access patterns, PIC codes on multi-block structured meshes may offer the best compromise for capturing complex geometries while also maintaining solution accuracy and computational efficiency.

An electrostatic Particle-In-Cell code on multi-block structured meshes

DOE PAGES

Meierbachtol, Collin S.; Svyatskiy, Daniil; Delzanno, Gian Luca; ...

2017-09-14

We present an electrostatic Particle-In-Cell (PIC) code on multi-block, locally structured, curvilinear meshes called Curvilinear PIC (CPIC). Multi-block meshes are essential to capture complex geometries accurately and with good mesh quality, something that would not be possible with single-block structured meshes that are often used in PIC and for which CPIC was initially developed. In spite of the structured nature of the individual blocks, multi-block meshes resemble unstructured meshes in a global sense and introduce several new challenges, such as the presence of discontinuities in the mesh properties and coordinate orientation changes across adjacent blocks, and polyjunction points where anmore » arbitrary number of blocks meet. In CPIC, these challenges have been met by an approach that features: (1) a curvilinear formulation of the PIC method: each mesh block is mapped from the physical space, where the mesh is curvilinear and arbitrarily distorted, to the logical space, where the mesh is uniform and Cartesian on the unit cube; (2) a mimetic discretization of Poisson's equation suitable for multi-block meshes; and (3) a hybrid (logical-space position/physical-space velocity), asynchronous particle mover that mitigates the performance degradation created by the necessity to track particles as they move across blocks. The numerical accuracy of CPIC was verified using two standard plasma–material interaction tests, which demonstrate good agreement with the corresponding analytic solutions. And compared to PIC codes on unstructured meshes, which have also been used for their flexibility in handling complex geometries but whose performance suffers from issues associated with data locality and indirect data access patterns, PIC codes on multi-block structured meshes may offer the best compromise for capturing complex geometries while also maintaining solution accuracy and computational efficiency.« less

An electrostatic Particle-In-Cell code on multi-block structured meshes

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

Meierbachtol, Collin S.; Svyatskiy, Daniil; Delzanno, Gian Luca

We present an electrostatic Particle-In-Cell (PIC) code on multi-block, locally structured, curvilinear meshes called Curvilinear PIC (CPIC). Multi-block meshes are essential to capture complex geometries accurately and with good mesh quality, something that would not be possible with single-block structured meshes that are often used in PIC and for which CPIC was initially developed. In spite of the structured nature of the individual blocks, multi-block meshes resemble unstructured meshes in a global sense and introduce several new challenges, such as the presence of discontinuities in the mesh properties and coordinate orientation changes across adjacent blocks, and polyjunction points where anmore » arbitrary number of blocks meet. In CPIC, these challenges have been met by an approach that features: (1) a curvilinear formulation of the PIC method: each mesh block is mapped from the physical space, where the mesh is curvilinear and arbitrarily distorted, to the logical space, where the mesh is uniform and Cartesian on the unit cube; (2) a mimetic discretization of Poisson's equation suitable for multi-block meshes; and (3) a hybrid (logical-space position/physical-space velocity), asynchronous particle mover that mitigates the performance degradation created by the necessity to track particles as they move across blocks. The numerical accuracy of CPIC was verified using two standard plasma–material interaction tests, which demonstrate good agreement with the corresponding analytic solutions. And compared to PIC codes on unstructured meshes, which have also been used for their flexibility in handling complex geometries but whose performance suffers from issues associated with data locality and indirect data access patterns, PIC codes on multi-block structured meshes may offer the best compromise for capturing complex geometries while also maintaining solution accuracy and computational efficiency.« less

Effect of pH on the structure and drug release profiles of layer-by-layer assembled films containing polyelectrolyte, micelles, and graphene oxide.

PubMed

Han, Uiyoung; Seo, Younghye; Hong, Jinkee

2016-04-07

Layer by layer (lbl) assembled multilayer thin films are used in drug delivery systems with attractive advantages such as unlimited selection of building blocks and free modification of the film structure. In this paper, we report the fundamental properties of lbl films constructed from different substances such as PS-b-PAA amphiphilic block copolymer micelles (BCM) as nano-sized drug vehicles, 2D-shaped graphene oxide (GO), and branched polyethylenimine (bPEI). These films were fabricated by successive lbl assembly as a result of electrostatic interactions between the carboxyl group of BCM and amine group of functionalized GO or bPEI under various pH conditions. We also compared the thickness, roughness, morphology and degree of adsorption of the (bPEI/BCM) films to those in the (GO/BCM) films. The results showed significant difference because of the distinct pH dependence of each material. In addition, drug release rates of the GO/BCM film were more rapid those of the (bPEI/BCM) film in pH 7.4 and pH 2 PBS buffer solutions. In (bPEI/BCM/GO/BCM) film, the inserted GO layers into bPEI/BCM multilayer induced rapid drug release. We believe that these materials &pH dependent film properties allow developments in the control of coating techniques for biological and biomedical applications.

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

PubMed

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

2008-10-01

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

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

PubMed Central

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

2013-01-01

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

Odorants selectively activate distinct G protein subtypes in olfactory cilia.

PubMed

Schandar, M; Laugwitz, K L; Boekhoff, I; Kroner, C; Gudermann, T; Schultz, G; Breer, H

1998-07-03

Chemoelectrical signal transduction in olfactory neurons appears to involve intracellular reaction cascades mediated by heterotrimeric GTP-binding proteins. In this study attempts were made to identify the G protein subtype(s) in olfactory cilia that are activated by the primary (odorant) signal. Antibodies directed against the alpha subunits of distinct G protein subtypes interfered specifically with second messenger reponses elicited by defined subsets of odorants; odor-induced cAMP-formation was attenuated by Galphas antibodies, whereas Galphao antibodies blocked odor-induced inositol 1,4, 5-trisphosphate (IP3) formation. Activation-dependent photolabeling of Galpha subunits with [alpha-32P]GTP azidoanilide followed by immunoprecipitation using subtype-specific antibodies enabled identification of particular individual G protein subtypes that were activated upon stimulation of isolated olfactory cilia by chemically distinct odorants. For example odorants that elicited a cAMP response resulted in labeling of a Galphas-like protein, whereas odorants that elicited an IP3 response led to the labeling of a Galphao-like protein. Since odorant-induced IP3 formation was also blocked by Gbeta antibodies, activation of olfactory phospholipase C might be mediated by betagamma subunits of a Go-like G protein. These results indicate that different subsets of odorants selectively trigger distinct reaction cascades and provide evidence for dual transduction pathways in olfactory signaling.

Superalloy Lattice Block Structures

NASA Technical Reports Server (NTRS)

Nathal, M. V.; Whittenberger, J. D.; Hebsur, M. G.; Kantzos, P. T.; Krause, D. L.

2004-01-01

Initial investigations of investment cast superalloy lattice block suggest that this technology will yield a low cost approach to utilize the high temperature strength and environmental resistance of superalloys in lightweight, damage tolerant structural configurations. Work to date has demonstrated that relatively large superalloy lattice block panels can be successfully investment cast from both IN-718 and Mar-M247. These castings exhibited mechanical properties consistent with the strength of the same superalloys measured from more conventional castings. The lattice block structure also accommodates significant deformation without failure, and is defect tolerant in fatigue. The potential of lattice block structures opens new opportunities for the use of superalloys in future generations of aircraft applications that demand strength and environmental resistance at elevated temperatures along with low weight.

Defining Hsp70 Subnetworks in Dengue Virus Replication Reveals Key Vulnerability in Flavivirus Infection.

PubMed

Taguwa, Shuhei; Maringer, Kevin; Li, Xiaokai; Bernal-Rubio, Dabeiba; Rauch, Jennifer N; Gestwicki, Jason E; Andino, Raul; Fernandez-Sesma, Ana; Frydman, Judith

2015-11-19

Viral protein homeostasis depends entirely on the machinery of the infected cell. Accordingly, viruses can illuminate the interplay between cellular proteostasis components and their distinct substrates. Here, we define how the Hsp70 chaperone network mediates the dengue virus life cycle. Cytosolic Hsp70 isoforms are required at distinct steps of the viral cycle, including entry, RNA replication, and virion biogenesis. Hsp70 function at each step is specified by nine distinct DNAJ cofactors. Of these, DnaJB11 relocalizes to virus-induced replication complexes to promote RNA synthesis, while DnaJB6 associates with capsid protein and facilitates virion biogenesis. Importantly, an allosteric Hsp70 inhibitor, JG40, potently blocks infection of different dengue serotypes in human primary blood cells without eliciting viral resistance or exerting toxicity to the host cells. JG40 also blocks replication of other medically-important flaviviruses including yellow fever, West Nile and Japanese encephalitis viruses. Thus, targeting host Hsp70 subnetworks provides a path for broad-spectrum antivirals. Copyright © 2015 Elsevier Inc. All rights reserved.

Svecofennian orogeny in an evolving convergent margin setting

NASA Astrophysics Data System (ADS)

Korja, Annakaisa

2015-04-01

The dominant tectonic mode changes from extension to convergence at around 1.9 Ga in Fennoscandian. The lithological record suggests short lived subduction-related magmatic events followed by deformation and low-pressure high temperature metamorphism. At around 1.8 Ga the subduction systems seem to have stabilized implying continuous supply of oceanic lithosphere. The evolution of the convergent margin is recorded in the rock record and crustal architecture of the long lived Svecofennian orogeny (1.9-1.7 Ga). A closer look at the internal structure of the Svecofennian orogen reveals distinct regional differences. The northern and central parts of the Svecofennian orogen that have been formed during the initial accretionary phase - or compilation of the nucleus - have a thick three-layer crust and with thick mafic lower crust (10-30 km) and block-like internal architecture. Reflection profiles (FIRE1-3) image listric structures flattening on crustal scale décollement zones at the upper-middle crust and middle-upper crust boundaries. The crustal architecture together with large volumes of exposed granitoid rocks suggests spreading of the orogen and the development of an orogenic plateau west of the continental convergence boundary. The architecture is reminiscent of a large hot orogen. Within the western and southwestern part of the Svecofennian orogen (BABEL B, 1, 2, 3&4), which have been envisioned to have formed during continuous subduction phase, the crust is thinner (45-50 km) and it is hosting crustal blocks having one to two crustal layers. Layering is poorly developed in crustal blocks that are found S-SW of NE-dipping mantle reflections previously interpreted as paleo-subduction zones. Within these blocks, the crustal scale reflective structures dip NE (prowedge) or form pop-up wedges (uplifted plug) above the paleo-subduction zones. Crustal blocks with well-developed two-layer crust are located NE of the paleo-subduction zone. The architecture can be interpreted to image a series of abandoned accretion zones where the orogenic structure has developed from a young and cold orogen (BABEL 2,3&4) to a transitional (BABEL 1,6,B) one as the plate boundary is retreating during SW wards. The fast retreating rate of the subduction zone may not only have formed continental back-arc environment but may have restricted the thickening of the upper plate and the growth rate of the orogen. Altogether the architecture suggests a long-lived southwesterly retreating subduction system, with continental back-arc formation in its rear parts and well developed system of prowedge-retrowedge-uplifted plug close to a subduction conduit. Changes in the relative velocities of the upper and lower plate may have resulted in repetitive extensional and compressional phases of the orogeny as has been previously suggested for the southern part of the Svecofennian orogen.

Application of stochastic automata networks for creation of continuous time Markov chain models of voltage gating of gap junction channels.

PubMed

Snipas, Mindaugas; Pranevicius, Henrikas; Pranevicius, Mindaugas; Pranevicius, Osvaldas; Paulauskas, Nerijus; Bukauskas, Feliksas F

2015-01-01

The primary goal of this work was to study advantages of numerical methods used for the creation of continuous time Markov chain models (CTMC) of voltage gating of gap junction (GJ) channels composed of connexin protein. This task was accomplished by describing gating of GJs using the formalism of the stochastic automata networks (SANs), which allowed for very efficient building and storing of infinitesimal generator of the CTMC that allowed to produce matrices of the models containing a distinct block structure. All of that allowed us to develop efficient numerical methods for a steady-state solution of CTMC models. This allowed us to accelerate CPU time, which is necessary to solve CTMC models, ~20 times.

Magnetic domain wall engineering in a nanoscale permalloy junction

NASA Astrophysics Data System (ADS)

Wang, Junlin; Zhang, Xichao; Lu, Xianyang; Zhang, Jason; Yan, Yu; Ling, Hua; Wu, Jing; Zhou, Yan; Xu, Yongbing

2017-08-01

Nanoscale magnetic junctions provide a useful approach to act as building blocks for magnetoresistive random access memories (MRAM), where one of the key issues is to control the magnetic domain configuration. Here, we study the domain structure and the magnetic switching in the Permalloy (Fe20Ni80) nanoscale magnetic junctions with different thicknesses by using micromagnetic simulations. It is found that both the 90-° and 45-° domain walls can be formed between the junctions and the wire arms depending on the thickness of the device. The magnetic switching fields show distinct thickness dependencies with a broad peak varying from 7 nm to 22 nm depending on the junction sizes, and the large magnetic switching fields favor the stability of the MRAM operation.

NUCLEAR REACTORS

DOEpatents

Long, E.; Ashley, J.W.

1958-12-16

A graphite moderator structure is described for a gas-cooled nuclear reactor having a vertical orlentation wherein the structure is physically stable with regard to dlmensional changes due to Wigner growth properties of the graphite, and leakage of coolant gas along spaces in the structure is reduced. The structure is comprised of stacks of unlform right prismatic graphite blocks positioned in layers extending in the direction of the lengths of the blocks, the adjacent end faces of the blocks being separated by pairs of tiles. The blocks and tiles have central bores which are in alignment when assembled and are provided with cooperatlng keys and keyways for physical stability.

Basement structure based on gravity anomaly in the northern Noto peninsula, Central Japan

NASA Astrophysics Data System (ADS)

Mizubayashi, T.; Sawada, A.; Hamada, M.; Hiramatsu, Y.; Honda, R.

2012-12-01

Upper crustal block structures are usually defined by using surface information, such as geological and morphological data. The northern Noto Peninsula, central Japan, is divided into four geological block structures from tectonic geomorphologic perspectives (Ota and Hirakawa, 1979). This division is based on the surface crustal movement. To image the geological blocks three-dimensionally, it is necessary to construct a subsurface structure model. Gravity survey can clarify the detailed subsurface structure with dense gravity measurement. From the detailed Bouguer anomalies in the northwestern Noto Peninsula, Honda et al. (2008) suggested that the rupture size of the 2007 Noto Hanto earthquake was constrained by the geological block structures. Hiramatsu et al. (2008) also suggested the active faults on the seafloor, such as the source fault of the 2007 Noto Hanto earthquake plays a major role for the formation of the geological block structures. In this study, we analyze subsurface density structure based on the Bouguer anomaly and estimate the distribution of basement depth in the northern Noto Peninsula. We focus the relationship among the basement depth, the block structures and the active faults on the seafloor and discuss the block movement in the northern Noto Peninsula. We compiled the data measured and published previously (Gravity Database of Southwest Japan, 2001; Geological survey of Japan, 2004; Geographical survey institute of Japan, 2006; The Gravity Research Group in Southwest Japan, 2001; Komazawa and Okuma, 2010; Hokuriku electric power Co. Ltd., undisclosed) and calculated Bouguer anomaly in the northern Noto Peninsula. Based on this Bouguer anomaly, we analyzed subsurface density structures along 13 northeastern-southwestern profiles and 35 northwestern-southeastern profiles with the interval of 2 km using the two dimensional Talwani's method (Talwani et al., 1959). In the analysis, we assumed a density structure with four layers: basement (density is 2670kg/m3), Neocene volcanic rock (density is 2400kg/m3, or 2550kg/m3), Neocene sedimentary rock (density is 2200kg/m3), and Quaternary sedimentary rock (density is 1800kg/m3, or 1500kg/m3) (Honda et al., 2008). To compare our basement model to the geological block structures, we focus on a transition zone of the basement depth. We recognize that two of three geological block boundaries correspond to the transition zones. These boundaries also correspond to the boundary of active fault segments on the seafloor. Therefore, based on the relationship between the source fault of the 2007 Noto Hanto earthquake and the geological block, we suggest that the movement of those geological blocks is possibly controlled by the corresponding active fault segments. However, we find that the other block boundary doesn't correspond to the transition zone.

Seismic stratigraphic characteristics of upper Louisiana continental slope: an area east of Green Canyon

USGS Publications Warehouse

Bouma, Arnold H.; Feeley, Mary H.; Kindinger, Jack G.; Stelting, Charles E.; Hilde, Thomas W.C.

1981-01-01

A high-resolution seismic reflection survey was conducted in a small area of the upper Louisiana Continental Slope known as Green Canyon Area. This area includes tracts 427, 428, 471, 472, 515, and 516, that will be offered for sale in March 1982 as part of Lease Sale 67.The sea floor of this region is, slightly hummocky and is underlain by salt diapirs that are mantled by early Tertiary shale. Most of the shale is overlain by younger Tertiary and Quaternary deposits, although locally some of the shale protrudes the sea floor. Because of proximity to older Mississippi River sources, the sediments are thick. The sediment cover shows an abundance of geologic phenomena such as horsts, grabens, growth faults, normal faults, and consolidation faults, zones with distinct and indistinct parallel reflections, semi-transparent zones, distorted zones, and angular unconformities.The major feature of this region is a N-S linear zone of uplifted and intruded sedimentary deposits formed due to diapiric intrusion.Small scale graben development over the crest of the structure can be attributed to extension and collapse. Large scale undulations of reflections well off the flanks of the uplifted structure suggest sediment creep and slumping. Dipping of parallel reflections show block faulting and tilting.Air gun (5 and 40 cubic inch) records reveal at least five major sequences that show masked onlap and slumping in their lower parts grading into more distinct parallel reflections in their upper parts. Such sequences can be related to local uplift and sea level changes. Minisparker records of this area show similar sequences but on a smaller scale. The distinct parallel reflections often onlap the diapir flanks. The highly reflective parts of these sequences may represent turbidite-type deposition, possibly at times of lower sea level. The acoustically more transparent parts of each sequence may represent deposits containing primarily hemipelagic and pelagic sediment.A complex ridge system is present along the west side of the area and distinct parallel reflections onlap onto this structure primarily from the east. Much of this deposition may be ascribed to sedimentation within a submarine canyon whose position is controlled by this ridge.

Nano-structured polymer composites and process for preparing same

DOEpatents

Hillmyer, Marc; Chen, Liang

2013-04-16

A process for preparing a polymer composite that includes reacting (a) a multi-functional monomer and (b) a block copolymer comprising (i) a first block and (ii) a second block that includes a functional group capable of reacting with the multi-functional monomer, to form a crosslinked, nano-structured, bi-continuous composite. The composite includes a continuous matrix phase and a second continuous phase comprising the first block of the block copolymer.

Bacterial effectors target the common signaling partner BAK1 to disrupt multiple MAMP receptor-signaling complexes and impede plant immunity.

PubMed

Shan, Libo; He, Ping; Li, Jianming; Heese, Antje; Peck, Scott C; Nürnberger, Thorsten; Martin, Gregory B; Sheen, Jen

2008-07-17

Successful pathogens have evolved strategies to interfere with host immune systems. For example, the ubiquitous plant pathogen Pseudomonas syringae injects two sequence-distinct effectors, AvrPto and AvrPtoB, to intercept convergent innate immune responses stimulated by multiple microbe-associated molecular patterns (MAMPs). However, the direct host targets and precise molecular mechanisms of bacterial effectors remain largely obscure. We show that AvrPto and AvrPtoB bind the Arabidopsis receptor-like kinase BAK1, a shared signaling partner of both the flagellin receptor FLS2 and the brassinosteroid receptor BRI1. This targeting interferes with ligand-dependent association of FLS2 with BAK1 during infection. It also impedes BAK1-dependent host immune responses to diverse other MAMPs and brassinosteroid signaling. Significantly, the structural basis of AvrPto-BAK1 interaction appears to be distinct from AvrPto-Pto association required for effector-triggered immunity. These findings uncover a unique strategy of bacterial pathogenesis where virulence effectors block signal transmission through a key common component of multiple MAMP-receptor complexes.

Evolutionary Limitation and Opportunities for Developing tRNA Synthetase Inhibitors with 5-Binding-Mode Classification

PubMed Central

Fang, Pengfei; Guo, Min

2015-01-01

Aminoacyl-tRNA synthetases (aaRSs) are enzymes that catalyze the transfer of amino acids to their cognate tRNAs as building blocks for translation. Each of the aaRS families plays a pivotal role in protein biosynthesis and is indispensable for cell growth and survival. In addition, aaRSs in higher species have evolved important non-translational functions. These translational and non-translational functions of aaRS are attractive for developing antibacterial, antifungal, and antiparasitic agents and for treating other human diseases. The interplay between amino acids, tRNA, ATP, EF-Tu and non-canonical binding partners, had shaped each family with distinct pattern of key sites for regulation, with characters varying among species across the path of evolution. These sporadic variations in the aaRSs offer great opportunity to target these essential enzymes for therapy. Up to this day, growing numbers of aaRS inhibitors have been discovered and developed. Here, we summarize the latest developments and structural studies of aaRS inhibitors, and classify them with distinct binding modes into five categories. PMID:26670257

Sample size determination for GEE analyses of stepped wedge cluster randomized trials.

PubMed

Li, Fan; Turner, Elizabeth L; Preisser, John S

2018-06-19

In stepped wedge cluster randomized trials, intact clusters of individuals switch from control to intervention from a randomly assigned period onwards. Such trials are becoming increasingly popular in health services research. When a closed cohort is recruited from each cluster for longitudinal follow-up, proper sample size calculation should account for three distinct types of intraclass correlations: the within-period, the inter-period, and the within-individual correlations. Setting the latter two correlation parameters to be equal accommodates cross-sectional designs. We propose sample size procedures for continuous and binary responses within the framework of generalized estimating equations that employ a block exchangeable within-cluster correlation structure defined from the distinct correlation types. For continuous responses, we show that the intraclass correlations affect power only through two eigenvalues of the correlation matrix. We demonstrate that analytical power agrees well with simulated power for as few as eight clusters, when data are analyzed using bias-corrected estimating equations for the correlation parameters concurrently with a bias-corrected sandwich variance estimator. © 2018, The International Biometric Society.

An Examination of the Nature of Global MODIS Cloud Regimes

NASA Technical Reports Server (NTRS)

Oreopoulos, Lazaros; Cho, Nayeong; Lee, Dongmin; Kato, Seiji; Huffman, George J.

2014-01-01

We introduce global cloud regimes (previously also referred to as "weather states") derived from cloud retrievals that use measurements by the Moderate Resolution Imaging Spectroradiometer (MODIS) instrument aboard the Aqua and Terra satellites. The regimes are obtained by applying clustering analysis on joint histograms of retrieved cloud top pressure and cloud optical thickness. By employing a compositing approach on data sets from satellites and other sources, we examine regime structural and thermodynamical characteristics. We establish that the MODIS cloud regimes tend to form in distinct dynamical and thermodynamical environments and have diverse profiles of cloud fraction and water content. When compositing radiative fluxes from the Clouds and the Earth's Radiant Energy System instrument and surface precipitation from the Global Precipitation Climatology Project, we find that regimes with a radiative warming effect on the atmosphere also produce the largest implied latent heat. Taken as a whole, the results of the study corroborate the usefulness of the cloud regime concept, reaffirm the fundamental nature of the regimes as appropriate building blocks for cloud system classification, clarify their association with standard cloud types, and underscore their distinct radiative and hydrological signatures.

Efficient Imaging and Real-Time Display of Scanning Ion Conductance Microscopy Based on Block Compressive Sensing

NASA Astrophysics Data System (ADS)

Li, Gongxin; Li, Peng; Wang, Yuechao; Wang, Wenxue; Xi, Ning; Liu, Lianqing

2014-07-01

Scanning Ion Conductance Microscopy (SICM) is one kind of Scanning Probe Microscopies (SPMs), and it is widely used in imaging soft samples for many distinctive advantages. However, the scanning speed of SICM is much slower than other SPMs. Compressive sensing (CS) could improve scanning speed tremendously by breaking through the Shannon sampling theorem, but it still requires too much time in image reconstruction. Block compressive sensing can be applied to SICM imaging to further reduce the reconstruction time of sparse signals, and it has another unique application that it can achieve the function of image real-time display in SICM imaging. In this article, a new method of dividing blocks and a new matrix arithmetic operation were proposed to build the block compressive sensing model, and several experiments were carried out to verify the superiority of block compressive sensing in reducing imaging time and real-time display in SICM imaging.

Resolving writer's block.

PubMed Central

Huston, P.

1998-01-01

PROBLEM BEING ADDRESSED: Writer's block, or a distinctly uncomfortable inability to write, can interfere with professional productivity. OBJECTIVE OF PROGRAM: To identify writer's block and to outline suggestions for its early diagnosis, treatment, and prevention. MAIN COMPONENTS OF PROGRAM: Once the diagnosis has been established, a stepwise approach to care is recommended. Mild blockage can be resolved by evaluating and revising expectations, conducting a task analysis, and giving oneself positive feedback. Moderate blockage can be addressed by creative exercises, such as brainstorming and role-playing. Recalcitrant blockage can be resolved with therapy. Writer's block can be prevented by taking opportunities to write at the beginning of projects, working with a supportive group of people, and cultivating an ongoing interest in writing. CONCLUSIONS: Writer's block is a highly treatable condition. A systematic approach can help to alleviate anxiety, build confidence, and give people the information they need to work productively. PMID:9481467

Oil migration in a major growth fault: Structural analysis of the Pathfinder core, South Eugene Island Block 330, offshore Louisiana

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

Losh, S.

1998-09-01

The Pathfinder core, collected in the South Eugene Island Block 330 field, offshore Louisiana, provides an outstanding sample of structures associated with a major growth fault that abuts a giant oil field and that is thought to have acted as a conduit for hydrocarbon migration into the producing reservoirs. The fault zone in the core consists of three structural domains, each characterized by a distinct rock type, distribution of fault dips and dip azimuths, and distribution of spacing between adjacent faults and fractures. Although all of the domains contain oil-bearing sands, only faults and fractures in the deepest domain containmore » oil, even though the oil-barren fault domains contain numerous faults and fractures that are parallel to those containing oil in the deepest domain. The deepest domain is also distinguished from the other two domains by a greater degree of structural complexity and by a well-defined power-law distribution of fault and fracture spacings. Even though oil is present in sands throughout the core, its restriction to faults and fractures in the youngest sampled portion of the fault zone implies that oil migrated only through that part of the fault that was active during the time when oil had access to it. The absence of oil in fractures or faults in the other, probably older, fault domains indicates that the oil was never sufficiently pressured to flow up the fault zone on its own, either by hydraulic fracture or by increased permeability as a result of decreased effective stress. Instead, fluid migration along faults and fractures in the Pathfinder core was enhanced by permeability created in response to relatively far-field stresses related to minibasin subsidence.« less

Structural fluctuation governed dynamic diradical character in pentacene.

PubMed

Yang, Hongfang; Chen, Mengzhen; Song, Xinyu; Bu, Yuxiang

2015-06-07

We unravel intriguing dynamical diradical behavior governed by structural fluctuation in pentacene using ab initio molecular dynamics simulation. In contrast to static equilibrium configuration of pentacene with a closed-shell ground state without diradical character, due to structural fluctuation, some of its dynamical snapshot configurations exhibit an open-shell broken-symmetry singlet ground state with diradical character, and such diradical character presents irregular pulsing behavior in time evolution. Not all structural changes can lead to diradical character, only those involving the shortening of cross-linking C-C bonds and variations of the C-C bonds in polyacetylene chains are the main contributors. This scenario about diradicalization is distinctly different from that in long acenes. The essence is that structural distortion cooperatively raises the HOMO and lowers the LUMO, efficiently reducing the HOMO-LUMO and singlet-triplet energy gaps, which facilitate the formation of a broken-symmetry open-shell singlet state. The irregular pulsing behavior originates from the mixing of normal vibrations in pentacene. This fascinating behavior suggests the potential application of pentacene as a suitable building block in the design of new electronic devices due to its magnetism-controllability through energy induction. This work provides new insight into inherent electronic property fluctuation in acenes.

Detrital zircon provenance of the Late Triassic Songpan-Ganzi complex: Sedimentary record of collision of the North and South China blocks

USGS Publications Warehouse

Weislogel, A.L.; Graham, S.A.; Chang, E.Z.; Wooden, J.L.; Gehrels, G.E.; Yang, H.

2006-01-01

Using detrital zircon geochronology, turbidite deposystems fed from distinct sediment sources can be distinguished within the Songpan-Ganzi complex, a collapsed Middle to Late Triassic turbidite basin of central China. A southern Songpan-Ganzi deposystem initially was sourced solely by erosion of the Qinling-Dabie orogen during early Late Triassic time, then by Qinling-Dabie orogen, North China block, and South China block sources during middle to late Late Triassic time. A northern Songpan-Ganzi system was sourced by erosion of the Qinling-Dabie orogen and the North China block throughout its deposition. These separate deposystems were later tectonically amalgamated to form one complex and then uplifted as the eastern Tibet Plateau. ?? 2006 Geological Society of America.

Theory of the interplay between the superconductivity and the blocked antiferromagnetic order in A(y)Fe(2-x)Se2.

PubMed

Jiang, Hong-Min

2012-09-26

Based on an effective two-orbital tight-binding model, we examine the possible superconducting states in iron-vacancy-ordered A(y)Fe(2-x)Se(2). In the presence of ordered vacancies and blocked antiferromagnetic order, it is shown that the emergent SC pairing is the nodeless next-nearest-neighbor (NNN)-pairing due to the dominant antiferromagnetic (AFM) interaction between the inter-block NNN sites. In particular, we show that due to the ordered vacancies and the associated blocked AFM order, the interplay between the superconducting and AFM states results in three distinct states in the phase diagram as doping is varied. The divergent experimental observations can be accounted for by considering the different charge carrier concentrations in their respective compounds.

Modularity in protein structures: study on all-alpha proteins.

PubMed

Khan, Taushif; Ghosh, Indira

2015-01-01

Modularity is known as one of the most important features of protein's robust and efficient design. The architecture and topology of proteins play a vital role by providing necessary robust scaffolds to support organism's growth and survival in constant evolutionary pressure. These complex biomolecules can be represented by several layers of modular architecture, but it is pivotal to understand and explore the smallest biologically relevant structural component. In the present study, we have developed a component-based method, using protein's secondary structures and their arrangements (i.e. patterns) in order to investigate its structural space. Our result on all-alpha protein shows that the known structural space is highly populated with limited set of structural patterns. We have also noticed that these frequently observed structural patterns are present as modules or "building blocks" in large proteins (i.e. higher secondary structure content). From structural descriptor analysis, observed patterns are found to be within similar deviation; however, frequent patterns are found to be distinctly occurring in diverse functions e.g. in enzymatic classes and reactions. In this study, we are introducing a simple approach to explore protein structural space using combinatorial- and graph-based geometry methods, which can be used to describe modularity in protein structures. Moreover, analysis indicates that protein function seems to be the driving force that shapes the known structure space.

Image Processing Research

DTIC Science & Technology

1975-09-30

systems a linear model results in an object f being mappad into an image _ by a point spread function matrix H. Thus with noise j +Hf +n (1) The simplest... linear models for imaging systems are given by space invariant point spread functions (SIPSF) in which case H is block circulant. If the linear model is...Ij,...,k-IM1 is a set of two dimensional indices each distinct and prior to k. Modeling Procedare: To derive the linear predictor (block LP of figure

Identification of an antagonist that selectively blocks the activity of prostamides (prostaglandin-ethanolamides) in the feline iris.

PubMed

Woodward, D F; Krauss, A H; Wang, J W; Protzman, C E; Nieves, A L; Liang, Y; Donde, Y; Burk, R M; Landsverk, K; Struble, C

2007-02-01

The prostamides (prostaglandin-ethanolamides) and prostaglandin (PG) glyceryl esters are biosynthesized by COX-2 from the respective endocannabinoids anandamide and 2-arachidonyl glycerol. Agonist studies suggest that their pharmacologies are unique and unrelated to prostanoid receptors. This concept was further investigated using antagonists. The isolated feline iris was used as a key preparation, where prostanoid FP receptors and prostamide activity co-exist. Activity at human recombinant FP and other prostanoid receptors was determined using stable transfectants. In the feline iris, AGN 204396 produced a rightward shift of the dose-response curves for prostamide F2alpha and the prostamide F2alpha analog bimatoprost but did not block the effects of PGF2alpha and synthetic FP receptor agonists. Studies on human recombinant prostanoid receptors confirmed that AGN 204396 did not behave as a prostanoid FP receptor antagonist. AGN 204396 exhibited no antagonism at DP and EP1-4, but was a highly effective TP receptor antagonist. Contrary to expectation, the FP receptor antagonist AL-8810 efficaciously contracted the cat iris. AGN 204396 did not affect AL-8810 induced contractions, demonstrating that AL-8810 and AGN 204396 are pharmacologically distinct. Unlike AL-8810, the ethylamide derivate of AL-8810 was not an agonist. Al-8810 did not block prostamide F2alpha activity. Finally, AGN 204396 did not block PGE2-glyceryl ester activity. The ability of AGN 204396 to selectively block prostamide responses suggests the existence of prostamide sensitive receptors as entities distinct from receptors recognizing PGF2alpha and PGE2-glyceryl ester.

Large space erectable structures - building block structures study

NASA Technical Reports Server (NTRS)

Armstrong, W. H.; Skoumal, D. E.; Straayer, J. W.

1977-01-01

A modular planar truss structure and a long slender boom concept identified as building block approaches to construction of large spacecraft configurations are described. The concepts are compatible in weight and volume goals with the Space Transportation System, use standard structural units, and represent high on-orbit productivity in terms of structural area or beam length. Results of structural trade studies involving static and dynamic analyses of a single module and rigid body deployment analyses to assess kinetics and kinematics of automatic deployment of the building block modules are presented.

An Accelerated Recursive Doubling Algorithm for Block Tridiagonal Systems

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

Seal, Sudip K

2014-01-01

Block tridiagonal systems of linear equations arise in a wide variety of scientific and engineering applications. Recursive doubling algorithm is a well-known prefix computation-based numerical algorithm that requires O(M^3(N/P + log P)) work to compute the solution of a block tridiagonal system with N block rows and block size M on P processors. In real-world applications, solutions of tridiagonal systems are most often sought with multiple, often hundreds and thousands, of different right hand sides but with the same tridiagonal matrix. Here, we show that a recursive doubling algorithm is sub-optimal when computing solutions of block tridiagonal systems with multiplemore » right hand sides and present a novel algorithm, called the accelerated recursive doubling algorithm, that delivers O(R) improvement when solving block tridiagonal systems with R distinct right hand sides. Since R is typically about 100 1000, this improvement translates to very significant speedups in practice. Detailed complexity analyses of the new algorithm with empirical confirmation of runtime improvements are presented. To the best of our knowledge, this algorithm has not been reported before in the literature.« less

Novel Self-Assembling Amino Acid-Derived Block Copolymer with Changeable Polymer Backbone Structure.

PubMed

Koga, Tomoyuki; Aso, Eri; Higashi, Nobuyuki

2016-11-29

Block copolymers have attracted much attention as potentially interesting building blocks for the development of novel nanostructured materials in recent years. Herein, we report a new type of self-assembling block copolymer with changeable polymer backbone structure, poly(Fmoc-Ser) ester -b-PSt, which was synthesized by combining the polycondensation of 9-fluorenylmethoxycarbonyl-serine (Fmoc-Ser) with the reversible addition-fragmentation chain transfer (RAFT) polymerization of styrene (St). This block copolymer showed the direct conversion of the backbone structure from polyester to polypeptide through a multi O,N-acyl migration triggered by base-induced deprotection of Fmoc groups in organic solvent. Such polymer-to-polymer conversion was found to occur quantitatively without decrease in degree of polymerization and to cause a drastic change in self-assembling property of the block copolymer. On the basis of several morphological analyses using FTIR spectroscopy, atomic force, and transmission and scanning electron microscopies, the resulting peptide block copolymer was found to self-assemble into a vesicle-like hollow nanosphere with relatively uniform diameter of ca. 300 nm in toluene. In this case, the peptide block generated from polyester formed β-sheet structure, indicating the self-assembly via peptide-guided route. We believe the findings presented in this study offer a new concept for the development of self-assembling block copolymer system.

Differentiation in the angiotensin II receptor 1 blocker class on autonomic function.

PubMed

Krum, H

2001-09-01

Autonomic function is disordered in cardiovascular disease states such as chronic heart failure (CHF) and hypertension. Interactions between the renin-angiotensin-aldosterone system (RAAS) and the sympathetic nervous system (SNS) may potentially occur at a number of sites. These include central sites (eg, rostral ventrolateral medulla), at the level of baroreflex control, and at the sympathetic prejunctional angiotensin II receptor 1 (AT(1)) receptor, which is facilitatory for norepinephrine release from the sympathetic nerve terminal. Therefore, drugs that block the RAAS may be expected to improve autonomic dysfunction in cardiovascular disease states. In order to test the hypothesis that RAAS inhibition directly reduces SNS activity, a pithed rat model of sympathetic stimulation has been established. In this model, an increase in frequency of stimulation results in a pressor response that is sympathetically mediated and highly reproducible. This pressor response is enhanced in the presence of angiotensin II and is reduced in the presence of nonselective AIIRAs that block both AT(1) and AT(2) receptor subtypes (eg, saralasin). AT(1)-selective antagonists have also been studied in this model, at pharmacologically relevant doses. In one such study, only the AT(1) blocker eprosartan reduced sympathetically stimulated increases in blood pressure, whereas comparable doses of losartan, valsartan, and irbesartan did not. The reason(s) for the differences between eprosartan and other agents of this class on sympathetic modulation are not clear, but may relate to the chemical structure of the drug (a non- biphenyl tetrazole structure that is chemically distinct from the structure of other AIIRAs), receptor binding characteristics (competitive), or unique effects on presynaptic AT(1) receptors.

Superalloy Lattice Block Structures

NASA Technical Reports Server (NTRS)

Whittenberger, J. D.; Nathal, M. V.; Hebsur, M. G.; Kraus, D. L.

2003-01-01

In their simplest form, lattice block panels are produced by direct casting and result in lightweight, fully triangulated truss-like configurations which provide strength and stiffness [2]. The earliest realizations of lattice block were made from A1 and steels, primarily under funding from the US Navy [3]. This work also showed that the mechanical efficiency (eg., specific stiffness) of lattice block structures approached that of honeycomb structures [2]. The lattice architectures are also less anisotropic, and the investment casting route should provide a large advantage in cost and temperature capability over honeycombs which are limited to alloys that can be processed into foils. Based on this early work, a program was initiated to determine the feasibility of extending the high temperature superalloy lattice block [3]. The objective of this effort was to provide an alternative to intermetallics and composites in achieving a lightweight high temperature structure without sacrificing the damage tolerance and moderate cost inherent in superalloys. To establish the feasibility of the superalloy lattice block concept, work was performed in conjunction with JAMCORP, Inc. Billerica, MA, to produce a number of lattice block panels from both IN71 8 and Mar-M247.

Structure and mechanism of the ATP synthase membrane motor inferred from quantitative integrative modeling.

PubMed

Leone, Vanessa; Faraldo-Gómez, José D

2016-12-01

Two subunits within the transmembrane domain of the ATP synthase-the c-ring and subunit a-energize the production of 90% of cellular ATP by transducing an electrochemical gradient of H + or Na + into rotational motion. The nature of this turbine-like energy conversion mechanism has been elusive for decades, owing to the lack of definitive structural information on subunit a or its c-ring interface. In a recent breakthrough, several structures of this complex were resolved by cryo-electron microscopy (cryo-EM), but the modest resolution of the data has led to divergent interpretations. Moreover, the unexpected architecture of the complex has cast doubts on a wealth of earlier biochemical analyses conducted to probe this structure. Here, we use quantitative molecular-modeling methods to derive a structure of the a-c complex that is not only objectively consistent with the cryo-EM data, but also with correlated mutation analyses of both subunits and with prior cross-linking and cysteine accessibility measurements. This systematic, integrative approach reveals unambiguously the topology of subunit a and its relationship with the c-ring. Mapping of known Cd 2+ block sites and conserved protonatable residues onto the structure delineates two noncontiguous pathways across the complex, connecting two adjacent proton-binding sites in the c-ring to the space on either side of the membrane. The location of these binding sites and of a strictly conserved arginine on subunit a, which serves to prevent protons from hopping between them, explains the directionality of the rotary mechanism and its strict coupling to the proton-motive force. Additionally, mapping of mutations conferring resistance to oligomycin unexpectedly reveals that this prototypical inhibitor may bind to two distinct sites at the a-c interface, explaining its ability to block the mechanism of the enzyme irrespective of the direction of rotation of the c-ring. In summary, this study is a stepping stone toward establishing the mechanism of the ATP synthase at the atomic level.

Beautiful Blocks of Bedrock

NASA Image and Video Library

2016-06-01

This image captured by NASA Mars Reconnaissance Orbiter spacecraft targets a 3-kilometer diameter crater that occurs within the ejecta blanket of the much older Bakhuysen Crater, a 150-kilometer diameter impact crater in Noachis Terra. Impact craters are interesting because they provide a mechanism to uplift and expose underlying bedrock, allowing for the study of the subsurface and the geologic past. An enhanced color image shows the wall of the crater, which exposes layering as well as blocks of rock. There is a distinctive large block in the upper left of the crater wall, generally referred to as a "mega-block." It is an angular, light-toned, highly fragmented block, about 100 meters across. Several smaller light-toned blocks are also in the crater wall, possibly of the same rock type as the "mega-block." Ejecta blocks are thrown outward during the initial excavation of a crater, or are deposited as part of the ground-hugging flows of which the majority of the ejecta blanket is comprised. Through images like these, we are able to study the deeper subsurface of Mars that is not otherwise exposed. http://photojournal.jpl.nasa.gov/catalog/PIA20728

Protein based Block Copolymers

PubMed Central

Rabotyagova, Olena S.; Cebe, Peggy; Kaplan, David L.

2011-01-01

Advances in genetic engineering have led to the synthesis of protein-based block copolymers with control of chemistry and molecular weight, resulting in unique physical and biological properties. The benefits from incorporating peptide blocks into copolymer designs arise from the fundamental properties of proteins to adopt ordered conformations and to undergo self-assembly, providing control over structure formation at various length scales when compared to conventional block copolymers. This review covers the synthesis, structure, assembly, properties, and applications of protein-based block copolymers. PMID:21235251

Accordant summit heights, summit levels and the origin of the ``upper denudation level'' in the Serra do Mar (SE-Brazil, São Paulo): A study of hillslope forms and processes

NASA Astrophysics Data System (ADS)

Römer, Wolfgang

2008-08-01

In southern São Paulo the Serra do Mar is characterized by three distinct terrain types: 1) highly dissected areas with closely spaced ridges and accordant summit heights; 2) multiconvex hills; and 3) terrains with highly elevated watershed areas, irregular summit heights, and locally subdued relief. The development of this landscape is considered to be the result of the Cenozoic block-faulting and of the influences that are exerted by the differing lithological and structural setting of block-faulted compartments on weathering and erosion processes. In areas characterized by pronounced accordant summits the close coincidence between hillslope angle and the angle of limiting stability against landsliding points to a close adjustment of hillslope gradients and the mechanical properties of the regolith. The relative height of the hillslopes is functionally related to the spacing of the valleys and the gradient of the hillslopes. In areas with a regular spacing of v-shaped valleys and uniform rocks, this leads to the intersection of valley-side slopes in summits and ridges at a certain elevation. This elevation is determined by the length and steepness of the valley-side slopes. Therefore, the heights of the summits are geometrically constrained and are likely to indicate the upper limit of summit heights or an "upper denudation level" that is adjusted by hillslope processes to the incising streams. Accordant summit heights of this type are poor indicators of formerly more extensive denudation surfaces as it is also likely that they are a result of the long-term adjustment of hillslopes to river incision. The steep mountain flanks of block-faulted compartments on the other hand, comprise regolith-covered hillslopes that are closely adjusted to the maximum stable gradient as well as rock-slopes that are controlled by the rock-mass strength. Their summits are usually not accommodated into uniform summit levels. Highly elevated watershed areas exhibiting a subdued relief are detached from the base level response. On granitoid rocks these areas are often characterized by the rocky hills and domal rock outcrops. However, differences in the elevation of interfluves and summits between rocks of differing resistance and in the elevation of lithologically distinct individual fault-blocks imply that long-term weathering and erosion has transformed and lowered these landscapes. Therefore, these areas cannot be interpreted as a remnant of a pre-uplift topography and it appears to be unlikely that the height of the summits correlates with formerly more widespread planation surfaces in the far hinterland. The studies indicate that concepts such as the parallel retreat of hillslopes cannot account for the observed differences in the landscape. It is suggested that the Serra do Mar is consumed from the Atlantic and the inland side by spatially non-uniform developmental states. These states are determined by local differences in the coupling and distance to the regional base level and sea-level or are due to lithological and structural controls between and within the block-faulted compartments.

Mechanical Testing of IN718 Lattice Block Structures

NASA Technical Reports Server (NTRS)

Krause, David L.; Whittenberger, John D.; Kantzos, Pete T.; Hebsur, Mohan G.

2002-01-01

Lattice block construction produces a flat, structurally rigid panel composed of thin ligaments of material arranged in a three-dimensional triangulated truss-like structure. Low-cost methods of producing cast metallic lattice block panels are now available that greatly expand opportunities for using this unique material system in today's high-performance structures. Additional advances are being made in NASA's Ultra Efficient Engine Technology (UEET) program to extend the lattice block concept to superalloy materials. Advantages offered by this combination include high strength, light weight, high stiffness, and elevated temperature capabilities. Recently under UEET, the nickel-based superalloy Inconel 718 (IN718) was investment cast into lattice block panels with great success. To evaluate casting quality and lattice block architecture merit, individual ligaments, and structural subelement specimens were extracted from the panels. Tensile tests, structural compression, and bending strength tests were performed on these specimens. Fatigue testing was also completed for several bend test specimens. This paper first presents metallurgical and optical microscopy analysis of the castings. This is followed by mechanical test results for the tensile ligament tests and the subelement compression and bending strength tests, as well as for the fatigue tests that were performed. These tests generally showed comparable properties to base IN718 with the same heat treatment, and they underscored the benefits offered by lattice block materials. These benefits might be extended with improved architecture such as face sheets.

Graphene-based membranes.

PubMed

Liu, Gongping; Jin, Wanqin; Xu, Nanping

2015-08-07

Graphene is a well-known two-dimensional material that exhibits preeminent electrical, mechanical and thermal properties owing to its unique one-atom-thick structure. Graphene and its derivatives (e.g., graphene oxide) have become emerging nano-building blocks for separation membranes featuring distinct laminar structures and tunable physicochemical properties. Extraordinary molecular separation properties for purifying water and gases have been demonstrated by graphene-based membranes, which have attracted a huge surge of interest during the past few years. This tutorial review aims to present the latest groundbreaking advances in both the theoretical and experimental chemical science and engineering of graphene-based membranes, including their design, fabrication and application. Special attention will be given to the progresses in processing graphene and its derivatives into separation membranes with three distinct forms: a porous graphene layer, assembled graphene laminates and graphene-based composites. Moreover, critical views on separation mechanisms within graphene-based membranes will be provided based on discussing the effect of inter-layer nanochannels, defects/pores and functional groups on molecular transport. Furthermore, the separation performance of graphene-based membranes applied in pressure filtration, pervaporation and gas separation will be summarized. This article is expected to provide a compact source of relevant and timely information and will be of great interest to all chemists, physicists, materials scientists, engineers and students entering or already working in the field of graphene-based membranes and functional films.

A cell wall-degrading esterase of Xanthomonas oryzae requires a unique substrate recognition module for pathogenesis on rice.

PubMed

Aparna, Gudlur; Chatterjee, Avradip; Sonti, Ramesh V; Sankaranarayanan, Rajan

2009-06-01

Xanthomonas oryzae pv oryzae (Xoo) causes bacterial blight, a serious disease of rice (Oryza sativa). LipA is a secretory virulence factor of Xoo, implicated in degradation of rice cell walls and the concomitant elicitation of innate immune responses, such as callose deposition and programmed cell death. Here, we present the high-resolution structural characterization of LipA that reveals an all-helical ligand binding module as a distinct functional attachment to the canonical hydrolase catalytic domain. We demonstrate that the enzyme binds to a glycoside ligand through a rigid pocket comprising distinct carbohydrate-specific and acyl chain recognition sites where the catalytic triad is situated 15 A from the anchored carbohydrate. Point mutations disrupting the carbohydrate anchor site or blocking the pocket, even at a considerable distance from the enzyme active site, can abrogate in planta LipA function, exemplified by loss of both virulence and the ability to elicit host defense responses. A high conservation of the module across genus Xanthomonas emphasizes the significance of this unique plant cell wall-degrading function for this important group of plant pathogenic bacteria. A comparison with the related structural families illustrates how a typical lipase is recruited to act on plant cell walls to promote virulence, thus providing a remarkable example of the emergence of novel functions around existing scaffolds for increased proficiency of pathogenesis during pathogen-plant coevolution.

Vasopressin up-regulates the expression of growth-related immediate-early genes via two distinct EGF receptor transactivation pathways

PubMed Central

Fuentes, Lida Q.; Reyes, Carlos E.; Sarmiento, José M.; Villanueva, Carolina I.; Figueroa, Carlos D.; Navarro, Javier; González, Carlos B.

2008-01-01

Activation of V1a receptor triggers the expression of growth-related immediate-early genes (IEGs), including c-Fos and Egr-1. Here we found that pre-treatment of rat vascular smooth muscle A-10 cell line with the EGF receptor inhibitor AG1478 or the over-expression of an EGFR dominant negative mutant (HEBCD533) blocked the vasopressin-induced expression of IEGs, suggesting that activation of these early genes mediated by V1a receptor is via transactivation of the EGF receptor. Importantly, the inhibition of the metalloproteinases, which catalyzed the shedding of the EGF receptor agonist HB-EGF, selectively blocked the vasopressin-induced expression c-Fos. On the other hand, the inhibition of c-Src selectively blocked the vasopressin-induced expression of Egr-1. Interestingly, in contrast to the expression of c-Fos, the expression of Egr-1 was mediated via the Ras/MEK/MAPK-dependent signalling pathway. Vasopressin-triggered expression of both genes required the release of intracellular calcium, activation of PKC and β-arrestin 2. These findings demonstrated that vasopressin up-regulated the expression of c-Fos and Erg-1 via transactivation of two distinct EGF receptor-dependent signalling pathways. PMID:18571897

Selective Erasure of Distinct Forms of Long-Term Synaptic Plasticity Underlying Different Forms of Memory in the Same Postsynaptic Neuron.

PubMed

Hu, Jiangyuan; Ferguson, Larissa; Adler, Kerry; Farah, Carole A; Hastings, Margaret H; Sossin, Wayne S; Schacher, Samuel

2017-07-10

Generalization of fear responses to non-threatening stimuli is a feature of anxiety disorders. It has been challenging to target maladaptive generalized memories without affecting adaptive memories. Synapse-specific long-term plasticity underlying memory involves the targeting of plasticity-related proteins (PRPs) to activated synapses. If distinct tags and PRPs are used for different forms of plasticity, one could selectively remove distinct forms of memory. Using a stimulation paradigm in which associative long-term facilitation (LTF) occurs at one input and non-associative LTF at another input to the same postsynaptic neuron in an Aplysia sensorimotor preparation, we found that each form of LTF is reversed by inhibiting distinct isoforms of protein kinase M (PKM), putative PRPs, in the postsynaptic neuron. A dominant-negative (dn) atypical PKM selectively reversed associative LTF, while a dn classical PKM selectively reversed non-associative LTF. Although both PKMs are formed from calpain-mediated cleavage of protein kinase C (PKC) isoforms, each form of LTF is sensitive to a distinct dn calpain expressed in the postsynaptic neuron. Associative LTF is blocked by dn classical calpain, whereas non-associative LTF is blocked by dn small optic lobe (SOL) calpain. Interfering with a putative synaptic tag, the adaptor protein KIBRA, which protects the atypical PKM from degradation, selectively erases associative LTF. Thus, the activity of distinct PRPs and tags in a postsynaptic neuron contribute to the maintenance of different forms of synaptic plasticity at separate inputs, allowing for selective reversal of synaptic plasticity and providing a cellular basis for developing therapeutic strategies for selectively reversing maladaptive memories. Copyright © 2017 Elsevier Ltd. All rights reserved.

Multiple capsid-stabilizing interactions revealed in a high-resolution structure of an emerging picornavirus causing neonatal sepsis

NASA Astrophysics Data System (ADS)

Shakeel, Shabih; Westerhuis, Brenda M.; Domanska, Ausra; Koning, Roman I.; Matadeen, Rishi; Koster, Abraham J.; Bakker, Arjen Q.; Beaumont, Tim; Wolthers, Katja C.; Butcher, Sarah J.

2016-07-01

The poorly studied picornavirus, human parechovirus 3 (HPeV3) causes neonatal sepsis with no therapies available. Our 4.3-Å resolution structure of HPeV3 on its own and at 15 Å resolution in complex with human monoclonal antibody Fabs demonstrates the expected picornavirus capsid structure with three distinct features. First, 25% of the HPeV3 RNA genome in 60 sites is highly ordered as confirmed by asymmetric reconstruction, and interacts with conserved regions of the capsid proteins VP1 and VP3. Second, the VP0 N terminus stabilizes the capsid inner surface, in contrast to other picornaviruses where on expulsion as VP4, it forms an RNA translocation channel. Last, VP1's hydrophobic pocket, the binding site for the antipicornaviral drug, pleconaril, is blocked and thus inappropriate for antiviral development. Together, these results suggest a direction for development of neutralizing antibodies, antiviral drugs based on targeting the RNA-protein interactions and dissection of virus assembly on the basis of RNA nucleation.

Synthesis and characterization of hexaarylbenzenes with five or six different substituents enabled by programmed synthesis

NASA Astrophysics Data System (ADS)

Suzuki, Shin; Segawa, Yasutomo; Itami, Kenichiro; Yamaguchi, Junichiro

2015-03-01

Since its discovery in 1825, benzene has served as one of the most used and indispensable building blocks of chemical compounds, ranging from pharmaceuticals and agrochemicals to plastics and those used in organic electronic devices. Benzene has six hydrogen atoms that can each be replaced by different substituents, which means that the structural diversity of benzene derivatives is intrinsically extraordinary. The number of possible substituted benzenes from n different substituents is (2n + 2n2 + 4n3 + 3n4 + n6)/12. However, owing to a lack of general synthetic methods for making multisubstituted benzenes, this potentially huge structural diversity has not been fully exploited. Here, we describe a programmed synthesis of hexaarylbenzenes using C-H activation, cross-coupling and [4+2] cycloaddition reactions. The present method allows for the isolation and structure-property characterization of hexaarylbenzenes with distinctive aryl substituents at all positions for the first time. Moreover, the established protocol can be applied to the synthesis of tetraarylnaphthalenes and pentaarylpyridines.

Do priority effects outweigh environmental filtering in a guild of dominant freshwater macroinvertebrates?

PubMed

Little, Chelsea J; Altermatt, Florian

2018-04-11

Abiotic conditions have long been considered essential in structuring freshwater macroinvertebrate communities. Ecological drift, dispersal and biotic interactions also structure communities, and although these mechanisms are more difficult to detect, they may be of equal importance in natural communities. Here, we hypothesized that in 10 naturally replicated headwater streams in eastern Switzerland, locally dominant amphipod species would be associated with differences in environmental conditions. We conducted repeated surveys of amphipods and used a hierarchical joint species distribution model to assess the influence of different drivers on species co-occurrences. The species had unique environmental requirements, but a distinct spatial structure in their distributions was unrelated to habitat. Species co-occurred much less frequently than predicted by the model, which was surprising because laboratory and field evidence suggests they are capable of coexisting in equal densities. We suggest that niche preemption may limit their distribution and that a blocking effect related to the specific linear configuration of streams determines which species colonizes and dominates a given stream catchment, thus suggesting a new solution a long-standing conundrum in freshwater ecology. © 2018 The Author(s).

RTEL1 dismantles T loops and counteracts telomeric G4-DNA to maintain telomere integrity.

PubMed

Vannier, Jean-Baptiste; Pavicic-Kaltenbrunner, Visnja; Petalcorin, Mark I R; Ding, Hao; Boulton, Simon J

2012-05-11

T loops and telomeric G-quadruplex (G4) DNA structures pose a potential threat to genome stability and must be dismantled to permit efficient telomere replication. Here we implicate the helicase RTEL1 in the removal of telomeric DNA secondary structures, which is essential for preventing telomere fragility and loss. In the absence of RTEL1, T loops are inappropriately resolved by the SLX4 nuclease complex, resulting in loss of the telomere as a circle. Depleting SLX4 or blocking DNA replication abolished telomere circles (TCs) and rescued telomere loss in RTEL1(-/-) cells but failed to suppress telomere fragility. Conversely, stabilization of telomeric G4-DNA or loss of BLM dramatically enhanced telomere fragility in RTEL1-deficient cells but had no impact on TC formation or telomere loss. We propose that RTEL1 performs two distinct functions at telomeres: it disassembles T loops and also counteracts telomeric G4-DNA structures, which together ensure the dynamics and stability of the telomere. Copyright © 2012 Elsevier Inc. All rights reserved.

Using Distinct Sectors in Media Sampling and Full Media Analysis to Detect Presence of Documents from a Corpus

DTIC Science & Technology

2012-09-01

relative performance of several conventional SQL and NoSQL databases with a set of one billion file block hashes. Digital Forensics, Sector Hashing, Full... NoSQL databases with a set of one billion file block hashes. v THIS PAGE INTENTIONALLY LEFT BLANK vi Table of Contents List of Acronyms and...Operating System NOOP No Operation assembly instruction NoSQL “Not only SQL” model for non-relational database management NSRL National Software

Hydrolytic degradation of poly(ethylene oxide)-block-polycaprolactone worm micelles.

PubMed

Geng, Yan; Discher, Dennis E

2005-09-21

Spherical micelles and nanoparticles made with degradable polymers have been of great interest for therapeutic application, but degradation-induced changes in a spherical morphology can be subtle and mechanism/kinetics appears poorly understood. Here, we report the first preparation of giant and flexible worm micelles self-assembled from degradable copolymer poly(ethylene oxide)-block-polycaprolactone. Such worm micelles spontaneously shorten to generate spherical micelles, triggered by polycaprolactone hydrolysis, with distinct mechanism and kinetics from that which occurs in bulk material.

Genetics Home Reference: maple syrup urine disease

MedlinePlus

... disease is an inherited disorder in which the body is unable to process certain protein building blocks (amino acids) properly. The condition gets its name from the distinctive sweet odor of affected infants' urine. It is also characterized ...

The vaccinia virus I3L gene product is localized to a complex endoplasmic reticulum-associated structure that contains the viral parental DNA.

PubMed

Welsch, Sonja; Doglio, Laura; Schleich, Sibylle; Krijnse Locker, Jacomine

2003-05-01

The vaccinia virus (VV) I3L gene product is a single-stranded DNA-binding protein made early in infection that localizes to the cytoplasmic sites of viral DNA replication (S. C. Rochester and P. Traktman, J. Virol. 72:2917-2926, 1998). Surprisingly, when replication was blocked, the protein localized to distinct cytoplasmic spots (A. Domi and G. Beaud, J. Gen. Virol. 81:1231-1235, 2000). Here these I3L-positive spots were characterized in more detail. By using an anti-I3L peptide antibody we confirmed that the protein localized to the cytoplasmic sites of viral DNA replication by both immunofluorescence and electron microscopy (EM). Before replication had started or when replication was inhibited with hydroxyurea or cytosine arabinoside, I3L localized to distinct cytoplasmic punctate structures of homogeneous size. We show that these structures are not incoming cores or cytoplasmic sites of VV early mRNA accumulation. Instead, morphological and quantitative data indicate that they are specialized sites where the parental DNA accumulates after its release from incoming viral cores. By EM, these sites appeared as complex, electron-dense structures that were intimately associated with the cellular endoplasmic reticulum (ER). By double labeling of cryosections we show that they contain DNA and a viral early protein, the gene product of E8R. Since E8R is a membrane protein that is able to bind to DNA, the localization of this protein to the I3L puncta suggests that they are composed of membranes. The results are discussed in relation to our previous data showing that the process of viral DNA replication also occurs in close association with the ER.

Structural Basis for FcγRIIa Recognition of Human IgG and Formation of Inflammatory Signaling Complexes

PubMed Central

Ramsland, Paul A.; Farrugia, William; Bradford, Tessa M.; Tan Sardjono, Caroline; Esparon, Sandra; Trist, Halina M.; Powell, Maree S.; Szee Tan, Peck; Cendron, Angela C.; Wines, Bruce D.; Scott, Andrew M.; Hogarth, P. Mark

2012-01-01

The interaction of Abs with their specific FcRs is of primary importance in host immune effector systems involved in infection and inflammation, and are the target for immune evasion by pathogens. FcγRIIa is a unique and the most widespread activating FcR in humans that through avid binding of immune complexes potently triggers inflammation. Polymorphisms of FcγRIIa (high responder/low responder [HR/LR]) are linked to susceptibility to infections, autoimmune diseases, and the efficacy of therapeutic Abs. In this article, we define the three-dimensional structure of the complex between the HR (arginine, R134) allele of FcγRIIa (FcγRIIa-HR) and the Fc region of a humanized IgG1 Ab, hu3S193. The structure suggests how the HR/LR polymorphism may influence FcγRIIa interactions with different IgG subclasses and glycoforms. In addition, mutagenesis defined the basis of the epitopes detected by FcR blocking mAbs specific for FcγRIIa (IV.3), FcγRIIb (X63-21), and a pan FcγRII Ab (8.7). The epitopes detected by these Abs are distinct, but all overlap with residues defined by crystallography to contact IgG. Finally, crystal structures of LR (histidine, H134) allele of FcγRIIa and FcγRIIa-HR reveal two distinct receptor dimers that may represent quaternary states on the cell surface. A model is presented whereby a dimer of FcγRIIa-HR binds Ag–Ab complexes in an arrangement that possibly occurs on the cell membrane as part of a larger signaling assembly. PMID:21856937

Response of cells on surface-induced nanopatterns: fibroblasts and mesenchymal progenitor cells.

PubMed

Khor, Hwei Ling; Kuan, Yujun; Kukula, Hildegard; Tamada, Kaoru; Knoll, Wolfgang; Moeller, Martin; Hutmacher, Dietmar W

2007-05-01

Ultrathin films of a poly(styrene)-block-poly(2-vinylpyrindine) diblock copolymer (PS-b-P2VP) and poly(styrene)-block-poly(4-vinylpyrindine) diblock copolymer (PS-b-P4VP) were used to form surface-induced nanopattern (SINPAT) on mica. Surface interaction controlled microphase separation led to the formation of chemically heterogeneous surface nanopatterns on dry ultrathin films. Two distinct nanopatterned surfaces, namely, wormlike and dotlike patterns, were used to investigate the influence of topography in the nanometer range on cell adhesion, proliferation, and migration. Atomic force microscopy was used to confirm that SINPAT was stable under cell culture conditions. Fibroblasts and mesenchymal progenitor cells were cultured on the nanopatterned surfaces. Phase contrast and confocal laser microscopy showed that fibroblasts and mesenchymal progenitor cells preferred the densely spaced wormlike patterns. Atomic force microscopy showed that the cells remodelled the extracellular matrix differently as they migrate over the two distinctly different nanopatterns.

Distinct Adsorption Configurations and Self-Assembly Characteristics of Fibrinogen on Chemically Uniform and Alternating Surfaces including Block Copolymer Nanodomains

PubMed Central

2015-01-01

Understanding protein–surface interactions is crucial to solid-state biomedical applications whose functionality is directly correlated with the precise control of the adsorption configuration, surface packing, loading density, and bioactivity of protein molecules. Because of the small dimensions and highly amphiphilic nature of proteins, investigation of protein adsorption performed on nanoscale topology can shed light on subprotein-level interaction preferences. In this study, we examine the adsorption and assembly behavior of a highly elongated protein, fibrinogen, on both chemically uniform (as-is and buffered HF-treated SiO2/Si, and homopolymers of polystyrene and poly(methyl methacrylate)) and varying (polystyrene-block-poly(methyl methacrylate)) surfaces. By focusing on high-resolution imaging of individual protein molecules whose configurations are influenced by protein–surface rather than protein–protein interactions, fibrinogen conformations characteristic to each surface are identified and statistically analyzed for structural similarities/differences in key protein domains. By exploiting block copolymer nanodomains whose repeat distance is commensurate with the length of the individual protein, we determine that fibrinogen exhibits a more neutral tendency for interaction with both polystyrene and poly(methyl methacrylate) blocks relative to the case of common globular proteins. Factors affecting fibrinogen–polymer interactions are discussed in terms of hydrophobic and electrostatic interactions. In addition, assembly and packing attributes of fibrinogen are determined at different loading conditions. Primary orientations of fibrinogen and its rearrangements with respect to the underlying diblock nanodomains associated with different surface coverage are explained by pertinent protein interaction mechanisms. On the basis of two-dimensional stacking behavior, a protein assembly model is proposed for the formation of an extended fibrinogen network on the diblock copolymer. PMID:24708538

Beating the curse of dimension with accurate statistics for the Fokker-Planck equation in complex turbulent systems.

PubMed

Chen, Nan; Majda, Andrew J

2017-12-05

Solving the Fokker-Planck equation for high-dimensional complex dynamical systems is an important issue. Recently, the authors developed efficient statistically accurate algorithms for solving the Fokker-Planck equations associated with high-dimensional nonlinear turbulent dynamical systems with conditional Gaussian structures, which contain many strong non-Gaussian features such as intermittency and fat-tailed probability density functions (PDFs). The algorithms involve a hybrid strategy with a small number of samples [Formula: see text], where a conditional Gaussian mixture in a high-dimensional subspace via an extremely efficient parametric method is combined with a judicious Gaussian kernel density estimation in the remaining low-dimensional subspace. In this article, two effective strategies are developed and incorporated into these algorithms. The first strategy involves a judicious block decomposition of the conditional covariance matrix such that the evolutions of different blocks have no interactions, which allows an extremely efficient parallel computation due to the small size of each individual block. The second strategy exploits statistical symmetry for a further reduction of [Formula: see text] The resulting algorithms can efficiently solve the Fokker-Planck equation with strongly non-Gaussian PDFs in much higher dimensions even with orders in the millions and thus beat the curse of dimension. The algorithms are applied to a [Formula: see text]-dimensional stochastic coupled FitzHugh-Nagumo model for excitable media. An accurate recovery of both the transient and equilibrium non-Gaussian PDFs requires only [Formula: see text] samples! In addition, the block decomposition facilitates the algorithms to efficiently capture the distinct non-Gaussian features at different locations in a [Formula: see text]-dimensional two-layer inhomogeneous Lorenz 96 model, using only [Formula: see text] samples. Copyright © 2017 the Author(s). Published by PNAS.

Motivational changes in response to blocked goals and foreshortened time: testing alternatives to socioemotional selectivity theory.

PubMed

Fung, Helene H; Carstensen, Laura L

2004-03-01

Socioemotional selectivity theory contends that when people perceive time as limited, they prioritize emotionally meaningful goals. Although empirical support for the theory has been found in several studies, 2 alternative explanations for the pattern of findings remain: (a) emotional goals are pursued by default because nonemotional goals are blocked, and (b) emotional goals are pursued in search of emotional support rather than emotional meaning. This study tested these alternatives by examining social goals in response to blocked goals and foreshortened time. Findings reveal distinct motivational patterns, as reflected in social preferences and self-reported social goals, in response to the 2 types of constraints.

Gaussian curvature analysis allows for automatic block placement in multi-block hexahedral meshing.

PubMed

Ramme, Austin J; Shivanna, Kiran H; Magnotta, Vincent A; Grosland, Nicole M

2011-10-01

Musculoskeletal finite element analysis (FEA) has been essential to research in orthopaedic biomechanics. The generation of a volumetric mesh is often the most challenging step in a FEA. Hexahedral meshing tools that are based on a multi-block approach rely on the manual placement of building blocks for their mesh generation scheme. We hypothesise that Gaussian curvature analysis could be used to automatically develop a building block structure for multi-block hexahedral mesh generation. The Automated Building Block Algorithm incorporates principles from differential geometry, combinatorics, statistical analysis and computer science to automatically generate a building block structure to represent a given surface without prior information. We have applied this algorithm to 29 bones of varying geometries and successfully generated a usable mesh in all cases. This work represents a significant advancement in automating the definition of building blocks.

How Young Children Learn to Program with Sensor, Action, and Logic Blocks

ERIC Educational Resources Information Center

Wyeth, Peta

2008-01-01

Electronic Blocks are a new programming environment designed specifically for children aged between 3 and 8 years. These physical, stackable blocks include sensor blocks, action blocks, and logic blocks. By connecting these blocks, children can program a wide variety of structures that interact with one another and the environment. Electronic…

Airborne and Ground Electrical Surveys for Subsurface Mapping of the Arbuckle Aquifer, Central Oklahoma

NASA Astrophysics Data System (ADS)

Smith, D.; Smith, B. D.; Blome, C. D.; Osborn, N.

2008-12-01

Airborne and ground electrical surveys have been conducted to map the subsurface hydrogeologic character of the Arbuckle-Simpson aquifer in south central Oklahoma. An understanding of the geologic framework and hydrogeologic characteristics is necessary to evaluate groundwater flow through the highly faulted, structurally complex, carbonate aquifer. Results from this research will further understanding of the aquifer and will assist in managing the water resources of the region. The major issues include water quality, the allocation of water rights, and the potential impacts of pumping on springs and stream. Four areas in the Hunton anticline area, with distinctly different geology, were flown with a frequency domain helicopter electromagnetic system (HEM) in March, 2007. Ground electrical studies include dc resistivity imaging and natural field audiomagnetotelluric (AMT), and magnetotelluric (MT) surveys. The HEM resistivity and total field magnetic survey was flown in four blocks, A through D, mostly with a line spacing of 400 m. Block A extends from the Chickasaw National Recreational Area (CHIC) to Mill Creek on the west side of the anticline. The surface geology of this block is mostly dolomitic limestone of the Arbuckle Group that is in fault contact with younger Paleozoic clastic rocks. The flight line spacing was 800 meters in the western half of the block and 400 meters in the eastern part. Airborne magnetic data indicate that the Sulphur fault bends south to merge with the Mill Creek fault which substantiates an earlier hypothesis first made from interpretation of gravity data. Block B, located on the north side of the anticline consists of mostly of Arbuckle and Simpson Group rocks. Block C, covering most of the Clarita horst on the east side of the anticline, consists of the Upper Ordovician to the Lower Pennsylvanian shales. Block D, which was flown to include a deep test well site at Spears ranch, consisted of eight lines spaced at 400 meters. The HEM data are being used to more precisely locate faults, refine the lithostratigraphic units, and to map the depth and extent of shallow epikarst. The MT and AMT data revealed deep structural contacts and a transition between fresh and highly mineralized ground water between springs in the CHIC. The dc resistivity survey has greatly helped in mapping major faults both within dolomitic limestone and clastic units. Ground resistivity surveys also suggest that, in places, the faults within limestone are zones of lower resistivity and map low resistivity surficial epikarst a several meters thick. Ground penetrometer data also has been used to define the depth extent of epikarst in selected areas and the data correlate well with the dc resistivity and HEM resistivity depth sections.

Resurgent current of voltage-gated Na+ channels

PubMed Central

Lewis, Amanda H; Raman, Indira M

2014-01-01

Resurgent Na+ current results from a distinctive form of Na+ channel gating, originally identified in cerebellar Purkinje neurons. In these neurons, the tetrodotoxin-sensitive voltage-gated Na+ channels responsible for action potential firing have specialized mechanisms that reduce the likelihood that they accumulate in fast inactivated states, thereby shortening refractory periods and permitting rapid, repetitive, and/or burst firing. Under voltage clamp, step depolarizations evoke transient Na+ currents that rapidly activate and quickly decay, and step repolarizations elicit slower channel reopening, or a ‘resurgent’ current. The generation of resurgent current depends on a factor in the Na+ channel complex, probably a subunit such as NaVβ4 (Scn4b), which blocks open Na+ channels at positive voltages, competing with the fast inactivation gate, and unblocks at negative voltages, permitting recovery from an open channel block along with a flow of current. Following its initial discovery, resurgent Na+ current has been found in nearly 20 types of neurons. Emerging research suggests that resurgent current is preferentially increased in a variety of clinical conditions associated with altered cellular excitability. Here we review the biophysical, molecular and structural mechanisms of resurgent current and their relation to the normal functions of excitable cells as well as pathophysiology. PMID:25172941

15 CFR 50.40 - Fee structure for statistics for city blocks in the 1980 Census of Population and Housing.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 15 Commerce and Foreign Trade 1 2011-01-01 2011-01-01 false Fee structure for statistics for city... SERVICES AND STUDIES BY THE BUREAU OF THE CENSUS § 50.40 Fee structure for statistics for city blocks in... for each city block, drawn from the subjects which are being covered on a 100-percent basis. For these...

15 CFR 50.40 - Fee structure for statistics for city blocks in the 1980 Census of Population and Housing.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Fee structure for statistics for city... SERVICES AND STUDIES BY THE BUREAU OF THE CENSUS § 50.40 Fee structure for statistics for city blocks in... for each city block, drawn from the subjects which are being covered on a 100-percent basis. For these...

Structural motifs of pre-nucleation clusters.

PubMed

Zhang, Y; Türkmen, I R; Wassermann, B; Erko, A; Rühl, E

2013-10-07

Structural motifs of pre-nucleation clusters prepared in single, optically levitated supersaturated aqueous aerosol microparticles containing CaBr2 as a model system are reported. Cluster formation is identified by means of X-ray absorption in the Br K-edge regime. The salt concentration beyond the saturation point is varied by controlling the humidity in the ambient atmosphere surrounding the 15-30 μm microdroplets. This leads to the formation of metastable supersaturated liquid particles. Distinct spectral shifts in near-edge spectra as a function of salt concentration are observed, in which the energy position of the Br K-edge is red-shifted by up to 7.1 ± 0.4 eV if the dilute solution is compared to the solid. The K-edge positions of supersaturated solutions are found between these limits. The changes in electronic structure are rationalized in terms of the formation of pre-nucleation clusters. This assumption is verified by spectral simulations using first-principle density functional theory and molecular dynamics calculations, in which structural motifs are considered, explaining the experimental results. These consist of solvated CaBr2 moieties, rather than building blocks forming calcium bromide hexahydrates, the crystal system that is formed by drying aqueous CaBr2 solutions.

Structural Characterization of Proline-rich Tyrosine Kinase 2 (PYK2) Reveals a Unique (DFG-out) Conformation and Enables Inhibitor Design

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

Han, Seungil; Mistry, Anil; Chang, Jeanne S.

Proline-rich tyrosine kinase 2 (PYK2) is a cytoplasmic, non-receptor tyrosine kinase implicated in multiple signaling pathways. It is a negative regulator of osteogenesis and considered a viable drug target for osteoporosis treatment. The high-resolution structures of the human PYK2 kinase domain with different inhibitor complexes establish the conventional bilobal kinase architecture and show the conformational variability of the DFG loop. The basis for the lack of selectivity for the classical kinase inhibitor, PF-431396, within the FAK family is explained by our structural analyses. Importantly, the novel DFG-out conformation with two diarylurea inhibitors (BIRB796, PF-4618433) reveals a distinct subclass of non-receptormore » tyrosine kinases identifiable by the gatekeeper Met-502 and the unique hinge loop conformation of Leu-504. This is the first example of a leucine residue in the hinge loop that blocks the ATP binding site in the DFG-out conformation. Our structural, biophysical, and pharmacological studies suggest that the unique features of the DFG motif, including Leu-504 hinge-loop variability, can be exploited for the development of selective protein kinase inhibitors.« less

NEUTRON-IRRADIATED STRUCTURES

DOEpatents

Ashley, E.L.; Ashley, J.W.; Bowker, H.W.; Hall, R.H.; Kendall, J.W.

1959-02-01

A moderator structure is described for a nuclear reactor of the heterogensous type wherein a large mass of moderator is provided with channels therethrough for the introduction of uranium serving as nuclear fuel and for the passage of a cooling fluid. The structure is comprised of blocks of moderator material in superposed horizontal layers, the blocks of each layer being tied together with spaces between them and oriented to have horizontal Wigner growth. The ties are strips of moderator material, the same as the blocks, with transverse Wigner growth, disposed horizontally along lines crossing at vertical axes of the blocks. The blocks are preferably rectangular with a larger or length dimension transverse to the directions of Wiguer growth and are stood on end to provide for horizontal growth.

Enhancing instruction scheduling with a block-structured ISA

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

Melvin, S.; Patt, Y.

It is now generally recognized that not enough parallelism exists within the small basic blocks of most general purpose programs to satisfy high performance processors. Thus, a wide variety of techniques have been developed to exploit instruction level parallelism across basic block boundaries. In this paper we discuss some previous techniques along with their hardware and software requirements. Then we propose a new paradigm for an instruction set architecture (ISA): block-structuring. This new paradigm is presented, its hardware and software requirements are discussed and the results from a simulation study are presented. We show that a block-structured ISA utilizes bothmore » dynamic and compile-time mechanisms for exploiting instruction level parallelism and has significant performance advantages over a conventional ISA.« less

Toddlers Default to Canonical Surface-to-Meaning Mapping When Learning Verbs

PubMed Central

Dautriche, Isabelle; Cristia, Alejandrina; Brusini, Perrine; Yuan, Sylvia; Fisher, Cynthia; Christophe, Anne

2013-01-01

Previous work has shown that toddlers readily encode each noun in the sentence as a distinct argument of the verb. However, languages allow multiple mappings between form and meaning which do not fit this canonical format. Two experiments examined French 28-month-olds’ interpretation of right-dislocated sentences (nouni-verb, nouni) where the presence of clear, language-specific cues should block such a canonical mapping. Toddlers (N = 96) interpreted novel verbs embedded in these sentences as transitive, disregarding prosodic cues to dislocation (Experiment 1) but correctly interpreted right-dislocated sentences containing well-known verbs (Experiment 2). These results suggest that toddlers can integrate multiple cues in ideal conditions, but default to canonical surface-to-meaning mapping when extracting structural information about novel verbs in semantically impoverished conditions. PMID:24117408

Chameleon-like elastomers with molecularly encoded strain-adaptive stiffening and coloration

NASA Astrophysics Data System (ADS)

Vatankhah-Varnosfaderani, Mohammad; Keith, Andrew N.; Cong, Yidan; Liang, Heyi; Rosenthal, Martin; Sztucki, Michael; Clair, Charles; Magonov, Sergei; Ivanov, Dimitri A.; Dobrynin, Andrey V.; Sheiko, Sergei S.

2018-03-01

Active camouflage is widely recognized as a soft-tissue feature, and yet the ability to integrate adaptive coloration and tissuelike mechanical properties into synthetic materials remains elusive. We provide a solution to this problem by uniting these functions in moldable elastomers through the self-assembly of linear-bottlebrush-linear triblock copolymers. Microphase separation of the architecturally distinct blocks results in physically cross-linked networks that display vibrant color, extreme softness, and intense strain stiffening on par with that of skin tissue. Each of these functional properties is regulated by the structure of one macromolecule, without the need for chemical cross-linking or additives. These materials remain stable under conditions characteristic of internal bodily environments and under ambient conditions, neither swelling in bodily fluids nor drying when exposed to air.

Application of Stochastic Automata Networks for Creation of Continuous Time Markov Chain Models of Voltage Gating of Gap Junction Channels

PubMed Central

Pranevicius, Henrikas; Pranevicius, Mindaugas; Pranevicius, Osvaldas; Bukauskas, Feliksas F.

2015-01-01

The primary goal of this work was to study advantages of numerical methods used for the creation of continuous time Markov chain models (CTMC) of voltage gating of gap junction (GJ) channels composed of connexin protein. This task was accomplished by describing gating of GJs using the formalism of the stochastic automata networks (SANs), which allowed for very efficient building and storing of infinitesimal generator of the CTMC that allowed to produce matrices of the models containing a distinct block structure. All of that allowed us to develop efficient numerical methods for a steady-state solution of CTMC models. This allowed us to accelerate CPU time, which is necessary to solve CTMC models, ∼20 times. PMID:25705700

Domain wall structure and interactions in 50 nm wide Cobalt nanowires

NASA Astrophysics Data System (ADS)

Tu, Kun-Hua; Ojha, Shuchi; Ross, Caroline A.

2018-05-01

Arrays of cobalt nanowires with widths of 50 nm, thickness of 5 and 20 nm and periodicity of 70 nm were fabricated by pattern transfer from a self-assembled block copolymer film. Transverse domain walls (DWs) were imaged by magnetic force microscopy, indicating repulsive interactions between DWs of the same sign in the 20 nm thick wires. Micromagnetic simulations were used to identify the interactions in the six distinct cases of a pair of transverse DWs in adjacent wires, considering all the possible combinations of head-to-head and tail-to-tail DWs and the orientation of the core magnetization. The boundary between repulsive and attractive DW interactions is mapped out for wires as a function of thickness, width and interwire spacing.

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

Ramsland, Paul A.; Farrugia, William; Bradford, Tessa M.

The interaction of Abs with their specific FcRs is of primary importance in host immune effector systems involved in infection and inflammation, and are the target for immune evasion by pathogens. Fc{gamma}RIIa is a unique and the most widespread activating FcR in humans that through avid binding of immune complexes potently triggers inflammation. Polymorphisms of Fc{gamma}RIIa (high responder/low responder [HR/LR]) are linked to susceptibility to infections, autoimmune diseases, and the efficacy of therapeutic Abs. In this article, we define the three-dimensional structure of the complex between the HR (arginine, R134) allele of Fc{gamma}RIIa (Fc{gamma}RIIa-HR) and the Fc region of amore » humanized IgG1 Ab, hu3S193. The structure suggests how the HR/LR polymorphism may influence Fc{gamma}RIIa interactions with different IgG subclasses and glycoforms. In addition, mutagenesis defined the basis of the epitopes detected by FcR blocking mAbs specific for Fc{gamma}RIIa (IV.3), Fc{gamma}RIIb (X63-21), and a pan Fc{gamma}RII Ab (8.7). The epitopes detected by these Abs are distinct, but all overlap with residues defined by crystallography to contact IgG. Finally, crystal structures of LR (histidine, H134) allele of Fc{gamma}RIIa and Fc{gamma}RIIa-HR reveal two distinct receptor dimers that may represent quaternary states on the cell surface. A model is presented whereby a dimer of Fc{gamma}RIIa-HR binds Ag-Ab complexes in an arrangement that possibly occurs on the cell membrane as part of a larger signaling assembly.« less

Characterization and Structural Analysis of a Novel exo-Type Enzyme Acting on β-1,2-Glucooligosaccharides from Parabacteroides distasonis.

PubMed

Shimizu, Hisaka; Nakajima, Masahiro; Miyanaga, Akimasa; Takahashi, Yuta; Tanaka, Nobukiyo; Kobayashi, Kaito; Sugimoto, Naohisa; Nakai, Hiroyuki; Taguchi, Hayao

2018-05-25

β-1,2-Glucan is a polysaccharide produced mainly by some Gram-negative bacteria as a symbiosis and infectious factor. We recently identified endo-β-1,2-glucanase from Chitinophaga pinensis ( CpSGL) as an enzyme comprising a new family. Here, we report the characteristics and crystal structure of a CpSGL homologue from Parabacteroides distasonis, an intestinal bacterium (BDI_3064 protein), which exhibits distinctive properties of known β-1,2-glucan-degrading enzymes. BDI_3064 hydrolyzed linear β-1,2-glucan and β-1,2-glucooligosaccharides with degrees of polymerization (DPs) of ≥4 to produce sophorose specifically but did not hydrolyze cyclic β-1,2-glucan. This result indicates that BDI_3064 is a new exo-type enzyme. BDI_3064 also produced sophorose from β-1,2-glucooligosaccharide analogues that have a modified reducing end, indicating that BDI_3064 acts on its substrates from the nonreducing end. The crystal structure showed that BDI_3064 possesses additional N-terminal domains 1 and 2, unlike CpSGL. Superimposition of BDI_3064 and CpSGL complexed with ligands showed that R93 in domain 1 overlapped subsite -3 in CpSGL. Docking analysis involving a β-1,2-glucooligosaccharide with DP4 showed that R93 completely blocks the nonreducing end of the docked β-1,2-glucooligosaccharide. This indicates that BDI_3064 employs a distinct mechanism of recognition at the nonreducing end of substrates to act as an exo-type enzyme. Thus, we propose 2-β-d-glucooligosaccharide sophorohydrolase (nonreducing end) as a systematic name for BDI_3064.

Crustal structure of Central Sicily

NASA Astrophysics Data System (ADS)

Giustiniani, Michela; Tinivella, Umberta; Nicolich, Rinaldo

2018-01-01

We processed crustal seismic profile SIRIPRO, acquired across Central Sicily. To improve the seismic image we utilized the wave equation datuming technique, a process of upward or downward continuation of the wave-field between two arbitrarily shaped surfaces. Wave equation datuming was applied to move shots and receivers to a given datum plane, removing time shifts related to topography and to near-surface velocity variations. The datuming procedure largely contributed to attenuate ground roll, enhance higher frequencies, increase resolution and improve the signal/noise ratio. Processed data allow recognizing geometries of crust structures differentiating seismic facies and offering a direct image of ongoing tectonic setting within variable lithologies characterizing the crust of Central Sicily. Migrated sections underline distinctive features of Hyblean Plateau foreland and above all a crustal thinning towards the Caltanissetta trough, to the contact with a likely deep Permo-Triassic rifted basin or rather a zone of a continent to oceanic transition. Inhomogeneity and fragmentation of Sicily crust, with a distinct separation of Central Sicily basin from western and eastern blocks, appear to have guided the tectonic transport inside the Caltanissetta crustal scale syncline and the accumulation of allochthonous terrains with south and north-verging thrusts. Major tectonic stack operated on the construction of a wide anticline of the Maghrebian chain in northern Sicily. Sequential south-verging imbrications of deep elements forming the anticline core denote a crust wedge indenting foreland structures. Deformation processes involved multiple detachment planes down to decoupling levels located near crust/mantle transition, supporting a presence of high-density lenses beneath the chain, interrelated to a southwards push of Tyrrhenian mantle and asthenosphere.

"Eyeball test" of thermographic patterns for predicting a successful lateral infraclavicular block.

PubMed

Andreasen, Asger M; Linnet, Karen E; Asghar, Semera; Rothe, Christian; Rosenstock, Charlotte V; Lange, Kai H W; Lundstrøm, Lars H

2017-11-01

Increased distal skin temperature can be used to predict the success of lateral infraclavicular (LIC) block. We hypothesized that an "eyeball test" of specific infrared thermographic patterns after LIC block could be used to determine block success. In this observational study, five observers trained in four distinct thermographic patterns independently evaluated thermographic images of the hands of 40 patients at baseline and at one-minute intervals for 30 min after a LIC block. Sensitivity, specificity, and predictive values of a positive and a negative test were estimated to evaluate the validity of specific thermographic patterns for predicting a successful block. Sensory and motor block of the musculocutaneous, radial, ulnar, and median nerves defined block success. Fleiss' kappa statistics of multiple interobserver agreements were used to evaluate reliability. As a diagnostic test, the defined specific thermographic patterns of the hand predicted a successful block with increasing accuracy over the 30-min observation period. Block success was predicted with a sensitivity of 92.4% (95% confidence interval [CI], 86.8 to 96.2) and with a specificity of 84.0% (95% CI, 70.3 to 92.4) at min 30. The Fleiss' kappa for the five observers was 0.87 (95% CI, 0.77 to 0.96). We conclude that visual evaluation by an eyeball test of specific thermographic patterns of the blocked hands may be useful as a valid and reliable diagnostic test for predicting a successful LIC block.

Coordination of Hepatitis C Virus Assembly by Distinct Regulatory Regions in Nonstructural Protein 5A

PubMed Central

Zayas, Margarita; Long, Gang; Madan, Vanesa; Bartenschlager, Ralf

2016-01-01

Hepatitis C virus (HCV) nonstructural protein (NS)5A is a RNA-binding protein composed of a N-terminal membrane anchor, a structured domain I (DI) and two intrinsically disordered domains (DII and DIII) interacting with viral and cellular proteins. While DI and DII are essential for RNA replication, DIII is required for assembly. How these processes are orchestrated by NS5A is poorly understood. In this study, we identified a highly conserved basic cluster (BC) at the N-terminus of DIII that is critical for particle assembly. We generated BC mutants and compared them with mutants that are blocked at different stages of the assembly process: a NS5A serine cluster (SC) mutant blocked in NS5A-core interaction and a mutant lacking the envelope glycoproteins (ΔE1E2). We found that BC mutations did not affect core-NS5A interaction, but strongly impaired core–RNA association as well as virus particle envelopment. Moreover, BC mutations impaired RNA-NS5A interaction arguing that the BC might be required for loading of core protein with viral RNA. Interestingly, RNA-core interaction was also reduced with the ΔE1E2 mutant, suggesting that nucleocapsid formation and envelopment are coupled. These findings argue for two NS5A DIII determinants regulating assembly at distinct, but closely linked steps: (i) SC-dependent recruitment of replication complexes to core protein and (ii) BC-dependent RNA genome delivery to core protein, triggering encapsidation that is tightly coupled to particle envelopment. These results provide a striking example how a single viral protein exerts multiple functions to coordinate the steps from RNA replication to the assembly of infectious virus particles. PMID:26727512

Unraveling the Agglomeration Mechanism in Charged Block Copolymer and Surfactant Complexes

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

Borreguero, Jose M.; Pincus, Philip A.; Sumpter, Bobby G.

Here, we report a molecular dynamics simulation investigation of self-assembly and complex formation of charged-neutral double hydrophilic and hydrophobic-hydrophilic block copolymers (BCP) with oppositely charged surfactants. Furthermore, the structure of the surfactant micelles and the BCP aggregation on the micelle surface is systematically studied for five different BCP volume fractions that also mimics a reduction of the surfactant concentration. The local electrostatic interactions between the oppositely charged species encourage the formation of core-shell structures between the surfactant micelles where the surfactants form the cores and the charged blocks of the BCP form the corona. The emergent morphologies of these aggregatesmore » are contingent upon the nature of the BCP neutral blocks. The hydrophilic neutral blocks agglomerate with the micelles as hairy colloidal structures while the hydrophobic neutrals agglomerate in lamellar structures with the surfactant micelles. The distribution of counterion charges along the simulation box show a close-to-normal density distribution for the hydrophilic neutral blocks and a binodal distribution for hydrophobic neutral blocks. No specific surfactant concentration dependent scaling relation is observed as opposed to the simpler case of homo-polyelectrolytes.« less

Unraveling the Agglomeration Mechanism in Charged Block Copolymer and Surfactant Complexes

DOE PAGES

Borreguero, Jose M.; Pincus, Philip A.; Sumpter, Bobby G.; ...

2017-01-27

Here, we report a molecular dynamics simulation investigation of self-assembly and complex formation of charged-neutral double hydrophilic and hydrophobic-hydrophilic block copolymers (BCP) with oppositely charged surfactants. Furthermore, the structure of the surfactant micelles and the BCP aggregation on the micelle surface is systematically studied for five different BCP volume fractions that also mimics a reduction of the surfactant concentration. The local electrostatic interactions between the oppositely charged species encourage the formation of core-shell structures between the surfactant micelles where the surfactants form the cores and the charged blocks of the BCP form the corona. The emergent morphologies of these aggregatesmore » are contingent upon the nature of the BCP neutral blocks. The hydrophilic neutral blocks agglomerate with the micelles as hairy colloidal structures while the hydrophobic neutrals agglomerate in lamellar structures with the surfactant micelles. The distribution of counterion charges along the simulation box show a close-to-normal density distribution for the hydrophilic neutral blocks and a binodal distribution for hydrophobic neutral blocks. No specific surfactant concentration dependent scaling relation is observed as opposed to the simpler case of homo-polyelectrolytes.« less

Unique Pressure Dependence of the Order-Disorder Transition Temperature of a Series of PEP-PDMS Diblock Copolymers

NASA Astrophysics Data System (ADS)

Mortensen, K.; Almdal, K.; Schwahn, D.; Frielinghaus, H.

1997-03-01

Studies of the phase behavior of polymer systems has proven that the sensitivity to fluctuations is much more distinct than originally anticipated based on theoretical arguments. In blends of homo-polymers, studies have revealed that fluctuations give rise to significant re-normalized critical behavior. It has been argued that the free volume causes an entropic contribution to the Flory-Huggins interaction parameter, \\chi, and is thereby responsible for the re-normalized behavior. In block copolymers fluctuations have even more pronounced effects, as it changes the second order critical point at f=0.5 to first order and additional complex phases are stabilized. Measurements of the structure factor S(q) of PEP-PDMS diblock copolymers have revealed unique character in the phase-diagram with re-entrant ordered structure. Moreover, an unexpected singularity in the conformational compressibility, as identified from the peak-position, q, is observed. In contrary to binary polymer blends, pressure does not affect the Ginzburg number.

Slowing down single-molecule trafficking through a protein nanopore reveals intermediates for peptide translocation

NASA Astrophysics Data System (ADS)

Mereuta, Loredana; Roy, Mahua; Asandei, Alina; Lee, Jong Kook; Park, Yoonkyung; Andricioaei, Ioan; Luchian, Tudor

2014-01-01

The microscopic details of how peptides translocate one at a time through nanopores are crucial determinants for transport through membrane pores and important in developing nano-technologies. To date, the translocation process has been too fast relative to the resolution of the single molecule techniques that sought to detect its milestones. Using pH-tuned single-molecule electrophysiology and molecular dynamics simulations, we demonstrate how peptide passage through the α-hemolysin protein can be sufficiently slowed down to observe intermediate single-peptide sub-states associated to distinct structural milestones along the pore, and how to control residence time, direction and the sequence of spatio-temporal state-to-state dynamics of a single peptide. Molecular dynamics simulations of peptide translocation reveal the time- dependent ordering of intermediate structures of the translocating peptide inside the pore at atomic resolution. Calculations of the expected current ratios of the different pore-blocking microstates and their time sequencing are in accord with the recorded current traces.

The Incremental Multiresolution Matrix Factorization Algorithm

PubMed Central

Ithapu, Vamsi K.; Kondor, Risi; Johnson, Sterling C.; Singh, Vikas

2017-01-01

Multiresolution analysis and matrix factorization are foundational tools in computer vision. In this work, we study the interface between these two distinct topics and obtain techniques to uncover hierarchical block structure in symmetric matrices – an important aspect in the success of many vision problems. Our new algorithm, the incremental multiresolution matrix factorization, uncovers such structure one feature at a time, and hence scales well to large matrices. We describe how this multiscale analysis goes much farther than what a direct “global” factorization of the data can identify. We evaluate the efficacy of the resulting factorizations for relative leveraging within regression tasks using medical imaging data. We also use the factorization on representations learned by popular deep networks, providing evidence of their ability to infer semantic relationships even when they are not explicitly trained to do so. We show that this algorithm can be used as an exploratory tool to improve the network architecture, and within numerous other settings in vision. PMID:29416293

Correlation of ash-flow tuffs.

USGS Publications Warehouse

Hildreth, W.; Mahood, G.

1985-01-01

Discrimination and correlation of ash-flow sheets is important in structurally complex, long-lived volcanic fields where such sheets provide the best keys to the regional stratigraphic framework. Three-dimensional complexities resulting from pulsatory eruptions, sectorial emplacement, mechanical sorting during outflow, thermal and compositional zoning of magmas, the physical zoning of cooling units, and structural and erosional disruption can make such correlation and discrimination difficult. When lithologic, magnetic, petrographic, chemical, and isotopic criteria for correlating ash-flow sheets are critically evaluated, many problems and pitfalls can be identified. Distinctive phenocrysts, pumice clasts, and lithic fragments are among the more reliable criteria, as are high-precision K-Ar ages and thermal remanent magnetization (TRM) directions in unaltered welded tuff. Chemical correlation methods should rely principally upon welded or nonwelded pumice blocks, not upon the ash-flow matrix, which is subject to fractionation, mixing, and contamination during emplacement. Compositional zoning of most large sheets requires that many samples be analyzed before phenocryst, glass or whole-rock chemical trends can be used confidently as correlation criteria.-Authors

Phase Behavior of a Single Structured Ionomer Chain in Solution

DOE PAGES

Aryal, Dipak; Etampawala, Thusitha; Perahia, Dvora; ...

2014-08-14

Structured polymers offer a means to tailor transport pathways within mechanically stable manifolds. Here we examine the building block of such a membrane, namely a single large pentablock co-polymer that consist of a center block of a randomly sulfonated polystyrene, designed for transport, tethered to poly-ethylene-r-propylene and end-capped by poly-t-butyl styrene, for mechanical stability,using molecular dynamics simulations. The polymer structure in a cyclohexane-heptane mixture, a technologically viable solvent, and in water, a poor solvent for all segments and a ubiquitous substance is extracted. In all solvents the pentablock collapsed into nearly spherical aggregates where the ionic block is segregated. Inmore » hydrophobic solvents, the ionic block resides in the center, surrounded by swollen intermix of flexible and end blocks. In water all blocks are collapsed with the sulfonated block residing on the surface. Our results demonstrate that solvents drive different local nano-segregation, providing a gateway to assemble membranes with controlled topology.« less

Identification of an antagonist that selectively blocks the activity of prostamides (prostaglandin-ethanolamides) in the feline iris

PubMed Central

Woodward, D F; Krauss, A H; Wang, J W; Protzman, C E; Nieves, A L; Liang, Y; Donde, Y; Burk, R M; Landsverk, K; Struble, C

2006-01-01

Background and Purpose: The prostamides (prostaglandin-ethanolamides) and prostaglandin (PG) glyceryl esters are biosynthesized by COX-2 from the respective endocannabinoids anandamide and 2-arachidonyl glycerol. Agonist studies suggest that their pharmacologies are unique and unrelated to prostanoid receptors. This concept was further investigated using antagonists. Experimental Approach: The isolated feline iris was used as a key preparation, where prostanoid FP receptors and prostamide activity co-exist. Activity at human recombinant FP and other prostanoid receptors was determined using stable transfectants. Key Results: In the feline iris, AGN 204396 produced a rightward shift of the dose-response curves for prostamide F2α and the prostamide F2α analog bimatoprost but did not block the effects of PGF2α and synthetic FP receptor agonists. Studies on human recombinant prostanoid receptors confirmed that AGN 204396 did not behave as a prostanoid FP receptor antagonist. AGN 204396 exhibited no antagonism at DP and EP1-4, but was a highly effective TP receptor antagonist. Contrary to expectation, the FP receptor antagonist AL-8810 efficaciously contracted the cat iris. AGN 204396 did not affect AL-8810 induced contractions, demonstrating that AL-8810 and AGN 204396 are pharmacologically distinct. Unlike AL-8810, the ethylamide derivate of AL-8810 was not an agonist. Al-8810 did not block prostamide F2α activity. Finally, AGN 204396 did not block PGE2-glyceryl ester activity. Conclusions and Implications: The ability of AGN 204396 to selectively block prostamide responses suggests the existence of prostamide sensitive receptors as entities distinct from receptors recognizing PGF2α and PGE2-glyceryl ester. PMID:17179945

Coastal protection using topological interlocking blocks

NASA Astrophysics Data System (ADS)

Pasternak, Elena; Dyskin, Arcady; Pattiaratchi, Charitha; Pelinovsky, Efim

2013-04-01

The coastal protection systems mainly rely on the self-weight of armour blocks to ensure its stability. We propose a system of interlocking armour blocks, which form plate-shape assemblies. The shape and the position of the blocks are chosen in such a way as to impose kinematic constraints that prevent the blocks from being removed from the assembly. The topological interlocking shapes include simple convex blocks such as platonic solids, the most practical being tetrahedra, cubes and octahedra. Another class of topological interlocking blocks is so-called osteomorphic blocks, which form plate-like assemblies tolerant to random block removal (almost 25% of blocks need to be removed for the assembly to loose integrity). Both classes require peripheral constraint, which can be provided either by the weight of the blocks or post-tensioned internal cables. The interlocking assemblies provide increased stability because lifting one block involves lifting (and bending) the whole assembly. We model the effect of interlocking by introducing an equivalent additional self-weight of the armour blocks. This additional self-weight is proportional to the critical pressure needed to cause bending of the interlocking assembly when it loses stability. Using beam approximation we find an equivalent stability coefficient for interlocking. It is found to be greater than the stability coefficient of a structure with similar blocks without interlocking. In the case when the peripheral constraint is provided by the weight of the blocks and for the slope angle of 45o, the effective stability coefficient for a structure of 100 blocks is 33% higher than the one for a similar structure without interlocking. Further increase in the stability coefficient can be reached by a specially constructed peripheral constraint system, for instance by using post-tension cables.

Mechanistic insights for block copolymer morphologies: how do worms form vesicles?

PubMed

Blanazs, Adam; Madsen, Jeppe; Battaglia, Giuseppe; Ryan, Anthony J; Armes, Steven P

2011-10-19

Amphiphilic diblock copolymers composed of two covalently linked, chemically distinct chains can be considered to be biological mimics of cell membrane-forming lipid molecules, but with typically more than an order of magnitude increase in molecular weight. These macromolecular amphiphiles are known to form a wide range of nanostructures (spheres, worms, vesicles, etc.) in solvents that are selective for one of the blocks. However, such self-assembly is usually limited to dilute copolymer solutions (<1%), which is a significant disadvantage for potential commercial applications such as drug delivery and coatings. In principle, this problem can be circumvented by polymerization-induced block copolymer self-assembly. Here we detail the synthesis and subsequent in situ self-assembly of amphiphilic AB diblock copolymers in a one pot concentrated aqueous dispersion polymerization formulation. We show that spherical micelles, wormlike micelles, and vesicles can be predictably and efficiently obtained (within 2 h of polymerization, >99% monomer conversion) at relatively high solids in purely aqueous solution. Furthermore, careful monitoring of the in situ polymerization by transmission electron microscopy reveals various novel intermediate structures (including branched worms, partially coalesced worms, nascent bilayers, "octopi", "jellyfish", and finally pure vesicles) that provide important mechanistic insights regarding the evolution of the particle morphology during the sphere-to-worm and worm-to-vesicle transitions. This environmentally benign approach (which involves no toxic solvents, is conducted at relatively high solids, and requires no additional processing) is readily amenable to industrial scale-up, since it is based on commercially available starting materials.

Gyroid structure via highly asymmetric ABC and AB blends

NASA Astrophysics Data System (ADS)

Ahn, Seonghyeon; Kwak, Jongheon; Choi, Chungryong; Kim, Jin Kon

Gyroid structures are very important because of their co-continuous and network structures. However, a block copolymer shows gyroid structures only at 35 % volume fraction of one block. In this study, we designed ABC/AB blend system. B (polystyrene (PS)) is the matrix, while A (polyisoprene (PI)) and C (poly(2-vinyl pridine (P2VP)) are the core part. This blend shows gyroid structures at 20 % volume fraction, that is smaller than that observed at diblock copolymer. Morphologies of neat block copolymers and blends were characterized by TEM and small angle X-ray scattering.

Neural correlates of differential retrieval orientation: Sustained and item-related components.

PubMed

Woodruff, C Chad; Uncapher, Melina R; Rugg, Michael D

2006-01-01

Retrieval orientation refers to a cognitive state that biases processing of retrieval cues in service of a specific goal. The present study used a mixed fMRI design to investigate whether adoption of different retrieval orientations - as indexed by differences in the activity elicited by retrieval cues corresponding to unstudied items - is associated with differences in the state-related activity sustained across a block of test trials sharing a common retrieval goal. Subjects studied mixed lists comprising visually presented words and pictures. They then undertook a series of short test blocks in which all test items were visually presented words. The blocks varied according to whether the test items were used to cue retrieval of studied words or studied pictures. In several regions, neural activity elicited by correctly classified new items differed according to whether words or pictures were the targeted material. The loci of these effects suggest that one factor driving differential cue processing is modulation of the degree of overlap between cue and targeted memory representations. In addition to these item-related effects, neural activity sustained throughout the test blocks also differed according to the nature of the targeted material. These findings indicate that the adoption of different retrieval orientations is associated with distinct neural states. The loci of these sustained effects were distinct from those where new item activity varied, suggesting that the effects may play a role in biasing retrieval cue processing in favor of the current retrieval goal.

A province-scale block model of Walker Lane and western Basin and Range crustal deformation constrained by GPS observations (Invited)

NASA Astrophysics Data System (ADS)

Hammond, W. C.; Bormann, J.; Blewitt, G.; Kreemer, C.

2013-12-01

The Walker Lane in the western Great Basin of the western United States is an 800 km long and 100 km wide zone of active intracontinental transtension that absorbs ~10 mm/yr, about 20% of the Pacific/North America plate boundary relative motion. Lying west of the Sierra Nevada/Great Valley microplate (SNGV) and adjoining the Basin and Range Province to the east, deformation is predominantly shear strain overprinted with a minor component of extension. The Walker Lane responds with faulting, block rotations, structural step-overs, and has distinct and varying partitioned domains of shear and extension. Resolving these complex deformation patterns requires a long term observation strategy with a dense network of GPS stations (spacing ~20 km). The University of Nevada, Reno operates the 373 station Mobile Array of GPS for Nevada transtension (MAGNET) semi-continuous network that supplements coverage by other networks such as EarthScope's Plate Boundary Observatory, which alone has insufficient density to resolve the deformation patterns. Uniform processing of data from these GPS mega-networks provides a synoptic view and new insights into the kinematics and mechanics of Walker Lane tectonics. We present velocities for thousands of stations with time series between 3 to 17 years in duration aligned to our new GPS-based North America fixed reference frame NA12. The velocity field shows a rate budget across the southern Walker Lane of ~10 mm/yr, decreasing northward to ~7 mm/yr at the latitude of the Mohawk Valley and Pyramid Lake. We model the data with a new block model that estimates rotations and slip rates of known active faults between the Mojave Desert and northern Nevada and northeast California. The density of active faults in the region requires including a relatively large number of blocks in the model to accurately estimate deformation patterns. With 49 blocks, our the model captures structural detail not represented in previous province-scale models, and improves our ability to compare results to geologic fault slip rates. Modeling the kinematics on this scale has the advantages of 1) reducing the impact of poorly constrained boundaries on small geographically limited models, 2) consistent modeling of rotations across major structural step-overs near the Mina deflection and Carson domain, 3) tracking the kinematics of the south-to-north varying budget of Walker Lane deformation by solving for extension in the Basin and Range to the east, and 4) using a contiguous SNGV as a uniform western kinematic boundary condition. We compare contemporary deformation to geologic slip rates and longer term rotation rates estimated from rock paleomagnetism. GPS-derived block rotation rates are somewhat dependent on model regularization, but are generally within 1° per million years, and tend to be slower than published paleomagnetic rotations rates. GPS data, together with neotectonic and rock paleomagnetism studies provide evidence that the relative importance of Walker Lane block rotations and fault slip continues to evolve, giving way to a more through-going system with slower rotation rates and higher slip rates on individual faults.

Structuralism, Post-Structuralism, and Neo-Liberalism: Assessing Foucault's Legacy.

ERIC Educational Resources Information Center

Olssen, Mark

2003-01-01

Traces Foucault's distinctive commitment to "post-structuralism." Argues that under the influence of Nietzsche, Foucault's approach marks a distinct break with structuralism in several crucial aspects. What results is a materialist post-structuralism that is also distinctively different from the post-structuralism of Derrida, Lyotard,…

Geological History of the Tyre Region of Europa: A Regional Perspective on Europan Surface Features and Ice Thickness

NASA Technical Reports Server (NTRS)

Kadel, Steven D.; Chuang, Frank C.; Greeley, Ronald; Moore, Jeffrey M.

2000-01-01

Galileo images of the Tyre Macula region of Europa at regional (170 m/pixel) and local (approx. 40 m/pixel) scales allow mapping and understanding of surface processes and landforms. Ridged plains, doublet and complex ridges, shallow pits, domes, "chaos" areas. impact structures, tilted blocks and massifs, and young fracture systems indicate a complex history of surface deformation on Europa. Regional and local morphologies of the Tyre region of Europa suggest that an impactor penetrated through several kilometers of water ice tc a mobile layer below. The surface morphology was initially dominated by formation of ridged plains, followed by development of ridge bands and doublet ridges, with chaos and fracture formation dominating the latter part of the geologic history of the Tyre region. Two distinct types of chaos have been identified which, along with upwarped dome materials, appear to represent a continuum of features (domes-play chaos-knobby chaos) resulting from increasing degree of surface disruption associated with local lithospheric heating and thinning. Local and regional stratigraphic relationships, block heights, and the morphology of the Tyre impact structure suggest the presence of low-viscosity ice or liquid water beneath a thin (severa1 kilometers) surface ice shell at the time of the impact. The very low impact crater density on the surface of Europa suggests that this thin shell has either formed or been thoroughly resurfaced in the very recent past.

RNA self-assembly and RNA nanotechnology.

PubMed

Grabow, Wade W; Jaeger, Luc

2014-06-17

CONSPECTUS: Nanotechnology's central goal involves the direct control of matter at the molecular nanometer scale to build nanofactories, nanomachines, and other devices for potential applications including electronics, alternative fuels, and medicine. In this regard, the nascent use of nucleic acids as a material to coordinate the precise arrangements of specific molecules marked an important milestone in the relatively recent history of nanotechnology. While DNA served as the pioneer building material in nucleic acid nanotechnology, RNA continues to emerge as viable alternative material with its own distinct advantages for nanoconstruction. Several complementary assembly strategies have been used to build a diverse set of RNA nanostructures having unique structural attributes and the ability to self-assemble in a highly programmable and controlled manner. Of the different strategies, the architectonics approach uniquely endeavors to understand integrated structural RNA architectures through the arrangement of their characteristic structural building blocks. Viewed through this lens, it becomes apparent that nature routinely uses thermodynamically stable, recurrent modular motifs from natural RNA molecules to generate unique and more complex programmable structures. With the design principles found in natural structures, a number of synthetic RNAs have been constructed. The synthetic nanostructures constructed to date have provided, in addition to affording essential insights into RNA design, important platforms to characterize and validate the structural self-folding and assembly properties of RNA modules or building blocks. Furthermore, RNA nanoparticles have shown great promise for applications in nanomedicine and RNA-based therapeutics. Nevertheless, the synthetic RNA architectures achieved thus far consist largely of static, rigid particles that are still far from matching the structural and functional complexity of natural responsive structural elements such as the ribosome, large ribozymes, and riboswitches. Thus, the next step in synthetic RNA design will involve new ways to implement these same types of dynamic and responsive architectures into nanostructures functioning as real nanomachines in and outside the cell. RNA nanotechnology will likely garner broader utility and influence with a greater focus on the interplay between thermodynamic and kinetic influences on RNA self-assembly and using natural RNAs as guiding principles.

Rates and timing of vertical-axis block rotations across the Sierra Nevada-Walker Lane transition in the Bodie Hills

NASA Astrophysics Data System (ADS)

Rood, D. H.; Herman, S.; Burbank, D.; Bogue, S.

2008-12-01

We use paleomagnetic data from Tertiary volcanic rocks to address the rates and timing of vertical-axis block rotation across the Sierra Nevada-Walker Lane transition in the Bodie Hills, California/Nevada. In zones of continental deformation, block rotations are an important mechanism for permanent stain accommodation, and thus may be crucial to testing geodetic block models and resolving geologic-geodetic slip discrepancies. In our study, data included in the paleomagetic site means are high quality AF demagnetization results (least squared fits that generally include 5-7 points with MAD values less than 1). Thermal demagnetization results match the AF directions, and both thermal demag and rockmag results indicate strong ChRM, mostly carried by single domain magnetite. The site means used to calculate the VGPs all have a95 values less than 10 (mostly 2-5) and include 6-11 sites each. Each site (and thus site mean) has a reasonably well-known structural correction. The VGP scatter values range from 12 to 16 degrees, indicating that they include appropriate secular variation. The mean declinations and 95 percent confidence limits for each VGP timeslice are statistically distinct from one another (71 ± 9, 39 ± 13, and 11 ± 11 degrees). The slope of a linear regression fit to the age versus declination data gives a rate of vertical axis block rotation of approximately 3-4 degrees/Myr. Fitting two separate lines to the age vs. declination data would indicate an increase in the rates of rotation since ~10 Ma. Two possible interpretations of the data are: (1) the rotations began during or before the Middle Miocene, or (2) rates of rotation were high initially (e.g. ~10 Ma) and decelerated until the Pliocene. These data have implications for the (1) timing and spatial extent of distributed strain accumulation related to the initiation of the San Andreas Fault-Eastern California Shear Zone-Walker Lane transform plate boundary, (2) transfer of transform plate boundary deformation into the maturing Walker Lane, and (3) the initiation of transtensional block rotations and bounding fault systems.

Comparative study of CAVET with dielectric and p-GaN gate and Mg ion-implanted current blocking layer

NASA Astrophysics Data System (ADS)

Mandal, Saptarshi; Agarwal, Anchal; Ahmadi, Elaheh; Mahadeva Bhat, K.; Laurent, Matthew A.; Keller, Stacia; Chowdhury, Srabanti

2017-08-01

In this work, a study of two different types of current aperture vertical electron transistor (CAVET) with ion-implanted blocking layer are presented. The device fabrication and performance limitation of a CAVET with a dielectric gate is discussed, and the breakdown limiting structure is evaluated using on-wafer test structures. The gate dielectric limited the device breakdown to 50V, while the blocking layer was able to withstand over 400V. To improve the device performance, an alternative CAVET structure with a p-GaN gate instead of dielectric is designed and realized. The pGaN gated CAVET structure increased the breakdown voltage to over 400V. Measurement of test structures on the wafer showed the breakdown was limited by the blocking layer instead of the gate p-n junction.

Sandstone provenance and tectonic evolution of the Xiukang Mélange from Neotethyan subduction to India-Asia collision (Yarlung-Zangbo suture, south Tibet)

NASA Astrophysics Data System (ADS)

An, Wei; Hu, Xiumian; Garzanti, Eduardo

2016-04-01

The Xiukang Mélange of the Yarlung-Zangbo suture zone in south Tibet documents low efficiency of accretion along the southern active margin of Asia during Cretaceous Neotethyan subduction, followed by final development during the early Paleogene stages of the India-Asia collision. Here we investigate four transverses in the Xigaze area (Jiding, Cuola Pass, Riwuqi and Saga), inquiry the composition in each transverse, and present integrated petrologic, U-Pb detrital-zircon geochronology and Hf isotope data on sandstone blocks. In fault contact with the Yarlung-Zangbo Ophiolite to the north and the Tethyan Himalaya to the south, the Xiukang mélange can be divided into three types: serpentinite-matrix mélange composed by broken Yarlung-Zangbo Ophiolite, thrust-sheets consisting mainly chert, quartzose or limestone sheets(>100m) with little intervening marix, and mudstone-matrix mélange displaying typical blocks-in-matrix texture. While serpentinite-matrix mélange is exposed adjacent to the ophiolite, distributions of thrust-sheets and blocks in mudstone-matrix mélange show along-strike diversities. For example, Jiding transverse is dominant by chert sheets and basalt blocks with scarcely sandstone blocks, while Cuola Pass and Saga transverses expose large amounts of limestone/quartzarenite sheets in the north and volcaniclastic blocks in the south. However, turbidite sheets and volcaniclastic blocks are outcropped in the north Riwuqi transverse with quartzarenite blocks preserved in the south. Three groups of sandstone blocks/sheets with different provenance and depositional setting are distinguished by their petrographic, geochronological and isotopic fingerprints. Sheets of turbiditic quartzarenite originally sourced from the Indian continent were deposited in pre-Cretaceous time on the northernmost edge of the Indian passive margin and eventually involved into the mélange at the early stage of the India-Asia collision. Two distinct groups of volcaniclastic-sandstone blocks were derived from the central Lhasa block and Gangdese magmatic arc. One group was deposited in the trench and/or on the trench slope of the Asian margin during the early Late Cretaceous, and the other group in a syn-collisional basin just after the onset of the India-Asia collision in the Early Eocene. The largely erosional character of the Asian active margin in the Late Cretaceous is indicated by the scarcity of off-scraped trench-fill deposits and the relatively small subduction complex developed during limited episodes of accretion. The Xiukang Mélange was finally structured in the Late Paleocene/Eocene, when sandstone of both Indian and Asian origin were progressively incorporated tectonically in the suture zone of the nascent Himalayan Orogen.

East Cameron Block 270, a Pleistocene field

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

Holland, D.S.; Sutley, C.E.; Berlitz, R.E.

1974-01-01

Exploration of the Plio-Pleistocene in the Gulf of Mexico since 1970 has discovered significant hydrocarbon reserves. One of the better gas fields to date has been the Block 270 E. Cameron field. Utilization of a coordinated exploitation plan with Schlumberger has allowed Pennzoil as operator, to develop and put on production the Block 270 field in a minimum time period. Block 270 field is a N.-S. trending faulted nose at 6,000 ft. At G-Sand depth (8,700 ft), the structure has closed, forming an elongated N.-S. structure with dip in all directions from the Block 270 area. Closure is the resultmore » of contemporaneous growth on the E. bounding regional fault. Structural and stratigraphic interpretations from dipmeters were used to help determine the most favorable offset locations.« less

Chain end distribution of block copolymer in two-dimensional microphase-separated structure studied by scanning near-field optical microscopy.

PubMed

Sekine, Ryojun; Aoki, Hiroyuki; Ito, Shinzaburo

2009-10-01

The chain end distribution of a block copolymer in a two-dimensional microphase-separated structure was studied by scanning near-field optical microscopy (SNOM). In the monolayer of poly(octadecyl methacrylate)-block-poly(isobutyl methacrylate) (PODMA-b-PiBMA), the free end of the PiBMA subchain was directly observed by SNOM, and the spatial distributions of the whole block and the chain end are examined and compared with the convolution of the point spread function of the microscope and distribution function of the model structures. It was found that the chain end distribution of the block copolymer confined in two dimensions has a peak near the domain center, being concentrated in the narrower region, as compared with three-dimensional systems.

Dynamics of propagation of premature impulses in structurally remodeled infarcted myocardium: a computational analysis

PubMed Central

Cabo, Candido

2014-01-01

Initiation of cardiac arrhythmias typically follows one or more premature impulses either occurring spontaneously or applied externally. In this study, we characterize the dynamics of propagation of single (S2) and double premature impulses (S3), and the mechanisms of block of premature impulses at structural heterogeneities caused by remodeling of gap junctional conductance (Gj) in infarcted myocardium. Using a sub-cellular computer model of infarcted tissue, we found that |INa,max|, prematurity (coupling interval with the previous impulse), and conduction velocity (CV) of premature impulses change dynamically as they propagate away from the site of initiation. There are fundamental differences between the dynamics of propagation of S2 and S3 premature impulses: for S2 impulses |INa,max| recovers fast, prematurity decreases and CV increases as propagation proceeds; for S3 impulses low values of |INa,max| persist, prematurity could increase, and CV could decrease as impulses propagate away from the site of initiation. As a consequence it is more likely that S3 impulses block at sites of structural heterogeneities causing source/sink mismatch than S2 impulses block. Whether premature impulses block at Gj heterogeneities or not is also determined by the values of Gj (and the space constant λ) in the regions proximal and distal to the heterogeneity: when λ in the direction of propagation increases >40%, premature impulses could block. The maximum slope of CV restitution curves for S2 impulses is larger than for S3 impulses. In conclusion: (1) The dynamics of propagation of premature impulses make more likely that S3 impulses block at sites of structural heterogeneities than S2 impulses block; (2) Structural heterogeneities causing an increase in λ (or CV) of >40% could result in block of premature impulses; (3) A decrease in the maximum slope of CV restitution curves of propagating premature impulses is indicative of an increased potential for block at structural heterogeneities. PMID:25566085

Dynamics of propagation of premature impulses in structurally remodeled infarcted myocardium: a computational analysis.

PubMed

Cabo, Candido

2014-01-01

Initiation of cardiac arrhythmias typically follows one or more premature impulses either occurring spontaneously or applied externally. In this study, we characterize the dynamics of propagation of single (S2) and double premature impulses (S3), and the mechanisms of block of premature impulses at structural heterogeneities caused by remodeling of gap junctional conductance (Gj) in infarcted myocardium. Using a sub-cellular computer model of infarcted tissue, we found that |INa,max|, prematurity (coupling interval with the previous impulse), and conduction velocity (CV) of premature impulses change dynamically as they propagate away from the site of initiation. There are fundamental differences between the dynamics of propagation of S2 and S3 premature impulses: for S2 impulses |INa,max| recovers fast, prematurity decreases and CV increases as propagation proceeds; for S3 impulses low values of |INa,max| persist, prematurity could increase, and CV could decrease as impulses propagate away from the site of initiation. As a consequence it is more likely that S3 impulses block at sites of structural heterogeneities causing source/sink mismatch than S2 impulses block. Whether premature impulses block at Gj heterogeneities or not is also determined by the values of Gj (and the space constant λ) in the regions proximal and distal to the heterogeneity: when λ in the direction of propagation increases >40%, premature impulses could block. The maximum slope of CV restitution curves for S2 impulses is larger than for S3 impulses. (1) The dynamics of propagation of premature impulses make more likely that S3 impulses block at sites of structural heterogeneities than S2 impulses block; (2) Structural heterogeneities causing an increase in λ (or CV) of >40% could result in block of premature impulses; (3) A decrease in the maximum slope of CV restitution curves of propagating premature impulses is indicative of an increased potential for block at structural heterogeneities.

Initial Mechanical Testing of Superalloy Lattice Block Structures Conducted

NASA Technical Reports Server (NTRS)

Krause, David L.; Whittenberger, J. Daniel

2002-01-01

The first mechanical tests of superalloy lattice block structures produced promising results for this exciting new lightweight material system. The testing was performed in-house at NASA Glenn Research Center's Structural Benchmark Test Facility, where small subelement-sized compression and beam specimens were loaded to observe elastic and plastic behavior, component strength levels, and fatigue resistance for hundreds of thousands of load cycles. Current lattice block construction produces a flat panel composed of thin ligaments arranged in a three-dimensional triangulated trusslike structure. Investment casting of lattice block panels has been developed and greatly expands opportunities for using this unique architecture in today's high-performance structures. In addition, advances made in NASA's Ultra-Efficient Engine Technology Program have extended the lattice block concept to superalloy materials. After a series of casting iterations, the nickel-based superalloy Inconel 718 (IN 718, Inco Alloys International, Inc., Huntington, WV) was successfully cast into lattice block panels; this combination offers light weight combined with high strength, high stiffness, and elevated-temperature durability. For tests to evaluate casting quality and configuration merit, small structural compression and bend test specimens were machined from the 5- by 12- by 0.5-in. panels. Linear elastic finite element analyses were completed for several specimen layouts to predict material stresses and deflections under proposed test conditions. The structural specimens were then subjected to room-temperature static and cyclic loads in Glenn's Life Prediction Branch's material test machine. Surprisingly, the test results exceeded analytical predictions: plastic strains greater than 5 percent were obtained, and fatigue lives did not depreciate relative to the base material. These assets were due to the formation of plastic hinges and the redundancies inherent in lattice block construction, which were not considered in the simplified computer models. The fatigue testing proved the value of redundancies since specimen strength was maintained even after the fracture of one or two ligaments. This ongoing test program is planned to continue through high-temperature testing. Also scheduled for testing are IN 718 lattice block panels with integral face sheets, as well as specimens cast from a higher temperature alloy. The initial testing suggests the value of this technology for large panels under low and moderate pressure loadings and for high-risk, damage-tolerant structures. Potential aeropropulsion uses for lattice blocks include turbine-engine actuated panels, exhaust nozzle flaps, and side panel structures.

Agar Block Smear Preparation: a Novel Method of Slide Preparation for Preservation of Native Fungal Structures for Microscopic Examination and Long-Term Storage▿

PubMed Central

Woo, Patrick C. Y.; Ngan, Antonio H. Y.; Chui, Hon-Kit; Lau, Susanna K. P.; Yuen, Kwok-Yung

2010-01-01

We describe a novel method of fungal slide preparation named “agar block smear preparation.” A total of 510 agar block smears of 25 fungal strains obtained from culture collections, 90 QC fungal strains, and 82 clinical fungal strains from our clinical microbiology laboratory, which included a total of 137 species of yeasts, molds, and thermal dimorphic fungi, were prepared and examined. In contrast to adhesive tape preparation, agar block smears preserved the native fungal structures, such as intact conidiophores of Aspergillus species and arrangements of conidia in Scopulariopsis brevicaulis. Furthermore, agar block smears allowed examination of fungal structures embedded in the agar, such as the ascomata with ascomal hairs in Chaetomium funicola; pycnidium of Phoma glomerata; the intercalary ovoidal chlamydospores arranged in chains of Fusarium dimerum; and the lateral, spherical chlamydospores arranged in pairs of Fusarium solani. After 1 year of storage, morphological integrity was found to have been maintained in 459 (90%) of the 510 agar block smears. After 3 years of storage, morphological integrity was found to have been maintained in 72 (71%) of the 102 smears prepared in 2006. Agar block smear preparation preserves the native fungal structures and allows long-term storage and examination of fungal structures embedded in the agar, hence overcoming the major drawbacks of adhesive tape preparation. The major roles of agar block smear should be diagnosis for difficult cases, accurate identification of fungal species for clinical management of patients and epidemiological studies, and long-term storage for transportation of slides and education purposes. PMID:20660221

Agar block smear preparation: a novel method of slide preparation for preservation of native fungal structures for microscopic examination and long-term storage.

PubMed

Woo, Patrick C Y; Ngan, Antonio H Y; Chui, Hon-Kit; Lau, Susanna K P; Yuen, Kwok-Yung

2010-09-01

We describe a novel method of fungal slide preparation named "agar block smear preparation." A total of 510 agar block smears of 25 fungal strains obtained from culture collections, 90 QC fungal strains, and 82 clinical fungal strains from our clinical microbiology laboratory, which included a total of 137 species of yeasts, molds, and thermal dimorphic fungi, were prepared and examined. In contrast to adhesive tape preparation, agar block smears preserved the native fungal structures, such as intact conidiophores of Aspergillus species and arrangements of conidia in Scopulariopsis brevicaulis. Furthermore, agar block smears allowed examination of fungal structures embedded in the agar, such as the ascomata with ascomal hairs in Chaetomium funicola; pycnidium of Phoma glomerata; the intercalary ovoidal chlamydospores arranged in chains of Fusarium dimerum; and the lateral, spherical chlamydospores arranged in pairs of Fusarium solani. After 1 year of storage, morphological integrity was found to have been maintained in 459 (90%) of the 510 agar block smears. After 3 years of storage, morphological integrity was found to have been maintained in 72 (71%) of the 102 smears prepared in 2006. Agar block smear preparation preserves the native fungal structures and allows long-term storage and examination of fungal structures embedded in the agar, hence overcoming the major drawbacks of adhesive tape preparation. The major roles of agar block smear should be diagnosis for difficult cases, accurate identification of fungal species for clinical management of patients and epidemiological studies, and long-term storage for transportation of slides and education purposes.

Detecting dominant motion patterns in crowds of pedestrians

NASA Astrophysics Data System (ADS)

Saqib, Muhammad; Khan, Sultan Daud; Blumenstein, Michael

2017-02-01

As the population of the world increases, urbanization generates crowding situations which poses challenges to public safety and security. Manual analysis of crowded situations is a tedious job and usually prone to errors. In this paper, we propose a novel technique of crowd analysis, the aim of which is to detect different dominant motion patterns in real-time videos. A motion field is generated by computing the dense optical flow. The motion field is then divided into blocks. For each block, we adopt an Intra-clustering algorithm for detecting different flows within the block. Later on, we employ Inter-clustering for clustering the flow vectors among different blocks. We evaluate the performance of our approach on different real-time videos. The experimental results show that our proposed method is capable of detecting distinct motion patterns in crowded videos. Moreover, our algorithm outperforms state-of-the-art methods.

Constraints Imposed by Rift Inheritance on the Compressional Reactivation of a Hyperextended Margin: Mapping Rift Domains in the North Iberian Margin and in the Cantabrian Mountains

NASA Astrophysics Data System (ADS)

Cadenas, P.; Fernández-Viejo, G.; Pulgar, J. A.; Tugend, J.; Manatschal, G.; Minshull, T. A.

2018-03-01

The Alpine Pyrenean-Cantabrian orogen developed along the plate boundary between Iberia and Europe, involving the inversion of Mesozoic hyperextended basins along the southern Biscay margin. Thus, this margin represents a natural laboratory to analyze the control of structural rift inheritance on the compressional reactivation of a continental margin. With the aim to identify former rift domains and investigate their role during the subsequent compression, we performed a structural analysis of the central and western North Iberian margin, based on the interpretation of seismic reflection profiles and local constraints from drill-hole data. Seismic interpretations and published seismic velocity models enabled the development of crustal thickness maps that helped to constrain further the offshore and onshore segmentation. Based on all these constraints, we present a rift domain map across the central and western North Iberian margin, as far as the adjacent western Cantabrian Mountains. Furthermore, we provide a first-order description of the margin segmentation resulting from its polyphase tectonic evolution. The most striking result is the presence of a hyperthinned domain (e.g., Asturian Basin) along the central continental platform that is bounded to the north by the Le Danois High, interpreted as a rift-related continental block separating two distinctive hyperextended domains. From the analysis of the rift domain map and the distribution of reactivation structures, we conclude that the landward limit of the necking domain and the hyperextended domains, respectively, guide and localize the compressional overprint. The Le Danois block acted as a local buttress, conditioning the inversion of the Asturian Basin.

The crustal structure of Ellesmere Island, Arctic Canada—teleseismic mapping across a remote intraplate orogenic belt

NASA Astrophysics Data System (ADS)

Schiffer, Christian; Stephenson, Randell; Oakey, Gordon N.; Jacobsen, Bo H.

2016-03-01

Ellesmere Island in Arctic Canada displays a complex geological evolution. The region was affected by two distinct orogenies, the Palaeozoic Ellesmerian orogeny (the Caledonian equivalent in Arctic Canada and Northern Greenland) and the Palaeogene Eurekan orogeny, related to the opening of Baffin Bay and the consequent convergence of the Greenland plate. The details of this complex evolution and the present-day deep structure are poorly constrained in this remote area and deep geophysical data are sparse. Receiver function analysis of seven temporary broad-band seismometers of the Ellesmere Island Lithosphere Experiment complemented by two permanent stations provides important data on the crustal velocity structure of Ellesmere Island. The crustal expression of the northernmost tectonic block of Ellesmere Island (˜82°-83°N), Pearya, which was accreted during the Ellesmerian orogeny, is similar to that at the southernmost part, which is part of the Precambrian Laurentian (North America-Greenland) craton. Both segments have thick crystalline crust (˜35-36 km) and comparable velocity-depth profiles. In contrast, crustal thickness in central Ellesmere Island decreases from ˜24-30 km in the Eurekan fold and thrust belt (˜79.7°-80.6°N) to ˜16-20 km in the Hazen Stable Block (HSB; ˜80.6°-81.4°N) and is covered by a thick succession of metasediments. A deep crustal root (˜48 km) at ˜79.6°N is interpreted as cratonic crust flexed beneath the Eurekan fold and thrust belt. The Carboniferous to Palaeogene sedimentary succession of the Sverdrup Basin is inferred to be up to 1-4 km thick, comparable to geologically-based estimates, near the western margin of the HSB.

Kinematic Model for the Sierra Nevada Frontal Fault Zone, California: Paleomagnetism of the Eureka Valley Tuff

NASA Astrophysics Data System (ADS)

Rood, D. H.; Burbank, D. W.; Luyendyk, B. P.

2005-12-01

We document the geometry, timing, rates, and kinematic style of Late Tertiary deformation between Sonora Pass and Mono Basin, central Sierra Nevada, California. Observed mismatches between geodetic and geologic deformation rates in the western Great Basin may be primarily due to underestimates of true geologic deformation. Relatively little attention has been paid to the role of permanent deformation between faults, i.e. folding or crustal block rotation. Current slip discrepancies may be accounted for if a significant component of off-fault transrotational deformation is present. We use geologic and paleomagnetic data to address the kinematic development of the Sierra Nevada frontal fault zone (SNFFZ), and to quantify both the elastic and inelastic strain accumulated across the Sierra Nevada-Basin and Range transition since ~9 Ma. The complex structure of this transition, between the regions of Sonora Pass and Mono Basin, may be a result of three distinct modes of dextral shear accommodation (transtensional, transpressional, and crustal thinning). The study area is characterized by four important structural elements that lie between the SNFFZ and Walker Lane Belt: (1) N- to NNW-striking normal and oblique faults, dominantly E-dipping, and associated W-tilted fault blocks; (2) NW-striking dextral faults; (3) ENE- to NE-striking left-lateral oblique faults that may accommodate overall dextral shear through clockwise vertical axis rotations of fault blocks; (4) E- to NE-trending folds, which may accommodate N-S shortening at large-scale left steps in the dextral transtensional fault system. Between Bridgeport and Mono Basins, a regional E- to NE-trending fold is present that affects both the Tertiary volcanic strata and a Quaternary glacial outwash surface. To the west, normal faulting rates on the SNFFZ are 1-2 mm/yr (Bursik and Sieh, 1989). This slip decreases to the north, into the folded region of the Bodie Hills. This kinematic relationship suggests that the region may be an accommodation zone between two linking faults, possibly an active fold that accommodates N-S shortening at a large-scale left step in the range front fault system. We collected ~200 paleomagnetic samples from the Late Miocene Eureka Valley Tuff of the Stanislaus Group at 21 sites over a 125-km-long, E-W transect (from the Sierra Nevada foothills to east of Mono Basin). Stepwise AF demagnetization reveals a stable characteristic remnant magnetization. Our preliminary data suggest 20-40 degrees of clockwise rotation adjacent to faults of the SNFFZ. An expanded dataset aims to identify specific structural domains, quantify differential vertical axis block rotations, and test geometric models of transrotation (i.e. block-specific versus gradational) during transtensional lithospheric deformation.

Fast Detection of Material Deformation through Structural Dissimilarity

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

Ushizima, Daniela; Perciano, Talita; Parkinson, Dilworth

2015-10-29

Designing materials that are resistant to extreme temperatures and brittleness relies on assessing structural dynamics of samples. Algorithms are critically important to characterize material deformation under stress conditions. Here, we report on our design of coarse-grain parallel algorithms for image quality assessment based on structural information and on crack detection of gigabyte-scale experimental datasets. We show how key steps can be decomposed into distinct processing flows, one based on structural similarity (SSIM) quality measure, and another on spectral content. These algorithms act upon image blocks that fit into memory, and can execute independently. We discuss the scientific relevance of themore » problem, key developments, and decomposition of complementary tasks into separate executions. We show how to apply SSIM to detect material degradation, and illustrate how this metric can be allied to spectral analysis for structure probing, while using tiled multi-resolution pyramids stored in HDF5 chunked multi-dimensional arrays. Results show that the proposed experimental data representation supports an average compression rate of 10X, and data compression scales linearly with the data size. We also illustrate how to correlate SSIM to crack formation, and how to use our numerical schemes to enable fast detection of deformation from 3D datasets evolving in time.« less

X-ray structure of the dopamine transporter in complex with tricyclic antidepressant

PubMed Central

Penmatsa, Aravind; Wang, Kevin H.; Gouaux, Eric

2013-01-01

Antidepressants targeting Na+/Cl−-coupled neurotransmitter uptake define a major therapeutic strategy to treat clinical depression and neuropathic pain. However, identifying the molecular interactions that underlie the pharmacological activity of these transport inhibitors and thus the mechanism by which the inhibitors lead to increased synaptic neurotransmitter levels has proven elusive. Here we present the crystal structure of the Drosophila melanogaster dopamine transporter (dDAT) at 3.0 Å resolution bound to the tricyclic antidepressant nortriptyline. The transporter is locked in an outward-open conformation with nortriptyline wedged between TMs1/6 and 3/8, blocking the transporter from binding substrate and from isomerizing to an inward facing conformation. While the overall structure of dDAT is similar to that of its prokaryotic relative LeuT, there are multiple distinctions that include a kink in TM12 halfway across the membrane bilayer, a latch-like C-terminal helix that caps the cytoplasmic gate, and a cholesterol molecule wedged within a groove formed by TMs 1a, 5 and 7. Taken together, the dDAT structure reveals the molecular basis for antidepressant action on sodium-coupled neurotransmitter symporters and illuminates critical elements of eukaryotic transporter structure and modulation by lipids, thus expanding our understanding of mechanism and regulation of neurotransmitter uptake at chemical synapses. PMID:24037379

Osmosis and thermodynamics explained by solute blocking.

PubMed

Nelson, Peter Hugo

2017-01-01

A solute-blocking model is presented that provides a kinetic explanation of osmosis and ideal solution thermodynamics. It validates a diffusive model of osmosis that is distinct from the traditional convective flow model of osmosis. Osmotic equilibrium occurs when the fraction of water molecules in solution matches the fraction of pure water molecules that have enough energy to overcome the pressure difference. Solute-blocking also provides a kinetic explanation for why Raoult's law and the other colligative properties depend on the mole fraction (but not the size) of the solute particles, resulting in a novel kinetic explanation for the entropy of mixing and chemical potential of ideal solutions. Some of its novel predictions have been confirmed; others can be tested experimentally or by simulation.

Osmosis and thermodynamics explained by solute blocking

PubMed Central

Nelson, Peter Hugo

2016-01-01

A solute-blocking model is presented that provides a kinetic explanation of osmosis and ideal solution thermodynamics. It validates a diffusive model of osmosis that is distinct from the traditional convective flow model of osmosis. Osmotic equilibrium occurs when the fraction of water molecules in solution matches the fraction of pure water molecules that have enough energy to overcome the pressure difference. Solute-blocking also provides a kinetic explanation for why Raoult’s law and the other colligative properties depend on the mole fraction (but not the size) of the solute particles, resulting in a novel kinetic explanation for the entropy of mixing and chemical potential of ideal solutions. Some of its novel predictions have been confirmed, others can be tested experimentally or by simulation. PMID:27225298

Fire Protection Specialist, Blocks IV and V, 17-3. Military Curriculum Materials for Vocational and Technical Education.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus. National Center for Research in Vocational Education.

This military-developed text contains the fourth and fifth blocks of a five-block course for use in training fire protection specialists. Covered in the individual volumes are the following topics: structural firefighting (operation and maintenance of hydrants, emergency response activities, structural pumpers, vehicle positioning and relay, hose…

Sandblasting may damage the surface of composite CAD-CAM blocks.

PubMed

Yoshihara, Kumiko; Nagaoka, Noriyuki; Maruo, Yukinori; Nishigawa, Goro; Irie, Masao; Yoshida, Yasuhiro; Van Meerbeek, Bart

2017-03-01

CAD-CAM blocks to fabricate semi-direct and indirect restorations are available in different sorts of ceramics as well as composite. In order to bond restorations prepared out of composite blocks into tooth cavities, it is recommended to gently sandblast the surface prior to the application of a primer/adhesive. Today, the effect of sandblasting composite block surfaces has not thoroughly been investigated. In this study, the ultra-structure of composite CAD-CAM blocks was investigated with special attention to the effect of sandblasting on the surface topography and of silanization on the bonding performance. Five different composite CAD-CAM blocks were involved. We correlatively investigated their structural and chemical composition using X-ray diffraction (XRD), energy dispersion spectroscopy (EDS), scanning electron microscopy (SEM) and (scanning) transmission electron microscopy ((S)TEM). The effect of sandblasting was also imaged in cross-section and at the interface with composite cement. Finally, we measured the shear bond strength to the sandblasted block surface with and without silanization. All composite blocks revealed a different ultra-structure. Sandblasting increased surface roughness and resulted in an irregular surface with some filler exposure. Sandblasting also damaged the surface. When the sandblasted composite blocks were silanized, superior bonding receptiveness in terms of higher bond strength was achieved except for Shofu Block HC. Sandblasting followed by silanization improved the bond strength to composite CAD-CAM blocks. However, sandblasting may also damage the composite CAD-CAM block surface. For the composite CAD-CAM block Shofu Block HC, the damage was so severe that silanization did not improve bond strength. Copyright © 2016 The Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure

PubMed Central

Basu, Analabha; Sarkar-Roy, Neeta; Majumder, Partha P.

2016-01-01

India, occupying the center stage of Paleolithic and Neolithic migrations, has been underrepresented in genome-wide studies of variation. Systematic analysis of genome-wide data, using multiple robust statistical methods, on (i) 367 unrelated individuals drawn from 18 mainland and 2 island (Andaman and Nicobar Islands) populations selected to represent geographic, linguistic, and ethnic diversities, and (ii) individuals from populations represented in the Human Genome Diversity Panel (HGDP), reveal four major ancestries in mainland India. This contrasts with an earlier inference of two ancestries based on limited population sampling. A distinct ancestry of the populations of Andaman archipelago was identified and found to be coancestral to Oceanic populations. Analysis of ancestral haplotype blocks revealed that extant mainland populations (i) admixed widely irrespective of ancestry, although admixtures between populations was not always symmetric, and (ii) this practice was rapidly replaced by endogamy about 70 generations ago, among upper castes and Indo-European speakers predominantly. This estimated time coincides with the historical period of formulation and adoption of sociocultural norms restricting intermarriage in large social strata. A similar replacement observed among tribal populations was temporally less uniform. PMID:26811443

Extrapunitive and intropunitive individuals activate different parts of the prefrontal cortex under an ego-blocking frustration.

PubMed

Minamoto, Takehiro; Osaka, Mariko; Yaoi, Ken; Osaka, Naoyuki

2014-01-01

Different people make different responses when they face a frustrating situation: some punish others (extrapunitive), while others punish themselves (intropunitive). Few studies have investigated the neural structures that differentiate extrapunitive and intropunitive individuals. The present fMRI study explored these neural structures using two different frustrating situations: an ego-blocking situation which blocks a desire or goal, and a superego-blocking situation which blocks self-esteem. In the ego-blocking condition, the extrapunitive group (n = 9) showed greater activation in the bilateral ventrolateral prefrontal cortex, indicating that these individuals prefer emotional processing. On the other hand, the intropunitive group (n = 9) showed greater activation in the left dorsolateral prefrontal cortex, possibly reflecting an effortful control for anger reduction. Such patterns were not observed in the superego-blocking condition. These results indicate that the prefrontal cortex is the source of individual differences in aggression direction in the ego-blocking situation.

Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci.

PubMed

Schardl, Christopher L; Young, Carolyn A; Hesse, Uljana; Amyotte, Stefan G; Andreeva, Kalina; Calie, Patrick J; Fleetwood, Damien J; Haws, David C; Moore, Neil; Oeser, Birgitt; Panaccione, Daniel G; Schweri, Kathryn K; Voisey, Christine R; Farman, Mark L; Jaromczyk, Jerzy W; Roe, Bruce A; O'Sullivan, Donal M; Scott, Barry; Tudzynski, Paul; An, Zhiqiang; Arnaoudova, Elissaveta G; Bullock, Charles T; Charlton, Nikki D; Chen, Li; Cox, Murray; Dinkins, Randy D; Florea, Simona; Glenn, Anthony E; Gordon, Anna; Güldener, Ulrich; Harris, Daniel R; Hollin, Walter; Jaromczyk, Jolanta; Johnson, Richard D; Khan, Anar K; Leistner, Eckhard; Leuchtmann, Adrian; Li, Chunjie; Liu, JinGe; Liu, Jinze; Liu, Miao; Mace, Wade; Machado, Caroline; Nagabhyru, Padmaja; Pan, Juan; Schmid, Jan; Sugawara, Koya; Steiner, Ulrike; Takach, Johanna E; Tanaka, Eiji; Webb, Jennifer S; Wilson, Ella V; Wiseman, Jennifer L; Yoshida, Ruriko; Zeng, Zheng

2013-01-01

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some-including the infamous ergot alkaloids-have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses.

Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci

PubMed Central

Schardl, Christopher L.; Young, Carolyn A.; Hesse, Uljana; Amyotte, Stefan G.; Andreeva, Kalina; Calie, Patrick J.; Fleetwood, Damien J.; Haws, David C.; Moore, Neil; Oeser, Birgitt; Panaccione, Daniel G.; Schweri, Kathryn K.; Voisey, Christine R.; Farman, Mark L.; Jaromczyk, Jerzy W.; Roe, Bruce A.; O'Sullivan, Donal M.; Scott, Barry; Tudzynski, Paul; An, Zhiqiang; Arnaoudova, Elissaveta G.; Bullock, Charles T.; Charlton, Nikki D.; Chen, Li; Cox, Murray; Dinkins, Randy D.; Florea, Simona; Glenn, Anthony E.; Gordon, Anna; Güldener, Ulrich; Harris, Daniel R.; Hollin, Walter; Jaromczyk, Jolanta; Johnson, Richard D.; Khan, Anar K.; Leistner, Eckhard; Leuchtmann, Adrian; Li, Chunjie; Liu, JinGe; Liu, Jinze; Liu, Miao; Mace, Wade; Machado, Caroline; Nagabhyru, Padmaja; Pan, Juan; Schmid, Jan; Sugawara, Koya; Steiner, Ulrike; Takach, Johanna E.; Tanaka, Eiji; Webb, Jennifer S.; Wilson, Ella V.; Wiseman, Jennifer L.; Yoshida, Ruriko; Zeng, Zheng

2013-01-01

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some—including the infamous ergot alkaloids—have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses. PMID:23468653

Physical modeling of geometrically confined disordered protein assemblies

NASA Astrophysics Data System (ADS)

Ando, David

2015-08-01

The transport of cargo across the nuclear membrane is highly selective and accomplished by a poorly understood mechanism involving hundreds of nucleoporins lining the inside of the nuclear pore complex (NPC). Currently, there is no clear picture of the overall structure formed by this collection of proteins within the pore, primarily due to their disordered nature and uncertainty regarding the properties of individual nucleoporins. We first study the defining characteristics of the amino acid sequences of nucleoporins through bioinformatics techniques, although bioinformatics of disordered proteins is especially challenging given high mutation rates for homologous proteins and that functionality may not be strongly related to sequence. Here we have performed a novel bioinformatic analysis, based on the spatial clustering of physically relevant features such as binding motifs and charges within disordered proteins, on thousands of FG motif containing nucleoporins (FG nups). The biophysical mechanism by which the critical FG nups regulate nucleocytoplasmic transport has remained elusive, yet our analysis revealed a set of highly conserved spatial features in the sequence structure of individual FG nups, such as the separation, localization, and ordering of FG motifs and charged residues along the protein chain. These sequence features are likely conserved due to a common functionality between species regarding how FG nups functionally regulate traffic, therefore these results constrain current models and eliminate proposed biophysical mechanisms responsible for regulation of nucleocytoplasmic traffic in the NPC which would not result in such a conserved amino acid sequence structure. Additionally, this method allows us to identify potentially functionally analogous disordered proteins across distantly related species. To understand the physical implications of the sequence features on structure and dynamics of the nucleoporins, we performed coarse-grained simulations of nucleoporins to understand their individual polymer properties. Our results indicate that different regions or blocks of an individual NPC protein can have distinctly different forms of disorder and that this property appears to be a conserved functional feature, consistent with the results of our physical bioinformatic analysis. Further simulations of grafted rings of FG nups mimicking the in vivo geometry of the NPC were performed and supplemented with polymer brush modeling to understand how aggregates of FG nups regulate transport in vivo. We found that the block structure at the individual protein level in terms of polymer properties is critical to the formation of a unique higher-order polymer brush architecture that can exist in distinct morphologies depending on the effective interaction energy between the phenylalanine glycine (FG) domains of different nups. Because the interactions between FG domains may be modulated by certain forms of transport factors, our results indicate that transitions between brush morphologies that correspond to open and closed states could play an important role in regulating transport across the NPC, suggesting novel forms of gated transport across membrane pores with wide biomimetic applicability in our Diblock Copolymer Brush Gate model. Previous experimental research has concluded that FG nups from S. cerevisiae are present in a bimodal distribution, with the "Forest Model" classifying FG nups as either diblock polymer like "trees" or single block polymer like "shrubs." Our simulation and polymer brush modeling results indicated that the function of the tree FG nups in the Diblock Copolymer Brush Gate (DCBG) model is to form a higher-order polymer brush architecture which can open and close to regulate transport across the NPC. Here we perform coarse grained simulations of the shrub FG nups which confirm that they have a single block polymer structure rather than the diblock structure of tree nups. Our molecular simulations also demonstrate that these single block FG nups are likely compact collapsed coil polymers, implying that shrubs are generally localized to their grafting location within the NPC. We find that adding a layer of shrub FG nups to the DCBG model increases the range of cargo sizes which are able to translocate the pore through a cooperative effect involving shrub and tree nups. This effect can explain the puzzling connection between shrub FG nup deletion mutants in S. cerevisiae and the resulting failure of certain large cargo transport through the NPC. Facilitation of large cargo transport via single block and diblock FG nup cooperativity in the nuclear pore could provide a model mechanism for designing future biomimetic pores of greater applicability. In summary, this dissertation presents a cohesive body of research that uses a combination of techniques including bioinformatics, coarse grained molecular modeling, and polymer brush theory to understand the properties of individual FG nups and how they behave in aggregate, strongly constraining possible biophysical mechanisms which may play a role in regulating traffic through the NPC. Our results are observed across different species and are consistent with many experimental observations which have been reported. Finally, our DCBG model for NPC function provides testable predictions for future experimental investigation and provides a foundation for the design and commercialization of biomimetic pores for filtering applications in vitro and industrial use.

Structural Color for Additive Manufacturing: 3D-Printed Photonic Crystals from Block Copolymers.

PubMed

Boyle, Bret M; French, Tracy A; Pearson, Ryan M; McCarthy, Blaine G; Miyake, Garret M

2017-03-28

The incorporation of structural color into 3D printed parts is reported, presenting an alternative to the need for pigments or dyes for colored parts produced through additive manufacturing. Thermoplastic build materials composed of dendritic block copolymers were designed, synthesized, and used to additively manufacture plastic parts exhibiting structural color. The reflection properties of the photonic crystals arise from the periodic nanostructure formed through block copolymer self-assembly during polymer processing. The wavelength of reflected light could be tuned across the visible spectrum by synthetically controlling the block copolymer molecular weight and manufacture parts that reflected violet, green, or orange light with the capacity to serve as selective optical filters and light guides.

Polymer-based platform for microfluidic systems

DOEpatents

Benett, William [Livermore, CA; Krulevitch, Peter [Pleasanton, CA; Maghribi, Mariam [Livermore, CA; Hamilton, Julie [Tracy, CA; Rose, Klint [Boston, MA; Wang, Amy W [Oakland, CA

2009-10-13

A method of forming a polymer-based microfluidic system platform using network building blocks selected from a set of interconnectable network building blocks, such as wire, pins, blocks, and interconnects. The selected building blocks are interconnectably assembled and fixedly positioned in precise positions in a mold cavity of a mold frame to construct a three-dimensional model construction of a microfluidic flow path network preferably having meso-scale dimensions. A hardenable liquid, such as poly (dimethylsiloxane) is then introduced into the mold cavity and hardened to form a platform structure as well as to mold the microfluidic flow path network having channels, reservoirs and ports. Pre-fabricated elbows, T's and other joints are used to interconnect various building block elements together. After hardening the liquid the building blocks are removed from the platform structure to make available the channels, cavities and ports within the platform structure. Microdevices may be embedded within the cast polymer-based platform, or bonded to the platform structure subsequent to molding, to create an integrated microfluidic system. In this manner, the new microfluidic platform is versatile and capable of quickly generating prototype systems, and could easily be adapted to a manufacturing setting.

North-South contraction of the mojave block and strike-slip tectonics in southern california.

PubMed

Bartley, J M; Glazner, A F; Schermer, E R

1990-06-15

The Mojave block of southern California has undergone significant late Cenozoic north-south contraction. This previously unappreciated deformation may account for part of the discrepancy between neotectonic and plate-tectonic estimates of Pacific-North American plate motion, and for part of the Big Bend in the San Andreas fault. In the eastern Mojave block, contraction is superimposed on early Miocene crustal extension. In the western Mojave block, contractional folds and reverse faults have been mistaken for extensional structures. The three-dimensional complexity of the contractional structures may mean that rigid-block tectonic models of the region based primarily on paleomagnetic data are unreliable.

Highχ block copolymers for directed self-assembly patterning without the need for topcoat or solvent annealing

NASA Astrophysics Data System (ADS)

Xu, Kui; Hockey, Mary Ann; Calderas, Eric; Guerrero, Douglas; Sweat, Daniel; Fiehler, Jeffrey

2017-03-01

High-χ block copolymers for directed self-assembly (DSA) patterning that do not need topcoat or solvent annealing have been developed. A variety of functionalities have been successfully added into the block copolymers, such as balanced surface energy between the polymer blocks, outstandingly high χ, tunable glass transition temperature (Tg), and selective crosslinking. Perpendicular orientation control, as desired for patterning, of the block copolymers can be simply achieved by thermal annealing due to the equal surface energy of the polymer blocks at the annealing temperatures, which allows avoiding solvent annealing or top-coat. The χ value can be tuned up to achieve L0 as low as 8-10 nm for lamellar-structured block copolymers and hole/pillar size as small as 5-6 nm for cylinder-structured block copolymers. The Tg of the block copolymers can be tuned to improve the kinetics of thermal annealing by enhancing the polymer chain mobility. Block-selective crosslinking facilitates the pattern transfer by mitigating pattern collapse during wet etching and improving oxygen plasma etching selectivity between the polymer blocks. This paper provides an introductory review of our high-χ block copolymer materials with various functionalities for achieving improved DSA performance.

Requirement for Lmo4 in the Vestibular Morphogenesis of Mouse Inner Ear

PubMed Central

Deng, Min; Pan, Ling; Xie, Xiaoling; Gan, Lin

2009-01-01

During development, compartmentalization of an early embryonic structure produces blocks of cells with distinct properties and developmental potentials. The auditory and vestibular components of vertebrate inner ears are derived from defined compartments within the otocyst during embryogenesis. The vestibular apparatus, including three semicircular canals, saccule, utricle, and their associated sensory organs, detects angular and linear acceleration of the head and relays the information through vestibular neurons to vestibular nuclei in the brainstem. How the early developmental events manifest vestibular structures at the molecular level is largely unknown. Here, we show that LMO4, a LIM-domain-only transcriptional regulator, is required for the formation of semicircular canals and their associated sensory cristae. Targeted disruption of Lmo4 resulted in the dysmorphogenesis of the vestibule and in the absence of three semicircular canals, anterior and posterior cristae. In Lmo4-null otocysts, canal outpouches failed to form and cell proliferation was reduced in the dorsolateral region. Expression analysis of the known otic markers showed that Lmo4 is essential for the normal expression of Bmp4, Fgf10, Msx1, Isl1, Gata3, and Dlx5 in the dorsolateral domain of the otocyst, whereas the initial compartmentalization of the otocyst remains unaffected. Our results demonstrate that Lmo4 controls the development of the dorsolateral otocyst into semicircular canals and cristae through two distinct mechanisms: regulating the expression of otic specific genes and stimulating the proliferation of the dorsolateral part of the otocyst. PMID:19913004

Emergency Management and Tourism Stakeholder Responses to Crises: A Global Survey.

PubMed

Morakabati, Yeganeh; Page, Stephen J; Fletcher, John

2017-03-01

This article examines the contested area of the responsibility for destinations and tourists, within emergency settings. It incorporates a Delphi-Scenario technique to facilitate a structured discussion of emergency management for different destination stakeholders. The Delphi exercise engaged 123 senior international stakeholders, from 9 different industry sectors, across 34 countries to provide a global perspective. The study's principal focus is on the notion of emergency management, to identify the challenges that stakeholders would face within a disaster scenario. The exercise asked stakeholders to identify with whom the responsibility rests for 18 distinct disaster-related activities. The study proposes a responsibility allocation building-block framework that could help speed up the emergency management responses by "knowing who is going to do what" with a particular focus on dealing with international tourists as a community in a disaster zone.

An evolutionary link between capsular biogenesis and surface motility in bacteria.

PubMed

Agrebi, Rym; Wartel, Morgane; Brochier-Armanet, Céline; Mignot, Tâm

2015-05-01

Studying the evolution of macromolecular assemblies is important to improve our understanding of how complex cellular structures evolved, and to identify the functional building blocks that are involved. Recent studies suggest that the macromolecular complexes that are involved in two distinct processes in Myxococcus xanthus - surface motility and sporulation - are derived from an ancestral polysaccharide capsule assembly system. In this Opinion article, we argue that the available data suggest that the motility machinery evolved from this capsule assembly system following a gene duplication event, a change in carbohydrate polymer specificity and the acquisition of additional proteins by the motility complex, all of which are key features that distinguish the motility and sporulation systems. Furthermore, the presence of intermediates of these systems in bacterial genomes suggests a testable evolutionary model for their emergence and spread.

Hexagonally Ordered Arrays of α-Helical Bundles Formed from Peptide-Dendron Hybrids

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

Barkley, Deborah A.; Rokhlenko, Yekaterina; Marine, Jeannette E.

Combining monodisperse building blocks that have distinct folding properties serves as a modular strategy for controlling structural complexity in hierarchically organized materials. We combine an α-helical bundle-forming peptide with self-assembling dendrons to better control the arrangement of functional groups within cylindrical nanostructures. Site-specific grafting of dendrons to amino acid residues on the exterior of the α-helical bundle yields monodisperse macromolecules with programmable folding and self-assembly properties. The resulting hybrid biomaterials form thermotropic columnar hexagonal mesophases in which the peptides adopt an α-helical conformation. Bundling of the α-helical peptides accompanies self-assembly of the peptide-dendron hybrids into cylindrical nanostructures. The bundle stoichiometrymore » in the mesophase agrees well with the size found in solution for α-helical bundles of peptides with a similar amino acid sequence.« less

Emergency Management and Tourism Stakeholder Responses to Crises

PubMed Central

Morakabati, Yeganeh; Page, Stephen J.; Fletcher, John

2016-01-01

This article examines the contested area of the responsibility for destinations and tourists, within emergency settings. It incorporates a Delphi-Scenario technique to facilitate a structured discussion of emergency management for different destination stakeholders. The Delphi exercise engaged 123 senior international stakeholders, from 9 different industry sectors, across 34 countries to provide a global perspective. The study’s principal focus is on the notion of emergency management, to identify the challenges that stakeholders would face within a disaster scenario. The exercise asked stakeholders to identify with whom the responsibility rests for 18 distinct disaster-related activities. The study proposes a responsibility allocation building-block framework that could help speed up the emergency management responses by “knowing who is going to do what” with a particular focus on dealing with international tourists as a community in a disaster zone. PMID:29708106

Quartetting in even-even and odd-odd N=Z nuclei

NASA Astrophysics Data System (ADS)

Sambataro, M.; Sandulescu, N.

2018-02-01

We report on a microscopic description of even-even N = Z nuclei in a formalism of quartets. Quartets are four-body correlated structures characterized by isospin T and angular momentum J. We show that the ground state correlations induced by a realistic shell model interaction can be well accounted for in terms of a restricted set of T = 0 low-J quartets, the J = 0 one playing by far a leading role among them. A conceptually similar description of odd-odd self-conjugate nuclei is given in terms of two distinct families of building blocks, one formed by the same T = 0 quartets employed for the even-even systems and the other by collective pairs with either T = 0 or T = 1. Some applications of this formalism are discussed for nuclei in the sd shell.

Evidence for a common mechanism of SIRT1 regulation by allosteric activators.

PubMed

Hubbard, Basil P; Gomes, Ana P; Dai, Han; Li, Jun; Case, April W; Considine, Thomas; Riera, Thomas V; Lee, Jessica E; E, Sook Yen; Lamming, Dudley W; Pentelute, Bradley L; Schuman, Eli R; Stevens, Linda A; Ling, Alvin J Y; Armour, Sean M; Michan, Shaday; Zhao, Huizhen; Jiang, Yong; Sweitzer, Sharon M; Blum, Charles A; Disch, Jeremy S; Ng, Pui Yee; Howitz, Konrad T; Rolo, Anabela P; Hamuro, Yoshitomo; Moss, Joel; Perni, Robert B; Ellis, James L; Vlasuk, George P; Sinclair, David A

2013-03-08

A molecule that treats multiple age-related diseases would have a major impact on global health and economics. The SIRT1 deacetylase has drawn attention in this regard as a target for drug design. Yet controversy exists around the mechanism of sirtuin-activating compounds (STACs). We found that specific hydrophobic motifs found in SIRT1 substrates such as PGC-1α and FOXO3a facilitate SIRT1 activation by STACs. A single amino acid in SIRT1, Glu(230), located in a structured N-terminal domain, was critical for activation by all previously reported STAC scaffolds and a new class of chemically distinct activators. In primary cells reconstituted with activation-defective SIRT1, the metabolic effects of STACs were blocked. Thus, SIRT1 can be directly activated through an allosteric mechanism common to chemically diverse STACs.

Evidence for a Common Mechanism of SIRT1 Regulation by Allosteric Activators

PubMed Central

Hubbard, Basil P.; Gomes, Ana P.; Dai, Han; Li, Jun; Case, April W.; Considine, Thomas; Riera, Thomas V.; Lee, Jessica E.; Sook Yen, E; Lamming, Dudley W.; Pentelute, Bradley L.; Schuman, Eli R.; Stevens, Linda A.; Ling, Alvin J. Y.; Armour, Sean M.; Michan, Shaday; Zhao, Huizhen; Jiang, Yong; Sweitzer, Sharon M.; Blum, Charles A.; Disch, Jeremy S.; Ng, Pui Yee; Howitz, Konrad T.; Rolo, Anabela P.; Hamuro, Yoshitomo; Moss, Joel; Perni, Robert B.; Ellis, James L.; Vlasuk, George P.; Sinclair, David A.

2013-01-01

A molecule that treats multiple age-related diseases would have a major impact on global health and economics. The SIRT1 deacetylase has drawn attention in this regard as a target for drug design. Yet controversy exists around the mechanism of sirtuin-activating compounds (STACs). We found that specific hydrophobic motifs found in SIRT1 substrates such as PGC-1α and FOXO3a facilitate SIRT1 activation by STACs. A single amino acid in SIRT1, Glu230, located in a structured N-terminal domain, was critical for activation by all previously reported STAC scaffolds and a new class of chemically distinct activators. In primary cells reconstituted with activation-defective SIRT1, the metabolic effects of STACs were blocked. Thus, SIRT1 can be directly activated through an allosteric mechanism common to chemically diverse STACs. PMID:23471411

An Ap-Structure with Finslerian Flavor I:. the Principal Idea

NASA Astrophysics Data System (ADS)

Wanas, M. I.

A geometric structure (FAP-structure), having both absolute parallelism and Finsler properties, is constructed. The building blocks of this structure are assumed to be functions of position and direction. A nonlinear connection emerges naturally and is defined in terms of the building blocks of the structure. Two linear connections, one of Berwald type and the other of the Cartan type, are defined using the nonlinear connection of the FAP. Both linear connections are nonsymmetric and consequently admit torsion. A metric tensor is defined in terms of the building blocks of the structure. The condition for this metric to be a Finslerian one is obtained. Also, the condition for an FAP-space to be an AP-one is given.

Random and Block Sulfonated Polyaramides as Advanced Proton Exchange Membranes

DOE PAGES

Kinsinger, Corey L.; Liu, Yuan; Liu, Feilong; ...

2015-10-09

We present here the experimental and computational characterization of two novel copolyaramide proton exchange membranes (PEMs) with higher conductivity than Nafion at relatively high temperatures, good mechanical properties, high thermal stability, and the capability to operate in low humidity conditions. The random and block copolyaramide PEMs are found to possess different ion exchange capacities (IEC) in addition to subtle structural and morphological differences, which impact the stability and conductivity of the membranes. SAXS patterns indicate the ionomer peak for the dry block copolymer resides at q = 0.1 Å –1, which increases in amplitude when initially hydrated to 25% relativemore » humidity, but then decrease in amplitude with additional hydration. This pattern is hypothesized to signal the transport of water into the polymer matrix resulting in a reduced degree of phase separation. Coupled to these morphological changes, the enhanced proton transport characteristics and structural/mechanical stability for the block copolymer are hypothesized to be primarily due to the ordered structure of ionic clusters that create connected proton transport pathways while reducing swelling upon hydration. Interestingly, the random copolymer did not possess an ionomer peak at any of the hydration levels investigated, indicating a lack of any significant ionomer structure. The random copolymer also demonstrated higher proton conductivity than the block copolymer, which is opposite to the trend normally seen in polymer membranes. However, it has reduced structural/mechanical stability as compared to the block copolymer. In conclusion, this reduction in stability is due to the random morphology formed by entanglements of polymer chains and the adverse swelling characteristics upon hydration. Therefore, the block copolymer with its enhanced proton conductivity characteristics, as compared to Nafion, and favorable structural/mechanical stability, as compared to the random copolymer, represents a viable alternative to current proton exchange membranes.« less

Fabrication of Carbonate Apatite Block through a Dissolution-Precipitation Reaction Using Calcium Hydrogen Phosphate Dihydrate Block as a Precursor.

PubMed

Tsuru, Kanji; Yoshimoto, Ayami; Kanazawa, Masayuki; Sugiura, Yuki; Nakashima, Yasuharu; Ishikawa, Kunio

2017-03-31

Carbonate apatite (CO₃Ap) block, which is a bone replacement used to repair defects, was fabricated through a dissolution-precipitation reaction using a calcium hydrogen phosphate dihydrate (DCPD) block as a precursor. When the DCPD block was immersed in NaHCO₃ or Na₂CO₃ solution at 80 °C, DCPD converted to CO₃Ap within 3 days. β-Tricalcium phosphate was formed as an intermediate phase, and it was completely converted to CO₃Ap within 2 weeks when the DCPD block was immersed in Na₂CO₃ solution. Although the crystal structures of the DCPD and CO₃Ap blocks were different, the macroscopic structure was maintained during the compositional transformation through the dissolution-precipitation reaction. CO₃Ap block fabricated in NaHCO₃ or Na₂CO₃ solution contained 12.9 and 15.8 wt % carbonate, respectively. The diametral tensile strength of the CO₃Ap block was 2 MPa, and the porosity was approximately 57% regardless of the carbonate solution. DCPD is a useful precursor for the fabrication of CO₃Ap block.

How do blockings relate to heavy precipitation events in Europe?

NASA Astrophysics Data System (ADS)

Lenggenhager, Sina; Romppainen, Olivia; Brönnimann, Stefan; Croci-Maspoli, Mischa

2017-04-01

Atmospheric blockings are quasi-stationary high pressure systems that persist for several days. Due to their longevity, blockings can be key features for extreme weather events. While several studies have shown their relevant role for temperatures extremes, the link between blockings and extreme precipitation and floods is still poorly understood. A case study of a Swiss lake flood event in the year 2000 reveals how different processes connected to blockings can favour the development of a flood. First upstream blocks helped to form strongly elongated troughs that are known to be associated with heavy precipitation events south of the Alps. Second recurrent precipitation events upstream of a block led to a moistening of the catchment and an increase of the lake level. Third the progression of the upstream weather systems was slowed and thereby the precipitation period over a catchment prolonged. Additionally, cloud diabatic processes in the flood region contributed to the establishment and maintenance of blocking anticyclones. Based on this case study we extend our analysis to all of Europe. Focusing on flood relevant precipitation events, i.e. extreme precipitation events that last for several days and affect larger areas, we show that different regions in Europe have very distinct seasonal precipitation patterns. Hence there is a strong seasonality in the occurrence of extreme events, depending on the geographical region. We further suggest that for different precipitation regimes, the preferred location of blockings varies strongly. Heavy precipitation events in southern France, for example, are often observed during Scandinavian blockings, while heavy precipitation events in south-eastern Europe coincide more often with eastern North-Atlantic blockings.

Dynamical Languages

NASA Astrophysics Data System (ADS)

Xie, Huimin

The following sections are included: * Definition of Dynamical Languages * Distinct Excluded Blocks * Definition and Properties * L and L″ in Chomsky Hierarchy * A Natural Equivalence Relation * Symbolic Flows * Symbolic Flows and Dynamical Languages * Subshifts of Finite Type * Sofic Systems * Graphs and Dynamical Languages * Graphs and Shannon-Graphs * Transitive Languages * Topological Entropy

The influence of polarity of additive molecules on micelle structures of polystyrene-block-poly(4-vinylpyridine) in the fabrication of nano-porous templates.

PubMed

Chua, Kee Sze; Koh, Ai Peng; Lam, Yeng Ming

2010-11-01

Block copolymers are useful for in situ synthesis of nanoparticles as well as producing nanoporous templates. As such, the effects of precursors on the block copolymer micelle structure is important. In this study, we investigate the effects of polarity of molecules introduced into block copolymer micelle cores on the micelle structure. The molecular dipole moment of the additive molecules has been evaluated and their effects on the block copolymer micelles investigated using light scattering spectroscopy, small-angle X-ray scattering, transmission electron microscopy and atomic force microscopy. The molecule with the largest dipole moment resulted in spherical structures with a polydispersity of less than 0.06 in a fully translational diffusion system. Surprisingly, the less polar additive molecules produced elongated micelles and the aspect ratio increases with decreasing polarity. The change in structure from spherical to elongated structure was attributed to P4VP chain extension, where compounds with polarity most similar to P4VP induce the most chain extension. The second virial coefficients of the solutions with elongated micelles are lower than that for spherical micelle systems by up to one order in magnitude, indicating a strong tendency for micelles to coalesce. On rinsing the spin-cast films, pores were obtained from spherical micelles and ridges from elongated micelles, suggesting a viable alternative for morphology modification using mild conditions where external annealing treatments to the film are not preferred. The knowledge of polarity effects of additive molecules on micelle structure has wider implications for supramolecular block copolymer systems where, depending on the application requirements, changes to the shape of the micelle structure can be induced or avoided. Copyright 2010 Elsevier Inc. All rights reserved.

Isolation of Fully Human Antagonistic RON Antibodies Showing Efficient Block of Downstream Signaling and Cell Migration1

PubMed Central

Gunes, Zeynep; Zucconi, Adriana; Cioce, Mario; Meola, Annalisa; Pezzanera, Monica; Acali, Stefano; Zampaglione, Immacolata; De Pratti, Valeria; Bova, Luca; Talamo, Fabio; Demartis, Anna; Monaci, Paolo; La Monica, Nicola; Ciliberto, Gennaro; Vitelli, Alessandra

2011-01-01

RON belongs to the c-MET family of receptor tyrosine kinases. As its well-known family member MET, RON and its ligand macrophage-stimulating protein have been implicated in the progression and metastasis of tumors and have been shown to be overexpressed in cancer. We generated and tested a large number of human monoclonal antibodies (mAbs) against human RON. Our screening yielded three high-affinity antibodies that efficiently block ligand-dependent intracellular AKT and MAPK signaling. This effect correlates with the strong reduction of ligand-activated migration of T47D breast cancer cell line. By cross-competition experiments, we showed that the antagonistic antibodies fall into three distinct epitope regions of the RON extracellular Sema domain. Notably, no inhibition of tumor growth was observed in different epithelial tumor xenografts in nude mice with any of the antibodies. These results suggest that distinct properties beside ligand antagonism are required for anti-RON mAbs to exert antitumor effects in vivo. PMID:21286376

Synthesis of poly(N-isopropylacrylamide)-co-poly(phenylboronate ester) acrylate and study on their glucose-responsive behavior.

PubMed

Yao, Yuan; Shen, Heyun; Zhang, Guanghui; Yang, Jing; Jin, Xu

2014-10-01

We introduced thermo-sensitive poly(N-isopropylacrylamide) (PNIPAM) into the polymer structure of poly(ethylene glycol)-block-poly(phenylboronate ester) acrylate (MPEG-block-PPBDEMA) by block and random polymerization pathways in order to investigate the effect of polymer architecture on the glucose-responsiveness and enhance their insulin release controllability. By following the structure, the continuous PNIPAM shell of the triblock polymer MPEG-block-PNIPAM-block-PPBDEMA collapsing on the glucose-responsive PPBDEMA core formed the polymeric micelles with a core-shell-corona structure, and MPEG-block-(PNIPAM-rand-PPBDEMA) exhibited core-corona micelles in which the hydrophobic core consisted of PNIPAM and PPBDEMA segments when the environmental temperature was increased above low critical solution temperature (LCST) of PNIPAM. The micellar morphologies can be precisely controlled by temperature change between 15 and 37°C. As a result, the introduction of PNIPAM greatly enhanced the overall stability of insulin encapsulated in the polymeric micelles in the absence of glucose over incubation 80 h at 37°C. Comparing to MPEG-block-PNIPAM-block-PPBDEMA, the nanocarriers from MPEG-block-(PNIPAM-rand-PPBDEMA) showed great insulin release behavior which is zero insulin release without glucose, low release at normal blood glucose concentration (1.0 mg/mL). Therefore, these nanocarriers may be served as promising self-regulated insulin delivery system for diabetes treatment. Copyright © 2014 Elsevier Inc. All rights reserved.

An outline of graphical Markov models in dentistry.

PubMed

Helfenstein, U; Steiner, M; Menghini, G

1999-12-01

In the usual multiple regression model there is one response variable and one block of several explanatory variables. In contrast, in reality there may be a block of several possibly interacting response variables one would like to explain. In addition, the explanatory variables may split into a sequence of several blocks, each block containing several interacting variables. The variables in the second block are explained by those in the first block; the variables in the third block by those in the first and the second block etc. During recent years methods have been developed allowing analysis of problems where the data set has the above complex structure. The models involved are called graphical models or graphical Markov models. The main result of an analysis is a picture, a conditional independence graph with precise statistical meaning, consisting of circles representing variables and lines or arrows representing significant conditional associations. The absence of a line between two circles signifies that the corresponding two variables are independent conditional on the presence of other variables in the model. An example from epidemiology is presented in order to demonstrate application and use of the models. The data set in the example has a complex structure consisting of successive blocks: the variable in the first block is year of investigation; the variables in the second block are age and gender; the variables in the third block are indices of calculus, gingivitis and mutans streptococci and the final response variables in the fourth block are different indices of caries. Since the statistical methods may not be easily accessible to dentists, this article presents them in an introductory form. Graphical models may be of great value to dentists in allowing analysis and visualisation of complex structured multivariate data sets consisting of a sequence of blocks of interacting variables and, in particular, several possibly interacting responses in the final block.

Effects of Interlocking and Supporting Conditions on Concrete Block Pavements

NASA Astrophysics Data System (ADS)

Mahapatra, Geetimukta; Kalita, Kuldeep

2018-02-01

Concrete Block Paving (CBP) is widely used as wearing course in flexible pavements, preferably under light and medium vehicular loadings. Construction of CBP at site is quick and easy in quality control. Usually, flexible pavement design philosophy is followed in CBP construction, though it is structurally different in terms of small block elements with high strength concrete and their interlocking aspects, frequent joints and discontinuity, restrained edge etc. Analytical solution for such group action of concrete blocks under loading in a three dimensional multilayer structure is complex and thus, the need of conducting experimental studies is necessitated for extensive understanding of the load—deformation characteristics and behavior of concrete blocks in pavement. The present paper focuses on the experimental studies for load transfer characteristics of CBP under different interlocking and supporting conditions. It is observed that both interlocking and supporting conditions affect significantly on the load transfer behavior in CBP structures. Coro-lock block exhibits better performance in terms of load carrying capacity and distortion behavior under static loads. Plate load tests are performed over subgrade, granular sub-base (GSB), CBP with and without GSB using different block shapes. For an example case, the comparison of CBP with conventional flexible pavement section is also presented and it is found that CBP provides considerable benefit in terms of construction cost of the road structure.

Controlled disulfonated poly(arylene ether sulfone) multiblock copolymers for direct methanol fuel cells.

PubMed

Li, Qing; Chen, Yu; Rowlett, Jarrett R; McGrath, James E; Mack, Nathan H; Kim, Yu Seung

2014-04-23

Structure-property-performance relationships of disulfonated poly(arylene ether sulfone) multiblock copolymer membranes were investigated for their use in direct methanol fuel cell (DMFC) applications. Multiple series of reactive polysulfone, polyketone, and polynitrile hydrophobic block segments having different block lengths and molecular composition were synthesized and reacted with a disulfonated poly(arylene ether sulfone) hydrophilic block segment by a coupling reaction. Large-scale morphological order of the multiblock copolymers evolved with the increase of block size that gave notable influence on mechanical toughness, water uptake, and proton/methanol transport. Chemical structural changes of the hydrophobic blocks through polar group, fluorination, and bisphenol type allowed further control of the specific properties. DMFC performance was analyzed to elicit the impact of structural variations of the multiblock copolymers. Finally, DMFC performances of selected multiblock copolymers were compared against that of the industrial standard Nafion in the DMFC system.

Hydrogen Bond Induces Hierarchical Self-Assembly in Liquid-Crystalline Block Copolymers.

PubMed

Huang, Shuai; Pang, Linlin; Chen, Yuxuan; Zhou, Liming; Fang, Shaoming; Yu, Haifeng

2018-03-01

Microphase-separated structures of block copolymers (BCs) with a size of sub-10 nm are usually obtained by hydrogen-bond-induced self-assembly of BCs through doping with small molecules as functional additives. Here, fabrication of hierarchically self-assembled sub-10 nm structures upon microphase separation of amphiphilic liquid-crystalline BCs (LCBCs) at the existence of hydrogen bonds but without any dopants is reported. The newly introduced urethane groups in the side chain of the hydrophobic block of LCBCs interact with the ether groups of the hydrophilic poly(ethylene oxide) (PEO) block, leading to imperfect crystallization of the PEO blocks. Both crystalline and amorphous domains coexist in the separated PEO phase, enabling a lamellar structure to appear inside the PEO nanocylinders. This provides an elegant method to fabricate controllable sub-10 nm microstructures in well-defined polymer systems without the introduction of any dopants. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Individual Differences in the Alignment of Structural and Functional Markers of the V5/MT Complex in Primates

PubMed Central

Large, I.; Bridge, H.; Ahmed, B.; Clare, S.; Kolasinski, J.; Lam, W. W.; Miller, K. L.; Dyrby, T. B.; Parker, A. J.; Smith, J. E. T.; Daubney, G.; Sallet, J.; Bell, A. H.; Krug, K.

2016-01-01

Extrastriate visual area V5/MT in primates is defined both structurally by myeloarchitecture and functionally by distinct responses to visual motion. Myelination is directly identifiable from postmortem histology but also indirectly by image contrast with structural magnetic resonance imaging (sMRI). First, we compared the identification of V5/MT using both sMRI and histology in Rhesus macaques. A section-by-section comparison of histological slices with in vivo and postmortem sMRI for the same block of cortical tissue showed precise correspondence in localizing heavy myelination for V5/MT and neighboring MST. Thus, sMRI in macaques accurately locates histologically defined myelin within areas known to be motion selective. Second, we investigated the functionally homologous human motion complex (hMT+) using high-resolution in vivo imaging. Humans showed considerable intersubject variability in hMT+ location, when defined with myelin-weighted sMRI signals to reveal structure. When comparing sMRI markers to functional MRI in response to moving stimuli, a region of high myelin signal was generally located within the hMT+ complex. However, there were considerable differences in the alignment of structural and functional markers between individuals. Our results suggest that variation in area identification for hMT+ based on structural and functional markers reflects individual differences in human regional brain architecture. PMID:27371764

[Interest of ultrasonographic guidance in paediatric regional anaesthesia].

PubMed

Dadure, C; Raux, O; Rochette, A; Capdevila, X

2009-10-01

The use of ultrasonographic guidance for regional anaesthesia has known recently a big interest in children in recent years. The linear ultrasound probes with a 25 mm active surface area (or probes with 38 mm active surface area in older children), with high sound frequencies in the range 8-14 MHz, allow a good compromise between excellent resolution for superficial structure and good penetration depths. In children, the easiest ultrasound guided blocks are axillar blocks, femoral blocks, fascia iliaca compartment blocks, ilio-inguinal blocks and para-umbilical blocks, caudal blocks. They permit a safe and easy learning curve of these techniques. The main advantage of ultrasound guided regional anaesthesia is the visualization of different anatomical structures and the approximate localization of the tip of needle. The other advantages for ultrasound guided peripheral nerve blocks in children are: faster onset time of sensory and motor block, longer duration of sensory blockade, increase of blockade quality and reduction of local anesthetic injection. The use of ultrasonographic guidance for central block allows to visualize different structures as well as spine and his content. Spinous process, ligament flavum, dura mater, conus medullaris and cerebrospinal fluid are identifiable, and give some information on spine, epidural space and the depth between epidural space and skin. At last, in caudal block, ultrasounds permit to evaluate the anatomy of caudal epidural space, especially the relation of the sacral hiatus to the dural sac and the search of occult spinal dysraphism. Benefit of this technique is the visualization of targeted nerves or spaces and the spread of injected local anaesthetic.

Evidences for Skeletal Structures in the Ocean from the Images Analyzed by Multilevel Dynamical Contrasting Method

NASA Astrophysics Data System (ADS)

Rantsev-Kartinov, Valentin A.

2004-11-01

An analysis of databases of photographic images of ocean's surface, taken from various altitudes and for various types of rough ocean surface, revealed the presence of an ocean's skeletal structures (OSS) = http://www.arxiv.org/ftp/physics/papers/0401/0401139.pdf [1] Rantsev-Kartinov V.A., Preprint, which exhibit a tendency toward self-similarity of structuring at various length scales (i.e., within various ``generations''). The topology of the OSS appears to be identical to that of skeletal structures which have been formerly found in a wide range of length scales, media and for various phenomena (Phys. Lett. A, 2002, 306). The typical OSS consists of separate identical blocks which are linked together to form a network. Two types of such blocks are found: (i) a coaxial tubular (CT) structures with internal radial bonds, and (ii) a cartwheel-like structures, located either on an axle or in the edges of the CT blocks. The OSSs differ from the formerly found SSs only by the fact that OSS, in their interior, are filled in with closely packed OSSs of a smaller size. We specially discuss the phenomenon of skeletal blocks in the form of vertically/horizontally oriented floating cylinders. The size of these observed blocks is shown to grow with increasing rough water.

High-concentration graphene dispersion stabilized by block copolymers in ethanol.

PubMed

Perumal, Suguna; Lee, Hyang Moo; Cheong, In Woo

2017-07-01

This article describes a comprehensive study for the preparation of graphene dispersions by liquid-phase exfoliation using amphiphilic diblock copolymers; poly(ethylene oxide)-block-poly(styrene) (PEO-b-PS), poly(ethylene oxide)-block-poly(4-vinylpyridine) (PEO-b-PVP), and poly(ethylene oxide)-block-poly(pyrenemethyl methacrylate) (PEO-b-PPy) with similar block lengths. Block copolymers were prepared from PEO using the Steglich coupling reaction followed by reversible addition-fragmentation chain transfer (RAFT) polymerization. Graphite platelets (G) and reduced graphene oxide (rGO) were used as graphene sources. The dispersion stability of graphene in ethanol was comparatively investigated by on-line turbidity, and the graphene concentration in the dispersions was determined gravimetrically. Our results revealed that the graphene dispersions with PEO-b-PVP were much more stable and included graphene with fewer defects than that with PEO-b-PS or PEO-b-PPy, as confirmed by turbidity and Raman analyses. Gravimetry confirmed that graphene concentrations up to 1.7 and 1.8mg/mL could be obtained from G and rGO dispersions, respectively, using PEO-b-PVP after one week. Distinctions in adhesion forces of PS, VP, PPy block units with graphene surface and the variation in solubility of the block copolymers in ethanol medium significantly affected the stability of the graphene dispersion. Copyright © 2017 Elsevier Inc. All rights reserved.

Genome-Wide Analysis of the Sucrose Synthase Gene Family in Grape (Vitis vinifera): Structure, Evolution, and Expression Profiles

PubMed Central

Zhu, Xudong; Wang, Mengqi; Li, Xiaopeng; Jiu, Songtao; Wang, Chen; Fang, Jinggui

2017-01-01

Sucrose synthase (SS) is widely considered as the key enzyme involved in the plant sugar metabolism that is critical to plant growth and development, especially quality of the fruit. The members of SS gene family have been identified and characterized in multiple plant genomes. However, detailed information about this gene family is lacking in grapevine (Vitis vinifera L.). In this study, we performed a systematic analysis of the grape (V. vinifera) genome and reported that there are five SS genes (VvSS1–5) in the grape genome. Comparison of the structures of grape SS genes showed high structural conservation of grape SS genes, resulting from the selection pressures during the evolutionary process. The segmental duplication of grape SS genes contributed to this gene family expansion. The syntenic analyses between grape and soybean (Glycine max) demonstrated that these genes located in corresponding syntenic blocks arose before the divergence of grape and soybean. Phylogenetic analysis revealed distinct evolutionary paths for the grape SS genes. VvSS1/VvSS5, VvSS2/VvSS3 and VvSS4 originated from three ancient SS genes, which were generated by duplication events before the split of monocots and eudicots. Bioinformatics analysis of publicly available microarray data, which was validated by quantitative real-time reverse transcription PCR (qRT-PCR), revealed distinct temporal and spatial expression patterns of VvSS genes in various tissues, organs and developmental stages, as well as in response to biotic and abiotic stresses. Taken together, our results will be beneficial for further investigations into the functions of SS gene in the processes of grape resistance to environmental stresses. PMID:28350372

A diversity-oriented synthesis strategy enabling the combinatorial-type variation of macrocyclic peptidomimetic scaffolds† †Electronic supplementary information (ESI) available: Experimental procedures, characterization data and details of the computational analyses. See DOI: 10.1039/c5ob00371g Click here for additional data file.

PubMed Central

Isidro-Llobet, Albert; Hadje Georgiou, Kathy; Galloway, Warren R. J. D.; Giacomini, Elisa; Hansen, Mette R.; Méndez-Abt, Gabriela; Tan, Yaw Sing; Carro, Laura; Sore, Hannah F.

2015-01-01

Macrocyclic peptidomimetics are associated with a broad range of biological activities. However, despite such potentially valuable properties, the macrocyclic peptidomimetic structural class is generally considered as being poorly explored within drug discovery. This has been attributed to the lack of general methods for producing collections of macrocyclic peptidomimetics with high levels of structural, and thus shape, diversity. In particular, there is a lack of scaffold diversity in current macrocyclic peptidomimetic libraries; indeed, the efficient construction of diverse molecular scaffolds presents a formidable general challenge to the synthetic chemist. Herein we describe a new, advanced strategy for the diversity-oriented synthesis (DOS) of macrocyclic peptidomimetics that enables the combinatorial variation of molecular scaffolds (core macrocyclic ring architectures). The generality and robustness of this DOS strategy is demonstrated by the step-efficient synthesis of a structurally diverse library of over 200 macrocyclic peptidomimetic compounds, each based around a distinct molecular scaffold and isolated in milligram quantities, from readily available building-blocks. To the best of our knowledge this represents an unprecedented level of scaffold diversity in a synthetically derived library of macrocyclic peptidomimetics. Cheminformatic analysis indicated that the library compounds access regions of chemical space that are distinct from those addressed by top-selling brand-name drugs and macrocyclic natural products, illustrating the value of our DOS approach to sample regions of chemical space underexploited in current drug discovery efforts. An analysis of three-dimensional molecular shapes illustrated that the DOS library has a relatively high level of shape diversity. PMID:25778821

The catalytic region and PEST domain of PTPN18 distinctly regulate the HER2 phosphorylation and ubiquitination barcodes.

PubMed

Wang, Hong-Mei; Xu, Yun-Fei; Ning, Shang-Lei; Yang, Du-Xiao; Li, Yi; Du, Yu-Jie; Yang, Fan; Zhang, Ya; Liang, Nan; Yao, Wei; Zhang, Ling-Li; Gu, Li-Chuan; Gao, Cheng-Jiang; Pang, Qi; Chen, Yu-Xin; Xiao, Kun-Hong; Ma, Rong; Yu, Xiao; Sun, Jin-Peng

2014-09-01

The tyrosine phosphorylation barcode encoded in C-terminus of HER2 and its ubiquitination regulate diverse HER2 functions. PTPN18 was reported as a HER2 phosphatase; however, the exact mechanism by which it defines HER2 signaling is not fully understood. Here, we demonstrate that PTPN18 regulates HER2-mediated cellular functions through defining both its phosphorylation and ubiquitination barcodes. Enzymologic characterization and three crystal structures of PTPN18 in complex with HER2 phospho-peptides revealed the molecular basis for the recognition between PTPN18 and specific HER2 phosphorylation sites, which assumes two distinct conformations. Unique structural properties of PTPN18 contribute to the regulation of sub-cellular phosphorylation networks downstream of HER2, which are required for inhibition of HER2-mediated cell growth and migration. Whereas the catalytic domain of PTPN18 blocks lysosomal routing and delays the degradation of HER2 by dephosphorylation of HER2 on pY(1112), the PEST domain of PTPN18 promotes K48-linked HER2 ubiquitination and its rapid destruction via the proteasome pathway and an HER2 negative feedback loop. In agreement with the negative regulatory role of PTPN18 in HER2 signaling, the HER2/PTPN18 ratio was correlated with breast cancer stage. Taken together, our study presents a structural basis for selective HER2 dephosphorylation, a previously uncharacterized mechanism for HER2 degradation and a novel function for the PTPN18 PEST domain. The new regulatory role of the PEST domain in the ubiquitination pathway will broaden our understanding of the functions of other important PEST domain-containing phosphatases, such as LYP and PTPN12.

Geology of the Zambales ophiolite, Luzon, Philippines

USGS Publications Warehouse

Rossman, D.L.; Castanada, G.C.; Bacuta, G.C.

1989-01-01

The Zambales ophiolite of western Luzon, Philippines, exposes a typical succession of basalt flows, diabasic dikes, gabbro and tectonized harzburgite. The age established by limiting strata is late Eocene. Lack of evidence of thrust faulting and the general domal disposition of the lithologie units indicate that the ophiolitic rocks are exposed by uplift. Highly complex internal layered structures within the complex are related to processes developed during formation of the ophiolite and the Zambales ophiolite may be one of the least disturbed (by emplacement) ophiolitic masses known. The exposed mass trends north and the upper surface plunges at low angles (a few degrees) to the north and south. The chemistry and composition of the rocks in the northwest part of the Zambales area (Acoje block) is distinct from that in the southeastern segment (Coto block). The Acoje block, according to Evans (1983) and Hawkins and Evans (1983), resembles (on a chemical basis) arc-tholeiite series rocks from intra-island arcs and the rocks in the Coto block are typical back-arc basin rock series. The present writer believes that the ophiolite composes a single genetic unit and that the changes in composition are the result of changes that took place during the initial formation. The gabbro probably formed below a spreading center in an elongate, in cross section, V-shaped, magma chamber. The gabbro is estimated by the writer to be less than 2 km thick and may be less than 1 km in places. Numerous erosional windows through the gabbro in the northern and eastern side of the Zambales area show that the gabbro remaining in those areas is likely to be only a few hundred meters thick. Harzburgite is exposed to a depth of about 800 m in the Bagsit River area and this may be the deepest part of the ophiolite accessible for study on which there is any control on depth. A transitional zone, about 200 m thick lying between the gabbro and harzburgite, is composed of serpentinized dunite. Commonly the dunite contains disseminated sulfide minerals and at the Acoje Mines, platinum-group elements. A compositional layering within the gabbro is in places cumulate in the lower part of the unit but may have formed by nucleation higher up on the relatively steep sides of the magma chamber. A widespread gneissic banding in the gabbro forms large mappable structures which are many times more complex than is the disposition of the major rock units. These structures are believed to be the result of extensive slumping in the magma chamber. The structure produced by the cumulate layering merges with the gneissic banding, commonly without discernible change in attitude. This tectonic layered structure crosses the gabbro-peridotite boundary at any angle without seeming to disturb the original rock distribution. At greater depths below the boundary (ca. 800 m), the harzburgite contains low dipping banding, which probably reflects the result of differential movement within the mantle. Chromite occurs almost exclusively in a zone that generally lies no more than 200-300 m below the gabbro-peridotite boundary. Refractory-grade chromite is found in this zone below the olivine gabbro in the Goto block and as low-grade metallurgical grade chromite below norite in the Acoje block. At Acoje Mines the chromite is present in layers in dunite, which the writer interprets as being distributed in a zone along the gently dipping (ca. 25??) gabbro-peridotite boundary. The steeply dipping (ca. 60-80 ?? ) individual layers lie en echelon along the boundary at an angle (ca. 50 ?? ) to the contact. At Coto the chromite forms large discontinuous masses in the lowest dunite and in the uppermost harzburgite. Except for the chromite present as layers at Acoje, the regional tectonic layering crosses the chromite deposits without structural deviation. The chromite deposits and associated peridotite may be cumulate in origin, but have been modified to such an extent that cumulate textures are gener

The use of blocking screws with internal lengthening nail and reverse rule of thumb for blocking screws in limb lengthening and deformity correction surgery.

PubMed

Muthusamy, Saravanaraja; Rozbruch, S Robert; Fragomen, Austin T

2016-11-01

Internal lengthening nail (ILN) is a recent development in limb lengthening and deformity correction specialty. The ILN has the distinct advantage of combining acute deformity correction with gradual lengthening of bone. While using ILN, the short metaphyseal bone fragment may develop a deformity at the time of osteotomy and nail insertion or during bone lengthening because of the wide medullary canal. These deformities are typically predictable, and blocking screws (Poller screws) are helpful in these situations. This manuscript describes the common deformities that occur in femur and tibia with osteotomies at different locations while using ILN in antegrade and retrograde nailing technique. Also, a systematic approach to the appropriate use of blocking screws in these deformities is described. In addition, the "reverse rule of thumb" is introduced as a quick reference to determine the ideal location(s) and number of blocking screws. These principles are applicable to limb lengthening and deformity correction as well as fracture fixation using intramedullary nails.

Anaesthetic Tricaine Acts Preferentially on Neural Voltage-Gated Sodium Channels and Fails to Block Directly Evoked Muscle Contraction

PubMed Central

Attili, Seetharamaiah; Hughes, Simon M.

2014-01-01

Movements in animals arise through concerted action of neurons and skeletal muscle. General anaesthetics prevent movement and cause loss of consciousness by blocking neural function. Anaesthetics of the amino amide-class are thought to act by blockade of voltage-gated sodium channels. In fish, the commonly used anaesthetic tricaine methanesulphonate, also known as 3-aminobenzoic acid ethyl ester, metacaine or MS-222, causes loss of consciousness. However, its role in blocking action potentials in distinct excitable cells is unclear, raising the possibility that tricaine could act as a neuromuscular blocking agent directly causing paralysis. Here we use evoked electrical stimulation to show that tricaine efficiently blocks neural action potentials, but does not prevent directly evoked muscle contraction. Nifedipine-sensitive L-type Cav channels affecting movement are also primarily neural, suggesting that muscle Nav channels are relatively insensitive to tricaine. These findings show that tricaine used at standard concentrations in zebrafish larvae does not paralyse muscle, thereby diminishing concern that a direct action on muscle could mask a lack of general anaesthesia. PMID:25090007

Nanogranular origin of concrete creep.

PubMed

Vandamme, Matthieu; Ulm, Franz-Josef

2009-06-30

Concrete, the solid that forms at room temperature from mixing Portland cement with water, sand, and aggregates, suffers from time-dependent deformation under load. This creep occurs at a rate that deteriorates the durability and truncates the lifespan of concrete structures. However, despite decades of research, the origin of concrete creep remains unknown. Here, we measure the in situ creep behavior of calcium-silicate-hydrates (C-S-H), the nano-meter sized particles that form the fundamental building block of Portland cement concrete. We show that C-S-H exhibits a logarithmic creep that depends only on the packing of 3 structurally distinct but compositionally similar C-S-H forms: low density, high density, ultra-high density. We demonstrate that the creep rate ( approximately 1/t) is likely due to the rearrangement of nanoscale particles around limit packing densities following the free-volume dynamics theory of granular physics. These findings could lead to a new basis for nanoengineering concrete materials and structures with minimal creep rates monitored by packing density distributions of nanoscale particles, and predicted by nanoscale creep measurements in some minute time, which are as exact as macroscopic creep tests carried out over years.

Finger posture modulates structural body representations

PubMed Central

Tamè, Luigi; Dransfield, Elanah; Quettier, Thomas; Longo, Matthew R.

2017-01-01

Patients with lesions of the left posterior parietal cortex commonly fail in identifying their fingers, a condition known as finger agnosia, yet are relatively unimpaired in sensation and skilled action. Such dissociations have traditionally been interpreted as evidence that structural body representations (BSR), such as the body structural description, are distinct from sensorimotor representations, such as the body schema. We investigated whether performance on tasks commonly used to assess finger agnosia is modulated by changes in hand posture. We used the ‘in between’ test in which participants estimate the number of unstimulated fingers between two touched fingers or a localization task in which participants judge which two fingers were stimulated. Across blocks, the fingers were placed in three levels of splay. Judged finger numerosity was analysed, in Exp. 1 by direct report and in Exp. 2 as the actual number of fingers between the fingers named. In both experiments, judgments were greater when non-adjacent stimulated fingers were positioned far apart compared to when they were close together or touching, whereas judgements were unaltered when adjacent fingers were stimulated. This demonstrates that BSRs are not fixed, but are modulated by the real-time physical distances between body parts. PMID:28223685

Materials Engineering by Ameloblasts

PubMed Central

2015-01-01

Enamel is unique. It is the only epithelial-derived mineralized tissue in mammals and has a distinct micro- and nanostructure with nanofibrous apatite crystals as building blocks. It is synthesized by a highly specialized cell, the ameloblast, which secretes matrix proteins with little homology to any other known amino acid sequence, but which is composed of a primary structure that makes it competent to self-assemble and control apatite crystal growth at the nanometer scale. The end-product of ameloblast activity is a marvel of structural engineering: a material optimized to provide the tooth with maximum biting force, withstanding millions of cycles of loads without catastrophic failure, while also protecting the dental pulp from bacterial attack. This review attempts to bring into context the mechanical behavior of enamel with the developmental process of amelogenesis and structural development, since they are linked to tissue function, and the importance of controlling calcium phosphate mineralization at the nanometer scale. The origins of apatite nanofibers, the development of a stiffness gradient, and the biological processes responsible for the synthesis of a hard and fracture-resistant dental tissue are discussed with reference to the evolution of enamel from a fibrous composite to a complex, tough, and damage-tolerant coating on dentin. PMID:25800708

Creating Reconfigurable Materials Using ``Colonies'' of Oscillating Polymer Gels

NASA Astrophysics Data System (ADS)

Deb, Debabrata; Dayal, Pratyush; Kuksenok, Olga; Balazs, Anna

2013-03-01

Species ranging from single-cell organisms to social insects can undergo auto-chemotaxis, where the entities move towards a chemo-attractant that they themselves emit. This mode of signaling allows the organisms to form large-scale structures. Using computational modeling, we show that millimeter-sized polymer gels can display similar auto-chemotaxis. In particular, we demonstrate that gels undergoing the self-oscillating Belousov-Zhabotinsky (BZ) reaction not only respond to a chemical signal from the surrounding solution, but also emit this signal and thus, multiple gel pieces can spontaneously self-aggregate. We focus on the collective behavior of ``colonies'' of BZ gels and show that communication between the individual pieces critically depends on all the neighboring gels. We isolate the conditions at which the BZ gels can undergo a type of self-recombining: if a larger gel is cut into distinct pieces that are moved relatively far apart, then their auto-chemotactic behavior drives them to move and autonomously recombine into a structure resembling the original, uncut sample. These findings reveal that the BZ gels can be used as autonomously moving building blocks to construct multiple structures and thus, provide a new route for creating dynamically reconfigurable materials.

Nanogranular origin of concrete creep

PubMed Central

Vandamme, Matthieu; Ulm, Franz-Josef

2009-01-01

Concrete, the solid that forms at room temperature from mixing Portland cement with water, sand, and aggregates, suffers from time-dependent deformation under load. This creep occurs at a rate that deteriorates the durability and truncates the lifespan of concrete structures. However, despite decades of research, the origin of concrete creep remains unknown. Here, we measure the in situ creep behavior of calcium–silicate–hydrates (C–S–H), the nano-meter sized particles that form the fundamental building block of Portland cement concrete. We show that C–S–H exhibits a logarithmic creep that depends only on the packing of 3 structurally distinct but compositionally similar C–S–H forms: low density, high density, ultra-high density. We demonstrate that the creep rate (≈1/t) is likely due to the rearrangement of nanoscale particles around limit packing densities following the free-volume dynamics theory of granular physics. These findings could lead to a new basis for nanoengineering concrete materials and structures with minimal creep rates monitored by packing density distributions of nanoscale particles, and predicted by nanoscale creep measurements in some minute time, which are as exact as macroscopic creep tests carried out over years. PMID:19541652

Structure-Guided Combinatorial Engineering Facilitates Affinity and Specificity Optimization of Anti-CD81 Antibodies.

PubMed

Nelson, Bryce; Adams, Jarrett; Kuglstatter, Andreas; Li, Zhijian; Harris, Seth F; Liu, Yang; Bohini, Sandya; Ma, Han; Klumpp, Klaus; Gao, Junjun; Sidhu, Sachdev S

2018-07-06

Hepatitis C viral infection is the major cause of chronic hepatitis that affects as many as 71 million people worldwide. Rather than target the rapidly shifting viruses and their numerous serotypes, four independent antibodies were made to target the host antigen CD81 and were shown to block hepatitis C viral entry. The single-chain variable fragment of each antibody was crystallized in complex with the CD81 large extracellular loop in order to guide affinity maturation of two distinct antibodies by phage display. Affinity maturation of antibodies using phage display has proven to be critical to therapeutic antibody development and typically involves modification of the paratope for increased affinity, improved specificity, enhanced stability or a combination of these traits. One antibody was engineered for increased affinity for human CD81 large extracellular loop that equated to increased efficacy, while the second antibody was engineered for cross-reactivity with cynomolgus CD81 to facilitate animal model testing. The use of structures to guide affinity maturation library design demonstrates the utility of combining structural analysis with phage display technologies. Copyright © 2018 Elsevier Ltd. All rights reserved.

Role of Polyalanine Domains in -Sheet Formation in Spider Silk Block Copolymers

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

Rabotyagova, O.; Cebe, P; Kaplan, D

2010-01-01

Genetically engineered spider silk-like block copolymers were studied to determine the influence of polyalanine domain size on secondary structure. The role of polyalanine block distribution on {beta}-sheet formation was explored using FT-IR and WAXS. The number of polyalanine blocks had a direct effect on the formation of crystalline {beta}-sheets, reflected in the change in crystallinity index as the blocks of polyalanines increased. WAXS analysis confirmed the crystalline nature of the sample with the largest number of polyalanine blocks. This approach provides a platform for further exploration of the role of specific amino acid chemistries in regulating the assembly of {beta}-sheetmore » secondary structures, leading to options to regulate material properties through manipulation of this key component in spider silks.« less

Cooperative storage of shared files in a parallel computing system with dynamic block size

DOEpatents

Bent, John M.; Faibish, Sorin; Grider, Gary

2015-11-10

Improved techniques are provided for parallel writing of data to a shared object in a parallel computing system. A method is provided for storing data generated by a plurality of parallel processes to a shared object in a parallel computing system. The method is performed by at least one of the processes and comprises: dynamically determining a block size for storing the data; exchanging a determined amount of the data with at least one additional process to achieve a block of the data having the dynamically determined block size; and writing the block of the data having the dynamically determined block size to a file system. The determined block size comprises, e.g., a total amount of the data to be stored divided by the number of parallel processes. The file system comprises, for example, a log structured virtual parallel file system, such as a Parallel Log-Structured File System (PLFS).

Fabrication of an open Au/nanoporous film by water-in-oil emulsion-induced block copolymer micelles.

PubMed

Koh, Haeng-Deog; Kang, Nam-Goo; Lee, Jae-Suk

2007-12-18

Water-in-oil (W/O) emulsion-induced micelles with narrow size distributions of approximately 140 nm were prepared by sonicating the polystyrene-b-poly(2-vinylpyridine) (PS-b-P2VP) block copolymer in the toluene/water (50:1 vol %). The ordered nanoporous block copolymer films with the hydrophilic P2VP interior and the PS matrix were distinctly fabricated by casting the resultant solution on substrates, followed by evaporating the organic solvent and water. The porous diameter was estimated to be about 70 nm. Here, we successfully prepared the open nanoporous nanocomposites, the P2VP domain decorated by Au (5+/-0.4 nm) nanoparticles based on the methodology mentioned. We anticipate that this novelty enhances the specific function of nanoporous films.

Origami-inspired building block and parametric design for mechanical metamaterials

NASA Astrophysics Data System (ADS)

Jiang, Wei; Ma, Hua; Feng, Mingde; Yan, Leilei; Wang, Jiafu; Wang, Jun; Qu, Shaobo

2016-08-01

An origami-based building block of mechanical metamaterials is proposed and explained by introducing a mechanism model based on its geometry. According to our model, this origami mechanism supports response to uniaxial tension that depends on structure parameters. Hence, its mechanical properties can be tunable by adjusting the structure parameters. Experiments for poly lactic acid (PLA) samples were carried out, and the results are in good agreement with those of finite element analysis (FEA). This work may be useful for designing building blocks of mechanical metamaterials or other complex mechanical structures.

Intermittent Granular Dynamics at a Seismogenic Plate Boundary.

PubMed

Meroz, Yasmine; Meade, Brendan J

2017-09-29

Earthquakes at seismogenic plate boundaries are a response to the differential motions of tectonic blocks embedded within a geometrically complex network of branching and coalescing faults. Elastic strain is accumulated at a slow strain rate on the order of 10^{-15}  s^{-1}, and released intermittently at intervals >100  yr, in the form of rapid (seconds to minutes) coseismic ruptures. The development of macroscopic models of quasistatic planar tectonic dynamics at these plate boundaries has remained challenging due to uncertainty with regard to the spatial and kinematic complexity of fault system behaviors. The characteristic length scale of kinematically distinct tectonic structures is particularly poorly constrained. Here, we analyze fluctuations in Global Positioning System observations of interseismic motion from the southern California plate boundary, identifying heavy-tailed scaling behavior. Namely, we show that, consistent with findings for slowly sheared granular media, the distribution of velocity fluctuations deviates from a Gaussian, exhibiting broad tails, and the correlation function decays as a stretched exponential. This suggests that the plate boundary can be understood as a densely packed granular medium, predicting a characteristic tectonic length scale of 91±20  km, here representing the characteristic size of tectonic blocks in the southern California fault network, and relating the characteristic duration and recurrence interval of earthquakes, with the observed sheared strain rate, and the nanosecond value for the crack tip evolution time scale. Within a granular description, fault and blocks systems may rapidly rearrange the distribution of forces within them, driving a mixture of transient and intermittent fault slip behaviors over tectonic time scales.

Intermittent Granular Dynamics at a Seismogenic Plate Boundary

NASA Astrophysics Data System (ADS)

Meroz, Yasmine; Meade, Brendan J.

2017-09-01

Earthquakes at seismogenic plate boundaries are a response to the differential motions of tectonic blocks embedded within a geometrically complex network of branching and coalescing faults. Elastic strain is accumulated at a slow strain rate on the order of 10-15 s-1 , and released intermittently at intervals >100 yr , in the form of rapid (seconds to minutes) coseismic ruptures. The development of macroscopic models of quasistatic planar tectonic dynamics at these plate boundaries has remained challenging due to uncertainty with regard to the spatial and kinematic complexity of fault system behaviors. The characteristic length scale of kinematically distinct tectonic structures is particularly poorly constrained. Here, we analyze fluctuations in Global Positioning System observations of interseismic motion from the southern California plate boundary, identifying heavy-tailed scaling behavior. Namely, we show that, consistent with findings for slowly sheared granular media, the distribution of velocity fluctuations deviates from a Gaussian, exhibiting broad tails, and the correlation function decays as a stretched exponential. This suggests that the plate boundary can be understood as a densely packed granular medium, predicting a characteristic tectonic length scale of 91 ±20 km , here representing the characteristic size of tectonic blocks in the southern California fault network, and relating the characteristic duration and recurrence interval of earthquakes, with the observed sheared strain rate, and the nanosecond value for the crack tip evolution time scale. Within a granular description, fault and blocks systems may rapidly rearrange the distribution of forces within them, driving a mixture of transient and intermittent fault slip behaviors over tectonic time scales.

De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks.

PubMed

Schneider, G; Lee, M L; Stahl, M; Schneider, P

2000-07-01

An evolutionary algorithm was developed for fragment-based de novo design of molecules (TOPAS, TOPology-Assigning System). This stochastic method aims at generating a novel molecular structure mimicking a template structure. A set of approximately 25,000 fragment structures serves as the building block supply, which were obtained by a straightforward fragmentation procedure applied to 36,000 known drugs. Eleven reaction schemes were implemented for both fragmentation and building block assembly. This combination of drug-derived building blocks and a restricted set of reaction schemes proved to be a key for the automatic development of novel, synthetically tractable structures. In a cyclic optimization process, molecular architectures were generated from a parent structure by virtual synthesis, and the best structure of a generation was selected as the parent for the subsequent TOPAS cycle. Similarity measures were used to define 'fitness', based on 2D-structural similarity or topological pharmacophore distance between the template molecule and the variants. The concept of varying library 'diversity' during a design process was consequently implemented by using adaptive variant distributions. The efficiency of the design algorithm was demonstrated for the de novo construction of potential thrombin inhibitors mimicking peptide and non-peptide template structures.

Extrapunitive and Intropunitive Individuals Activate Different Parts of the Prefrontal Cortex under an Ego-Blocking Frustration

PubMed Central

Minamoto, Takehiro; Osaka, Mariko; Yaoi, Ken; Osaka, Naoyuki

2014-01-01

Different people make different responses when they face a frustrating situation: some punish others (extrapunitive), while others punish themselves (intropunitive). Few studies have investigated the neural structures that differentiate extrapunitive and intropunitive individuals. The present fMRI study explored these neural structures using two different frustrating situations: an ego-blocking situation which blocks a desire or goal, and a superego-blocking situation which blocks self-esteem. In the ego-blocking condition, the extrapunitive group (n = 9) showed greater activation in the bilateral ventrolateral prefrontal cortex, indicating that these individuals prefer emotional processing. On the other hand, the intropunitive group (n = 9) showed greater activation in the left dorsolateral prefrontal cortex, possibly reflecting an effortful control for anger reduction. Such patterns were not observed in the superego-blocking condition. These results indicate that the prefrontal cortex is the source of individual differences in aggression direction in the ego-blocking situation. PMID:24454951

Kinetic control of block copolymer self-assembly into multicompartment and novel geometry nanoparticles

NASA Astrophysics Data System (ADS)

Chen, Yingchao; Wang, Xiaojun; Zhang, Ke; Wooley, Karen; Mays, Jimmy; Percec, Virgil; Pochan, Darrin

2012-02-01

Micelles with the segregation of hydrophobic blocks trapped in the same nanoparticle core have been produced through co-self-assembly of two block copolymers in THF/water dilute solution. The dissolution of two block copolymer sharing the same polyacrylic acid PAA blocks in THF undergoes consequent aggregation and phase separation through either slow water titration or quick water addition that triggers the micellar formation. The combination and comparison of the two water addition kinetic pathways are the keys of forming multicompartment structures at high water content. Importantly, the addition of organic diamine provides for acid-base complexation with the PAA side chains which, in turn, plays the key role of trapping unlike hydrophobic blocks from different block copolymers into one nanoparticle core. The kinetic control of solution assembly can be applied to other molecular systems such as dendrimers as well as other block copolymer molecules. Transmission electron microscopy, cryogenic transmission electron microscopy, light scattering have been applied to characterize the micelle structures.

Usage of digital image correlation in assessment of behavior of block element pavement structure

NASA Astrophysics Data System (ADS)

Grygierek, M.; Grzesik, B.; Rokitowski, P.; Rusin, T.

2018-05-01

In diagnostics of existing road pavement structures deflection measurements have fundamental meaning, because of ability to assess present stiffness (bearing capacity) of whole layered construction. During test loading the reaction of pavement structure to applied load is measured in central point or in a few points located along a straight on a 1.5 ÷ 1.8 m distance (i.e. Falling Weight Deflectometer) in similar spacing equal to 20 ÷ 30 cm. Typical measuring techniques are productive and precise enough for most common pavement structures such as flexible, semi-rigid and rigid. It should be noted that in experimental research as well as in pavements in complex stress state, measurement techniques allowing observation of pavement deformation in 3D would have been very helpful. A great example of that type of pavements is a block element pavement structure consisting of i.e. paving blocks or stone slabs. Due to high stiffness and confined ability of cooperation of surrounding block elements, in that type of pavements fatigue life is strongly connected with displacement distribution. Unfortunately, typical deflection measurement methods forefend displacement observations and rotation of single block elements like paving blocks or slabs. Another difficult problem is to carry out unmistakable analysis of cooperation between neighboring elements. For more precise observations of displacements state of block element pavements under a wheel load a Digital Image Correlation (DIC) was used. Application of this method for assessment of behavior of stone slabs pavement under a traffic load enabled the monitoring of deformations distribution and encouraged to formulate conclusions about the initiation mechanism and development of damages in this type of pavement structures. Results shown in this article were obtained in field tests executed on an exploited pavement structure with a surface course made of granite slabs with dimensions 0.5x1.0x0.14 m.

Effects of Polymer Structure and Relaxations on Ionic Conductivity in Anion Exchange Membranes with Quaternary Ammonium Functional Groups

NASA Astrophysics Data System (ADS)

Maes, Ashley M.

Anion exchange membranes (AEMs) are of considerable interest to developers and researchers of electrochemical conversion and storage devices such as anion exchange membrane fuel cells (AAEMFCs), alkaline polymer electrolyte electrolysers, redox flow batteries and bioelectrochemical devices. AEMs are generally in competition with more established proton exchange membranes (PEMs), but offer the potential for reduction of materials costs and greater fuel flexibility across these applications. This work includes an introduction to AEMs in the context of fuel cell technologies and some key techniques for AEM characterization. There are many synthetic strategies to incorporate cationic functional groups, which promote anion transport, into a polymer matrix. Two membrane chemistries are investigated in the following chapters. The first is based on a simple synthesis procedure that produced a membrane consisting of random, crosslinked polypropylene- ran-polyethyleneimine with quaternary ammonium functional groups. This membrane had moderate chloride ionic conductivity of 0.03 S cm -1 at 95 °C and high water uptake with minimal dimensional swelling. However, the lack of control of crosslink location and density during synthesis produced a material with a very random nature, making it a poor candidate for more fundamental transport studies. The second membrane chemistry is a block copolymer with a hydrophobic and hydrophilic block. The hydrophobic block was selected to provide favorable mechanical and barrier characteristics while a hydrophilic block was selected to provide water uptake and anion conducting functionalities. Poly(vinyl benzyl trimethyl ammonium bromide)-b-poly(methylbutylene) ([PVBTMA][Br]- b-PMB) was synthesized by partners at the University of Massachusetts-Amherst with varied degrees of functionalization (DF) along the hydrophilic block, resulting in ion exchange capacities ranging from 0.77 to 2.20 mmol g -1. Water uptake, in-plane ionic conductivity and membrane morphology were measured across a series of membranes with the original bromide (Br -) counter-ion. These bulk materials characterization experiments demonstrated that this polymer structure produces well-ordered lamellar morphology with moderate water uptake and competitive ionic conductivity (ca. 40 mS cm-1 at 90 °C and 95% relative humidity). These characteristics make it an appropriate candidate for the following more fundamental investigations of ionic conductivity mechanisms. Broadband electrical spectroscopy (BES) was conducted on one [PVBTMA][Br]- b-PMB sample in the Br- form and analyzed in conjunction with thermal stability and relaxation experiments in Chapter 4. We were able to propose two separate ionic conductivity mechanisms and relate each to physical attributes of the polymer structure. A significant thermal transition was observed at Tdelta , which resulted in a dramatic drop in conductivity. In a continued effort to characterize the ionic conductivity of these block-copolymer membranes, another BES study was conducted on three samples with varying DFs. Samples were converted to hydroxide (OH- ) form so we could contrast the Br- conductivity mechanisms to those in a more relevant counter-ion form. After analysis of the electric response of the material, combined with the thermal analysis by TGA, MDSC and DMA, conductivity mechanisms were described. As in the Br- study, conductivity involves two distinct conduction pathways, sigmaEP and sigmaIP,1. Importantly, we again observed a drop in conductivity at Tdelta in each of these samples, with Tdelta decreasing as the density of functional groups along the hydrophilic block increased. It is undesirable for this transition to occur during operation in a fuel cell or other electrochemical device, so future work to investigate strategies for inhibition are recommended.

Structural inhibition and reactivation of Escherichia coli septation by elements of the SOS and TER pathways

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

Dopazo, A.; Tormo, A.; Aldea, M.

1987-04-01

The inhibition of cell division caused by induction of the SOS pathway in Escherichia coli structurally blocks septation, as deduced from two sets of results. Potential septation sites active at the time of SOS induction became inactivated, while those initiated during the following doubling time were active. Penicillin resistance increased in wild-type UV light-irradiated cells, a behavior similar to that observed in mutants in which structural blocks were introduced by inactivation of FtsA. Potential septation sites that have been structurally blocked by either the SOS division inhibitor, furazlocillin inhibition of PBP3, or inactivation of a TER pathway component, FtsA3, couldmore » be reactivated one doubling time after removal of the inhibitory agent in the presence of an active lon gene product. Reactivation of potential septation sites blocked by the presence of an inactivated FtsA3 was significantly lower when the lon protease was not active, suggesting that Lon plays a role in the removal of inactivated TER pathway products from the blocked potential septation sites.« less

Novel dimeric interface and electrostatic recognition in bacterial Cu,Zn superoxide dismutase

PubMed Central

Bourne, Yves; Redford, Susan M.; Steinman, Howard M.; Lepock, James R.; Tainer, John A.; Getzoff, Elizabeth D.

1996-01-01

Eukaryotic Cu,Zn superoxide dismutases (CuZnSODs) are antioxidant enzymes remarkable for their unusually stable β-barrel fold and dimer assembly, diffusion-limited catalysis, and electrostatic guidance of their free radical substrate. Point mutations of CuZnSOD cause the fatal human neurodegenerative disease amyotrophic lateral sclerosis. We determined and analyzed the first crystallographic structure (to our knowledge) for CuZnSOD from a prokaryote, Photobacterium leiognathi, a luminescent symbiont of Leiognathid fish. This structure, exemplifying prokaryotic CuZnSODs, shares the active-site ligand geometry and the topology of the Greek key β-barrel common to the eukaryotic CuZnSODs. However, the β-barrel elements recruited to form the dimer interface, the strategy used to forge the channel for electrostatic recognition of superoxide radical, and the connectivity of the intrasubunit disulfide bond in P. leiognathi CuZnSOD are discrete and strikingly dissimilar from those highly conserved in eukaryotic CuZnSODs. This new CuZnSOD structure broadens our understanding of structural features necessary and sufficient for CuZnSOD activity, highlights a hitherto unrecognized adaptability of the Greek key β-barrel building block in evolution, and reveals that prokaryotic and eukaryotic enzymes diverged from one primordial CuZnSOD and then converged to distinct dimeric enzymes with electrostatic substrate guidance. PMID:8917495

North Atlantic Origin of Interdecadal variability of Siberian High

NASA Astrophysics Data System (ADS)

Kim, Seon-Hwa; Sung, Mi-Kyung; Kim, Baek-Min

2017-04-01

We suggest that the changes in the mean atmospheric circulation structure in the North Atlantic Ocean upstream region of Eurasian continent play an important role in the interdecadal variability of Siberian High (SH) through the modulation of Ural blocking frequency. Previous studies suggested that the interdecadal variability of SH is partly explained by the Arctic Oscillation. However, in this study, we emphasize the role of 'Warm Arctic and Cold Eurasia (WACE)', which is the second mode of winter surface air temperature variability over Eurasia. We show that the correlation between SH and WACE is high in general compared to that between SH and AO. However, the correlation between SH and WACE does not always exhibit high constant value. It shows a distinctive interdecadal fluctuation in the correlation. We found that this fluctuation in the correlation is due to the interdecadal fluctuation of the continental trough over the North Atlantic and the resultant strengthening of in-situ atmospheric baroclinicity. This accompanies changes in the transient vorticity flux divergence which leads to the downstream wave development and anomalous anticyclonic flow near Ural region. Obviously, the existence of anticyclonic flow over Ural region helps more frequent occurrence of Ural blocking and it is shown that this condition favors positive WACE event, which links to an intensified SH.

Fingerprinting Soybean Germplasm and Its Utility in Genomic Research

PubMed Central

Song, Qijian; Hyten, David L.; Jia, Gaofeng; Quigley, Charles V.; Fickus, Edward W.; Nelson, Randall L.; Cregan, Perry B.

2015-01-01

The United States Department of Agriculture, Soybean Germplasm Collection includes 18,480 domesticated soybean and 1168 wild soybean accessions introduced from 84 countries or developed in the United States. This collection was genotyped with the SoySNP50K BeadChip containing greater than 50K single-nucleotide polymorphisms. Redundant accessions were identified in the collection, and distinct genetic backgrounds of soybean from different geographic origins were observed that could be a unique resource for soybean genetic improvement. We detected a dramatic reduction of genetic diversity based on linkage disequilibrium and haplotype structure analyses of the wild, landrace, and North American cultivar populations and identified candidate regions associated with domestication and selection imposed by North American breeding. We constructed the first soybean haplotype block maps in the wild, landrace, and North American cultivar populations and observed that most recombination events occurred in the regions between haplotype blocks. These haplotype maps are crucial for association mapping aimed at the identification of genes controlling traits of economic importance. A case-control association test delimited potential genomic regions along seven chromosomes that most likely contain genes controlling seed weight in domesticated soybean. The resulting dataset will facilitate germplasm utilization, identification of genes controlling important traits, and will accelerate the creation of soybean varieties with improved seed yield and quality. PMID:26224783

A novel complexity-to-diversity strategy for the diversity-oriented synthesis of structurally diverse and complex macrocycles from quinine.

PubMed

Ciardiello, J J; Stewart, H L; Sore, H F; Galloway, W R J D; Spring, D R

2017-06-01

Recent years have witnessed a global decline in the productivity and advancement of the pharmaceutical industry. A major contributing factor to this is the downturn in drug discovery successes. This can be attributed to the lack of structural (particularly scaffold) diversity and structural complexity exhibited by current small molecule screening collections. Macrocycles have been shown to exhibit a diverse range of biological properties, with over 100 natural product-derived examples currently marketed as FDA-approved drugs. Despite this, synthetic macrocycles are widely considered to be a poorly explored structural class within drug discovery, which can be attributed to their synthetic intractability. Herein we describe a novel complexity-to-diversity strategy for the diversity-oriented synthesis of novel, structurally complex and diverse macrocyclic scaffolds from natural product starting materials. This approach exploits the inherent structural (including functional) and stereochemical complexity of natural products in order to rapidly generate diversity and complexity. Readily-accessible natural product-derived intermediates serve as structural templates which can be divergently functionalized with different building blocks to generate a diverse range of acyclic precursors. Subsequent macrocyclisation then furnishes compounds that are each based around a distinct molecular scaffold. Thus, high levels of library scaffold diversity can be rapidly achieved. In this proof-of-concept study, the natural product quinine was used as the foundation for library synthesis, and six novel structurally diverse, highly complex and functionalized macrocycles were generated. Copyright © 2017 Elsevier Ltd. All rights reserved.

Aerodynamics of a translating comb-like plate inspired by a fairyfly wing

NASA Astrophysics Data System (ADS)

Lee, Seung Hun; Kim, Daegyoum

2017-08-01

Unlike the smooth wings of common insects or birds, micro-scale insects such as the fairyfly have a distinctive wing geometry, comprising a frame with several bristles. Motivated by this peculiar wing geometry, we experimentally investigated the flow structure of a translating comb-like wing for a wide range of gap size, angle of attack, and Reynolds number, Re = O(10) - O(103), and the correlation of these parameters with aerodynamic performance. The flow structures of a smooth plate without a gap and a comb-like plate are significantly different at high Reynolds number, while little difference was observed at the low Reynolds number of O(10). At low Reynolds number, shear layers that were generated at the edges of the tooth of the comb-like plate strongly diffuse and eventually block a gap. This gap blockage increases the effective surface area of the plate and alters the formation of leading-edge and trailing-edge vortices. As a result, the comb-like plate generates larger aerodynamic force per unit area than the smooth plate. In addition to a quasi-steady phase after the comb-like plate travels several chords, we also studied a starting phase of the shear layer development when the comb-like plate begins to translate from rest. While a plate with small gap size can generate aerodynamic force at the starting phase as effectively as at the quasi-steady phase, the aerodynamic force drops noticeably for a plate with a large gap because the diffusion of the developing shear layers is not enough to block the gap.

Cyclodextrins as versatile building blocks for regenerative medicine.

PubMed

Alvarez-Lorenzo, Carmen; García-González, Carlos A; Concheiro, Angel

2017-12-28

Cyclodextrins (CDs) are one of the most versatile substances produced by nature, and it is in the aqueous biological environment where the multifaceted potential of CDs can be completely unveiled. CDs form inclusion complexes with a variety of guest molecules, including polymers, producing very diverse biocompatible supramolecular structures. Additionally, CDs themselves can trigger cell differentiation to distinct lineages depending on the substituent groups and also promote salt nucleation. These features together with the affinity-driven regulated release of therapeutic molecules, growth factors and gene vectors explain the rising interest for CDs as building blocks in regenerative medicine. Supramolecular poly(pseudo)rotaxane structures and zipper-like assemblies exhibit outstanding viscoelastic properties, performing as syringeable implants. The sharp shear-responsiveness of the supramolecular assemblies is opening new avenues for the design of bioinks for 3D printing and also of electrospun fibers. CDs can also be transformed into polymerizable monomers to prepare alternative nanostructured materials. The aim of this review is to analyze the role that CDs may play in regenerative medicine through the analysis of the last decade research. Most applications of CD-based scaffolds are focussed on non-healing bone fractures, cartilage reparation and skin recovery, but also on even more challenging demands such as neural grafts. For the sake of clarity, main sections of this review are organized according to the architecture of the CD-based scaffolds, mainly syringeable supramolecular hydrogels, 3D printed scaffolds, electrospun fibers, and composites, since the same scaffold type may find application in different tissues. Copyright © 2017 Elsevier B.V. All rights reserved.

A new view into the Cascadia subduction zone and volcanic arc: Implications for earthquake hazards along the Washington margin

USGS Publications Warehouse

Parsons, T.; Trehu, A.M.; Luetgert, J.H.; Miller, K.; Kilbride, F.; Wells, R.E.; Fisher, M.A.; Flueh, E.; ten Brink, Uri S.; Christensen, N.I.

1998-01-01

In light of suggestions that the Cascadia subduction margin may pose a significant seismic hazard for the highly populated Pacific Northwest region of the United States, the U.S. Geological Survey (USGS), the Research Center for Marine Geosciences (GEOMAR), and university collaborators collected and interpreted a 530-km-long wide-angle onshore-offshore seismic transect across the subduction zone and volcanic arc to study the major structures that contribute to seismogenic deformation. We observed (1) an increase in the dip of the Juan de Fuca slab from 2°–7° to 12° where it encounters a 20-km-thick block of the Siletz terrane or other accreted oceanic crust, (2) a distinct transition from Siletz crust into Cascade arc crust that coincides with the Mount St. Helens seismic zone, supporting the idea that the mafic Siletz block focuses seismic deformation at its edges, and (3) a crustal root (35–45 km deep) beneath the Cascade Range, with thinner crust (30–35 km) east of the volcanic arc beneath the Columbia Plateau flood basalt province. From the measured crustal structure and subduction geometry, we identify two zones that may concentrate future seismic activity: (1) a broad (because of the shallow dip), possibly locked part of the interplate contact that extends from ∼25 km depth beneath the coastline to perhaps as far west as the deformation front ∼120 km offshore and (2) a crustal zone at the eastern boundary between the Siletz terrane and the Cascade Range.

Morphological Evolution of Block Copolymer Particles: Effect of Solvent Evaporation Rate on Particle Shape and Morphology.

PubMed

Shin, Jae Man; Kim, YongJoo; Yun, Hongseok; Yi, Gi-Ra; Kim, Bumjoon J

2017-02-28

Shape and morphology of polymeric particles are of great importance in controlling their optical properties or self-assembly into unusual superstructures. Confinement of block copolymers (BCPs) in evaporative emulsions affords particles with diverse structures, including prolate ellipsoids, onion-like spheres, oblate ellipsoids, and others. Herein, we report that the evaporation rate of solvent from emulsions encapsulating symmetric polystyrene-b-polybutadiene (PS-b-PB) determines the shape and internal nanostructure of micron-sized BCP particles. A distinct morphological transition from the ellipsoids with striped lamellae to the onion-like spheres was observed with decreasing evaporation rate. Experiments and dissipative particle dynamics (DPD) simulations showed that the evaporation rate affected the organization of BCPs at the particle surface, which determined the final shape and internal nanostructure of the particles. Differences in the solvent diffusion rates in PS and PB at rapid evaporation rates induced alignment of both domains perpendicular to the particle surface, resulting in ellipsoids with axial lamellar stripes. Slower evaporation rates provided sufficient time for BCP organization into onion-like structures with PB as the outermost layer, owing to the preferential interaction of PB with the surroundings. BCP molecular weight was found to influence the critical evaporation rate corresponding to the morphological transition from ellipsoid to onion-like particles, as well as the ellipsoid aspect ratio. DPD simulations produced morphologies similar to those obtained from experiments and thus elucidated the mechanism and driving forces responsible for the evaporation-induced assembly of BCPs into particles with well-defined shapes and morphologies.

Double hydrophilic block copolymer controlled growth and self-assembly of CaCO3 multilayered structures at the air/water interface.

PubMed

Gao, Yun-Xiang; Yu, Shu-Hong; Guo, Xiao-Hui

2006-07-04

Double hydrophilic block copolymers PEG-b-PEI-linear with different PEI block lengths have been examined for CaCO3 mineralization at the air/water interface. The results demonstrated that either PEI length or the solution acidity had a significant influence on the morphogenesis of vaterite crystals at the air/water interface. A possible mechanism for the stratification of CaCO3 vaterite crystals has been proposed. Increasing either PEI length or the initial pH value of the solution will decrease the density of the PEG block anchored on the binding interface and result in exposing more space as binding interface to solution and favoring the subnucleation and stratification growth on the polymer-CaCO3 interface. In contrast, higher density of PEG blocks will stabilize the growing crystals more efficiently and inhibit subnucleation on the polymer-CaCO3 interface, and thus prevent the formation of stratified structures. This study provides an example that it is possible to access morphogenesis of calcium carbonate structures by a combination of a block copolymer with the air/water interface.

Role of solution structure in self-assembly of conjugated block copolymer thin films

DOE PAGES

Brady, Michael A.; Ku, Sung -Yu; Perez, Louis A.; ...

2016-10-24

Conjugated block copolymers provide a pathway to achieve thermally stable nanostructured thin films for organic solar cells. We characterized the structural evolution of poly(3-hexylthiophene)- block-poly(diketopyrrolopyrrole–terthiophene) (P3HT- b-DPPT-T) from solution to nanostructured thin films. Aggregation of the DPPT-T block of P3HT- b-DPPT-T was found in solution by small-angle X-ray scattering with the P3HT block remaining well-solvated. The nanostructure in thin films was determined using a combination of wide and small-angle X-ray scattering techniques as a function of processing conditions. The structure in solution controlled the initial nanostructure in spin-cast thin films, allowing subsequent thermal annealing processes to further improve the ordering.more » In contrast to the results for thin films, nanostructural ordering was not observed in the bulk samples by small-angle X-ray scattering. Finally, these results suggest the importance of controlling solvent induced aggregation in forming nanostructured thin films of conjugated block copolymers.« less

Inverse design of bulk morphologies in block copolymers using particle swarm optimization

NASA Astrophysics Data System (ADS)

Khadilkar, Mihir; Delaney, Kris; Fredrickson, Glenn

Multiblock polymers are a versatile platform for creating a large range of nanostructured materials with novel morphologies and properties. However, achieving desired structures or property combinations is difficult due to a vast design space comprised of parameters including monomer species, block sequence, block molecular weights and dispersity, copolymer architecture, and binary interaction parameters. Navigating through such vast design spaces to achieve an optimal formulation for a target structure or property set requires an efficient global optimization tool wrapped around a forward simulation technique such as self-consistent field theory (SCFT). We report on such an inverse design strategy utilizing particle swarm optimization (PSO) as the global optimizer and SCFT as the forward prediction engine. To avoid metastable states in forward prediction, we utilize pseudo-spectral variable cell SCFT initiated from a library of defect free seeds of known block copolymer morphologies. We demonstrate that our approach allows for robust identification of block copolymers and copolymer alloys that self-assemble into a targeted structure, optimizing parameters such as block fractions, blend fractions, and Flory chi parameters.

Role of solution structure in self-assembly of conjugated block copolymer thin films

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

Brady, Michael A.; Ku, Sung -Yu; Perez, Louis A.

Conjugated block copolymers provide a pathway to achieve thermally stable nanostructured thin films for organic solar cells. We characterized the structural evolution of poly(3-hexylthiophene)- block-poly(diketopyrrolopyrrole–terthiophene) (P3HT- b-DPPT-T) from solution to nanostructured thin films. Aggregation of the DPPT-T block of P3HT- b-DPPT-T was found in solution by small-angle X-ray scattering with the P3HT block remaining well-solvated. The nanostructure in thin films was determined using a combination of wide and small-angle X-ray scattering techniques as a function of processing conditions. The structure in solution controlled the initial nanostructure in spin-cast thin films, allowing subsequent thermal annealing processes to further improve the ordering.more » In contrast to the results for thin films, nanostructural ordering was not observed in the bulk samples by small-angle X-ray scattering. Finally, these results suggest the importance of controlling solvent induced aggregation in forming nanostructured thin films of conjugated block copolymers.« less

Complete A-V block: incidental or a part of cor triatriatum dexter.

PubMed

Guler, Y; Akgun, T; Toprak, C; Guler, A; Esen, A M

2014-05-01

Cor triatriatum dexter (CTD) is an extremely rare cardiac anomaly in which the right atrium is divided into two distinct chambers by a membrane. The persistence of the right valve of sinus venosus results in a complete septation of the right atrium. This anomaly is frequently associated with other right-sided cardiac abnormalities. Its clinical manifestation and the need for intervention are determined by the number and the size of the fenestrations on the membrane, associated cardiac anomalies and arrhythmias. We describe a case of CTD in a patient with complete atrioventricular (A-V) block.

Structure to function: Spider silk and human collagen

NASA Astrophysics Data System (ADS)

Rabotyagova, Olena S.

Nature has the ability to assemble a variety of simple molecules into complex functional structures with diverse properties. Collagens, silks and muscles fibers are some examples of fibrous proteins with self-assembling properties. One of the great challenges facing Science is to mimic these designs in Nature to find a way to construct molecules that are capable of organizing into functional supra-structures by self-assembly. In order to do so, a construction kit consisting of molecular building blocks along with a complete understanding on how to form functional materials is required. In this current research, the focus is on spider silk and collagen as fibrous protein-based biopolymers that can shed light on how to generate nanostructures through the complex process of self-assembly. Spider silk in fiber form offers a unique combination of high elasticity, toughness, and mechanical strength, along with biological compatibility and biodegrability. Spider silk is an example of a natural block copolymer, in which hydrophobic and hydrophilic blocks are linked together generating polymers that organize into functional materials with extraordinary properties. Since silks resemble synthetic block copolymer systems, we adopted the principles of block copolymer design from the synthetic polymer literature to build block copolymers based on spider silk sequences. Moreover, we consider spider silk to be an important model with which to study the relationships between structure and properties in our system. Thus, the first part of this work was dedicated to a novel family of spider silk block copolymers, where we generated a new family of functional spider silk-like block copolymers through recombinant DNA technology. To provide fundamental insight into relationships between peptide primary sequence, block composition, and block length and observed morphological and structural features, we used these bioengineered spider silk block copolymers to study secondary structure, morphological features and assembly. Aside from fundamental perspectives, we anticipate that these results will provide a blueprint for the design of precise materials for a range of potential applications such as controlled release devices, functional coatings, components of tissue regeneration materials and environmentally friendly polymers in future studies. In the second part of this work, human collagen type I was studied as another representative of the family of fibrous proteins. Collagen type I is the most abundant extracellular matrix protein in the human body, providing the basis for tissue structure and directing cellular functions. Collagen has a complex structural hierarchy, organized at different length scales, including the characteristic triple helical feature. In the present study we assessed the relationship between collagen structure (native vs. denatured) and sensitivity to UV radiation with a focus on changes in the primary structure, conformation, microstructure and material properties. Free radical reactions are involved in collagen degradation and a mechanism for UV-induced collagen degradation related to structure was proposed. The results from this study demonstrated the role of collagen supramolecular organization (triple helix) in the context of the effects of electromagnetic radiation on extracellular matrices. Owing to the fact that both silks and collagens are proteins that have found widespread interest for biomaterial related needs, we anticipate that the current studies will serve as a foundation for future biomaterial designs with controlled properties. Furthermore, fundamental insight into self-assembly and environmentally-2mediated degradation, will build a foundation for fundamental understanding of the remodeling and functions of these types of fibrous proteins in vivo and in vitro. This type of insight is essential for many areas of scientific inquiry, from drug delivery, to scaffolds for tissue engineering, and to the stability of materials in space.

A Combined Remote Sensing-Numerical Modelling Approach to the Stability Analysis of Delabole Slate Quarry, Cornwall, UK

NASA Astrophysics Data System (ADS)

Havaej, Mohsen; Coggan, John; Stead, Doug; Elmo, Davide

2016-04-01

Rock slope geometry and discontinuity properties are among the most important factors in realistic rock slope analysis yet they are often oversimplified in numerical simulations. This is primarily due to the difficulties in obtaining accurate structural and geometrical data as well as the stochastic representation of discontinuities. Recent improvements in both digital data acquisition and incorporation of discrete fracture network data into numerical modelling software have provided better tools to capture rock mass characteristics, slope geometries and digital terrain models allowing more effective modelling of rock slopes. Advantages of using improved data acquisition technology include safer and faster data collection, greater areal coverage, and accurate data geo-referencing far exceed limitations due to orientation bias and occlusion. A key benefit of a detailed point cloud dataset is the ability to measure and evaluate discontinuity characteristics such as orientation, spacing/intensity and persistence. This data can be used to develop a discrete fracture network which can be imported into the numerical simulations to study the influence of the stochastic nature of the discontinuities on the failure mechanism. We demonstrate the application of digital terrestrial photogrammetry in discontinuity characterization and distinct element simulations within a slate quarry. An accurately geo-referenced photogrammetry model is used to derive the slope geometry and to characterize geological structures. We first show how a discontinuity dataset, obtained from a photogrammetry model can be used to characterize discontinuities and to develop discrete fracture networks. A deterministic three-dimensional distinct element model is then used to investigate the effect of some key input parameters (friction angle, spacing and persistence) on the stability of the quarry slope model. Finally, adopting a stochastic approach, discrete fracture networks are used as input for 3D distinct element simulations to better understand the stochastic nature of the geological structure and its effect on the quarry slope failure mechanism. The numerical modelling results highlight the influence of discontinuity characteristics and kinematics on the slope failure mechanism and the variability in the size and shape of the failed blocks.

Physiological and ultrastructural analysis of elongating mitotic spindles reactivated in vitro

PubMed Central

1986-01-01

We have developed a simple procedure for isolating mitotic spindles from the diatom Stephanopyxis turris and have shown that they undergo anaphase spindle elongation in vitro upon addition of ATP. The isolated central spindle is a barrel-shaped structure with a prominent zone of microtubule overlap. After ATP addition greater than 75% of the spindle population undergoes distinct structural rearrangements: the spindles on average are longer and the two half-spindles are separated by a distinct gap traversed by only a small number of microtubules, the phase-dense material in the overlap zone is gone, and the peripheral microtubule arrays have depolymerized. At the ultrastructural level, we examined serial cross-sections of spindles after 1-, 5-, and 10-min incubations in reactivation medium. Microtubule depolymerization distal to the poles is confirmed by the increased number of incomplete, i.e., c-microtubule profiles specifically located in the region of overlap. After 10 min we see areas of reduced microtubule number which correspond to the gaps seen in the light microscope and an overall reduction in the number of half-spindle microtubules to about one-third the original number. The changes in spindle structure are highly specific for ATP, are dose-dependent, and do not occur with nonhydrolyzable nucleotide analogues. Spindle elongation and gap formation are blocked by 10 microM vanadate, equimolar mixtures of ATP and AMPPNP, and by sulfhydryl reagents. This process is not affected by nocodazole, erythro-9-[3-(2-hydroxynonyl)]adenine, cytochalasin D, and phalloidin. In the presence of taxol, the extent of spindle elongation is increased; however, distinct gaps still form between the two half- spindles. These results show that the response of isolated spindles to ATP is a complex process consisting of several discrete steps including initiation events, spindle elongation mechanochemistry, controlled central spindle microtubule plus-end depolymerization, and loss of peripheral microtubules. They also show that the microtubule overlap zone is an important site of ATP action and suggest that spindle elongation in vitro is best explained by a mechanism of microtubule- microtubule sliding. Spindle elongation in vitro cannot be accounted for by cytoplasmic forces pulling on the poles or by microtubule polymerization. PMID:3733882

Gravity anomaly and crustal structure characteristics in North-South Seismic Belt of China

NASA Astrophysics Data System (ADS)

Shen, Chongyang; Xuan, Songtbai; Yang, Guangliang; Wu, Guiju

2017-04-01

The North-South Seismic Belt (NSSB) is the binary system boundary what is formed by the western Indian plate subduction pushing and the eastern west Pacific asthenosphere rising, and it is one of the three major seismic belts (Tianshan, Taiwan and NSSB) and mainly located between E102°and E107°. And it is mainly composed of topographic gradient zones, faults, cenozoic basins and strong earthquake zones, which form two distinct parts of tectonic and physical features in the west and east. The research results of geophysical and deep tectonic setting in the NSSB show that it is not only a gravity anomaly gradient zone, it is but also a belt of crustal thickness increasing sharply westward of abrupt change. Seismic tomography results show that the anomaly zone is deeper than hundreds of kilometers in the NSSB, and the composition and structure of the crust are more complex. We deployed multiple Gravity and GNSS synchronous detection profiles in the NSSB, and these profiles crossed the mainly faults structure and got thousands of points data. In the research, source analysis, density structure inversion, residual gravity related imaging and normalized full gradient methods were used, and analyzed gravity field, density and their structure features in different positions, finally obtained the crustal density structure section characteristics and depth structure differences. The research results showed that the gravity Bouguer anomaly is similar to the existing large scale result. The Bouguer anomaly is rising significantly from west to east, its trend variation coincides well with the trend change of Moho depth, which is agreeing with the material flows to the peripheral situation of the Tibetan plateau. The obvious difference changes of the residual anomaly is relative to the boundary of structure or main tectonics, it's also connected with the stop degree of the eurasian plate when the material migrates around. The density structure of the gravity profiles mainly reflects basic frame work of the regional crust structure. The earth's crust basically present three layer structure, nearly horizontally distributes, undulation of Moho is obvious, which is consistent with the results of seismic sounding and seismic array detection; in the local area, there are lower density layer zonal distribution in the earth's crust what accelerates the lateral movement in up and middle crust; when the substance of the Tibetan plateau spreads around, the integrity in up and middle crust is well, and it is basically a coupling movement together; in the lower crust, the thickness of the Tibetan plateau is outward gradually thinning, there is decoupling phenomenon in crust-mantle; The results of the gravity and the crustal density structure show that the research area can be divided into several part such as Qinghai-Tibet Plateau, Sichuan-Yunnan block, Ordos block and Alxa block, the transitional zones of the Qinghai-Tibet Plateau and Sichuan basin, and Alxa and Ordos are complex, and Moho slope is bigger, where is the part of strong tectonic activity and strong earthquakes occur easily. The research is of great significance for study the crustal deep structure, geodynamic evolution process and environment of earthquake gestation of the NSSB region.

The Impact of Individual Differences, Types of Model and Social Settings on Block Building Performance among Chinese Preschoolers.

PubMed

Tian, Mi; Deng, Zhu; Meng, Zhaokun; Li, Rui; Zhang, Zhiyi; Qi, Wenhui; Wang, Rui; Yin, Tingting; Ji, Menghui

2018-01-01

Children's block building performances are used as indicators of other abilities in multiple domains. In the current study, we examined individual differences, types of model and social settings as influences on children's block building performance. Chinese preschoolers ( N = 180) participated in a block building activity in a natural setting, and performance was assessed with multiple measures in order to identify a range of specific skills. Using scores generated across these measures, three dependent variables were analyzed: block building skills, structural balance and structural features. An overall MANOVA showed that there were significant main effects of gender and grade level across most measures. Types of model showed no significant effect in children's block building. There was a significant main effect of social settings on structural features, with the best performance in the 5-member group, followed by individual and then the 10-member block building. These findings suggest that boys performed better than girls in block building activity. Block building performance increased significantly from 1st to 2nd year of preschool, but not from second to third. The preschoolers created more representational constructions when presented with a model made of wooden rather than with a picture. There was partial evidence that children performed better when working with peers in a small group than when working alone or working in a large group. It is suggested that future study should examine other modalities rather than the visual one, diversify the samples and adopt a longitudinal investigation.

Keeping the ball rolling: fullerene-like molecular clusters.

PubMed

Kong, Xiang-Jian; Long, La-Sheng; Zheng, Zhiping; Huang, Rong-Bin; Zheng, Lan-Sun

2010-02-16

The discovery of fullerenes in 1985 opened a new chapter in the chemistry of highly symmetric molecules. Fullerene-like metal clusters, characterized by (multi)shell-like structures, are one rapidly developing class of molecules that share this shape. In addition to creating aesthetically pleasing molecular structures, the ordered arrangement of metal atoms within such frameworks provides the opportunity to develop materials with properties not readily achieved in corresponding mononuclear or lower-nuclearity complexes. In this Account, we survey the great variety of fullerene-like metal-containing clusters with an emphasis on their synthetic and structural chemistry, a first step in the discussion of this fascinating field of cluster chemistry. We group the compounds of interest into three categories based on the atomic composition of the cluster core: those with formal metal-metal bonding, those characterized by ligand participation, and those supported by polyoxometalate building blocks. The number of clusters in the first group, containing metal-metal bonds, is relatively small. However, because of the unique and complex bonding scenarios observed for some of these species, these metalloid clusters present a number of research questions with significant ramifications. Because these cores contain molecular clusters of precious metals at the nanoscale, they offer an opportunity to study chemical properties at size ranges from the molecular to nanoscale and to gain insights into the electronic structures and properties of nanomaterials of similar chemical compositions. Clusters of the second type, whose core structures are facilitated by ligand participation, could aid in the development of functional materials. Of particular interest are the magnetic clusters containing both transition and lanthanide elements. A series of such heterometallic clusters that we prepared demonstrates diverse magnetic properties including antiferromagnetism, ferrimagnetism, and ferromagnetism. Considering the diversity of their composition, their distinct electronic structures, and the disparate coordination behaviors of the different metal elements, these materials suggest abundant opportunities for designing multifunctional materials with varied structures. The third type of clusters that we discuss are based on polyoxometalates, in particular those containing pentagonal units. However, unlike in fullerene chemistry, which does not allow the use of discrete pentagonal building blocks, the metal oxide-based pentagonal units can be used as fundamental building blocks for constructing various Keplerate structures. These structures also have a variety of functions, including intriguing magnetic properties in some cases. Coupled with different linking groups, such pentagonal units can be used for the assembly of a large number of spherical molecules whose properties can be tuned and optimized. Although this Account focuses on the topological aspects of fullerene-like metal clusters, we hope that this topical review will stimulate more efforts in the exploratory synthesis of new fullerene-like clusters. More importantly, we hope that further study of the bonding interactions and properties of these molecules will lead to the development of new functional materials.

An Archaean Tonalite-Trondhjemite-Granodiorite Association of the Kursk Block (Voronezh Massif): Composition, Age, and Correlation with the Ukrainian Shield

NASA Astrophysics Data System (ADS)

Savko, K. A.; Samsonov, A. V.; Larionov, A. N.; Korish, E. Kh.; Bazikov, N. S.

2018-01-01

Framing of the Archaean greenstone belts of the Kursk Block (KB) of the East Sarmatia preserves rocks of the TTG association: those do not form massifs with distinct boundaries, but occur as fields gradually transiting into gneisses and migmatites. According to Sm-Nd isotope-geochemical data, the TTG are characterized by positive values of ɛNd(2960) = +0.3…+1.6 and protolith model ages of T Nd( DM) = 3100-3200 Ma. Magmatic protoliths of the Kursk Block TTG were formed about 2960 Ma by melting from a juvenile basite source. These age estimates are significantly younger than heterochronous (3.19, 3.13 and 3.07 Ga) TTGs of the Middle Dnieper granite-greenstone terrane. On the other hand, the similarity of ɛNd(T) implies a single source of their protoliths. Consequently, the KB TTGs, apparently, are a result of transformation of an older sial crust preserved within the Middle Dnieper Block.

New database for improving virtual system “body-dress”

NASA Astrophysics Data System (ADS)

Yan, J. Q.; Zhang, S. C.; Kuzmichev, V. E.; Adolphe, D. C.

2017-10-01

The aim of this exploration is to develop a new database of solid algorithms and relations between the dress fit and the fabric mechanical properties, the pattern block construction for improving the reality of virtual system “body-dress”. In virtual simulation, the system “body-clothing” sometimes shown distinct results with reality, especially when important changes in pattern block and fabrics were involved. In this research, to enhance the simulation process, diverse fit parameters were proposed: bottom height of dress, angle of front center contours, air volume and its distribution between dress and dummy. Measurements were done and optimized by ruler, camera, 3D body scanner image processing software and 3D modeling software. In the meantime, pattern block indexes were measured and fabric properties were tested by KES. Finally, the correlation and linear regression equations between indexes of fabric properties, pattern blocks and fit parameters were investigated. In this manner, new database could be extended in programming modules of virtual design for more realistic results.

FunBlocks. A modular framework for AmI system development.

PubMed

Baquero, Rafael; Rodríguez, José; Mendoza, Sonia; Decouchant, Dominique; Papis, Alfredo Piero Mateos

2012-01-01

The last decade has seen explosive growth in the technologies required to implement Ambient Intelligence (AmI) systems. Technologies such as facial and speech recognition, home networks, household cleaning robots, to name a few, have become commonplace. However, due to the multidisciplinary nature of AmI systems and the distinct requirements of different user groups, integrating these developments into full-scale systems is not an easy task. In this paper we propose FunBlocks, a minimalist modular framework for the development of AmI systems based on the function module abstraction used in the IEC 61499 standard for distributed control systems. FunBlocks provides a framework for the development of AmI systems through the integration of modules loosely joined by means of an event-driven middleware and a module and sensor/actuator catalog. The modular design of the FunBlocks framework allows the development of AmI systems which can be customized to a wide variety of usage scenarios.

FunBlocks. A Modular Framework for AmI System Development

PubMed Central

Baquero, Rafael; Rodríguez, José; Mendoza, Sonia; Decouchant, Dominique; Papis, Alfredo Piero Mateos

2012-01-01

The last decade has seen explosive growth in the technologies required to implement Ambient Intelligence (AmI) systems. Technologies such as facial and speech recognition, home networks, household cleaning robots, to name a few, have become commonplace. However, due to the multidisciplinary nature of AmI systems and the distinct requirements of different user groups, integrating these developments into full-scale systems is not an easy task. In this paper we propose FunBlocks, a minimalist modular framework for the development of AmI systems based on the function module abstraction used in the IEC 61499 standard for distributed control systems. FunBlocks provides a framework for the development of AmI systems through the integration of modules loosely joined by means of an event-driven middleware and a module and sensor/actuator catalog. The modular design of the FunBlocks framework allows the development of AmI systems which can be customized to a wide variety of usage scenarios. PMID:23112599

Compartmentalization Technologies via Self-Assembly and Cross-Linking of Amphiphilic Random Block Copolymers in Water.

PubMed

Matsumoto, Mayuko; Terashima, Takaya; Matsumoto, Kazuma; Takenaka, Mikihito; Sawamoto, Mitsuo

2017-05-31

Orthogonal self-assembly and intramolecular cross-linking of amphiphilic random block copolymers in water afforded an approach to tailor-make well-defined compartments and domains in single polymer chains and nanoaggregates. For a double compartment single-chain polymer, an amphiphilic random block copolymer bearing hydrophilic poly(ethylene glycol) (PEG) and hydrophobic dodecyl, benzyl, and olefin pendants was synthesized by living radical polymerization (LRP) and postfunctionalization; the dodecyl and benzyl units were incorporated into the different block segments, whereas PEG pendants were statistically attached along a chain. The copolymer self-folded via the orthogonal self-assembly of hydrophobic dodecyl and benzyl pendants in water, followed by intramolecular cross-linking, to form a single-chain polymer carrying double yet distinct hydrophobic nanocompartments. A single-chain cross-linked polymer with a chlorine terminal served as a globular macroinitiator for LRP to provide an amphiphilic tadpole macromolecule comprising a hydrophilic nanoparticle and a hydrophobic polymer tail; the tadpole thus self-assembled into multicompartment aggregates in water.

IN UTERO EXPOSURE TO THE FUNGICIDE PROCYMIDONE AND DIBUTYL PHTHALATE PRODUCE DOSE ADDITIVE DISRUPTIONS OF MALE RAT SEXUAL DIFFERENTIATION

EPA Science Inventory

Procymidone (PRO) and dibutyl phthalate (DBP) alter male rat sexual differentiation by disrupting the androgen-signaling pathway via distinctly different cellular mechanisms of toxicity. DBP inhibits fetal Leydig cell androgen production whereas PRO binds AR and blocks androgen a...

Studies on the contributions of steric and polarity effects to the H2S-binding properties of Vitreoscilla hemoglobin

NASA Astrophysics Data System (ADS)

Wang, Dandan; Wang, Hui; Li, Haichao; Liu, Li; Li, Zhengqiang

2017-01-01

We have reported recently that Vitreoscilla hemoglobin (VHb) is a potential H2S receptor and storage molecule in bacterial metabolism. In this study, molecular cloning and site-directed mutagenesis were employed to investigate the structural basis for H2S binding. Association and dissociation rate constants (kon and koff) were determined using stopped-flow rapid-scanning spectrophotometry and compared with those for wild type VHb. Several unanticipated factors were found to govern H2S binding properties, due to the distinct structure of VHb. The results presented in this paper show that: i) bulkier residues at positions E7 and E11 decrease H2S binding accessibility, while the residue located at position B10 blocks bound H2S from escaping. ii) hydroxyl sidechains within the distal heme pocket reduce H2S reactivity to VHb; iii) Pro(E8) is involved in moving the E7-E10 loop region to trigger opening of the distal heme pocket to facilitate H2S binding.

Mechanistic basis for the recognition of a misfolded protein by the molecular chaperone Hsp90.

PubMed

Oroz, Javier; Kim, Jin Hae; Chang, Bliss J; Zweckstetter, Markus

2017-04-01

The critical toxic species in over 40 human diseases are misfolded proteins. Their interaction with molecular chaperones such as Hsp90, which preferentially interacts with metastable proteins, is essential for the blocking of disease progression. Here we used nuclear magnetic resonance (NMR) spectroscopy to determine the three-dimensional structure of the misfolded cytotoxic monomer of the amyloidogenic human protein transthyretin, which is characterized by the release of the C-terminal β-strand and perturbations of the A-B loop. The misfolded transthyretin monomer, but not the wild-type protein, binds to human Hsp90. In the bound state, the Hsp90 dimer predominantly populates an open conformation, and transthyretin retains its globular structure. The interaction surface for the transthyretin monomer comprises the N-terminal and middle domains of Hsp90 and overlaps with that of the Alzheimer's-disease-related protein tau. Taken together, the data suggest that Hsp90 uses a mechanism for the recognition of aggregation-prone proteins that is largely distinct from those of other Hsp90 clients.

Dual priming oligonucleotide system for the multiplex detection of respiratory viruses and SNP genotyping of CYP2C19 gene.

PubMed

Chun, Jong-Yoon; Kim, Kyoung-Joong; Hwang, In-Taek; Kim, Yun-Jee; Lee, Dae-Hoon; Lee, In-Kyoung; Kim, Jong-Kee

2007-01-01

Successful PCR starts with proper priming between an oligonucleotide primer and the template DNA. However, the inevitable risk of mismatched priming cannot be avoided in the currently used primer system, even though considerable time and effort are devoted to primer design and optimization of reaction conditions. Here, we report a novel dual priming oligonucleotide (DPO) which contains two separate priming regions joined by a polydeoxyinosine linker. The linker assumes a bubble-like structure which itself is not involved in priming, but rather delineates the boundary between the two parts of the primer. This structure results in two primer segments with distinct annealing properties: a longer 5'-segment that initiates stable priming, and a short 3'-segment that determines target-specific extension. This DPO-based system is a fundamental tool for blocking extension of non-specifically primed templates, and thereby generates consistently high PCR specificity even under less than optimal PCR conditions. The strength and utility of the DPO system are demonstrated here using multiplex PCR and SNP genotyping PCR.

Structural analysis of autoinhibition in the Ras-specific exchange factor RasGRP1

PubMed Central

Iwig, Jeffrey S; Vercoulen, Yvonne; Das, Rahul; Barros, Tiago; Limnander, Andre; Che, Yan; Pelton, Jeffrey G; Wemmer, David E; Roose, Jeroen P; Kuriyan, John

2013-01-01

RasGRP1 and SOS are Ras-specific nucleotide exchange factors that have distinct roles in lymphocyte development. RasGRP1 is important in some cancers and autoimmune diseases but, in contrast to SOS, its regulatory mechanisms are poorly understood. Activating signals lead to the membrane recruitment of RasGRP1 and Ras engagement, but it is unclear how interactions between RasGRP1 and Ras are suppressed in the absence of such signals. We present a crystal structure of a fragment of RasGRP1 in which the Ras-binding site is blocked by an interdomain linker and the membrane-interaction surface of RasGRP1 is hidden within a dimerization interface that may be stabilized by the C-terminal oligomerization domain. NMR data demonstrate that calcium binding to the regulatory module generates substantial conformational changes that are incompatible with the inactive assembly. These features allow RasGRP1 to be maintained in an inactive state that is poised for activation by calcium and membrane-localization signals. DOI: http://dx.doi.org/10.7554/eLife.00813.001 PMID:23908768

Shaping Crystal-Crystal Phase Transitions

NASA Astrophysics Data System (ADS)

Du, Xiyu; van Anders, Greg; Dshemuchadse, Julia; Glotzer, Sharon

Previous computational and experimental studies have shown self-assembled structure depends strongly on building block shape. New synthesis techniques have led to building blocks with reconfigurable shape and it has been demonstrated that building block reconfiguration can induce bulk structural reconfiguration. However, we do not understand systematically how this transition happens as a function of building block shape. Using a recently developed ``digital alchemy'' framework, we study the thermodynamics of shape-driven crystal-crystal transitions. We find examples of shape-driven bulk reconfiguration that are accompanied by first-order phase transitions, and bulk reconfiguration that occurs without any thermodynamic phase transition. Our results suggest that for well-chosen shapes and structures, there exist facile means of bulk reconfiguration, and that shape-driven bulk reconfiguration provides a viable mechanism for developing functional materials.

REACTOR MODERATOR STRUCTURE

DOEpatents

Fraas, A.P.; Tudor, J.J.

1963-08-01

An improved moderator structure for nuclear reactors consists of moderator blocks arranged in horizontal layers to form a multiplicity of vertically stacked columns of blocks. The blocks in each vertical column are keyed together, and a ceramic grid is disposed between each horizontal layer of blocks. Pressure plates cover- the lateral surface of the moderator structure in abutting relationship with the peripheral terminal lengths of the ceramic grids. Tubular springs are disposed between the pressure plates and a rigid external support. The tubular springs have their axes vertically disposed to facilitate passage of coolant gas through the springs and are spaced apart a selected distance such that at sonae preselected point of spring deflection, the sides of the springs will contact adjacent springs thereby causing a large increase in resistance to further spring deflection. (AEC)

Repair, Evaluation, Maintenance, and Rehabilitation Research Program: Case Histories of Corps Breakwater and Jetty Structures. Report 5. North Atlantic Division

DTIC Science & Technology

1988-11-01

TERMS (Continue on reverse if necessary and identify by block number) FIELD GROUP SUB-GROUP Breakwater REMR (Repair, Evaluation, Concrete armor units...Maintenance, and Rehabilitation) Jetty Rubble-mound structures 19. ABSTRACT (Continue on reverse if necessary and identify by block number) :-This...have been repaired since construction. Other construction materials that have been used include steel, dolosse, concrete cap, concrete block , and

Expansion and improvements of the FORMA system for response and load analysis. Volume 1: Programming manual

NASA Technical Reports Server (NTRS)

Wohlen, R. L.

1976-01-01

Techniques are presented for the solution of structural dynamic systems on an electronic digital computer using FORMA (FORTRAN Matrix Analysis). FORMA is a library of subroutines coded in FORTRAN 4 for the efficient solution of structural dynamics problems. These subroutines are in the form of building blocks that can be put together to solve a large variety of structural dynamics problems. The obvious advantage of the building block approach is that programming and checkout time are limited to that required for putting the blocks together in the proper order.

On the representation of atmospheric blocking in EURO-CORDEX control runs

NASA Astrophysics Data System (ADS)

Jury, Martin W.; García, Sixto; Gutiérrez, José M.

2017-04-01

While regional climate models (RCMs) have been shown to yield improved projections, due to better representations of orography and higher resolved scales, impacts on mesoscale phenomena like atmospheric blocking have been hardly addressed. In this study we clarify if the EURO-CORDEX domain is large enough to allow the RCMs to significantly amplify the blocking representation in reference to the underlying driving data. Therefore, we analyzed blocking accompanying anomalies in temperature near the surface (TAS) and precipitation rate (PR) for a set of RCMs. 5 RCMs stem from the ensemble of EURO-CORDEX control runs, while 3 RCMs are WRF models with different nudging realizations, all of them are driven by ERA-Interim. The used blocking detection method detects blockings by localizing high pressure systems between 55°N and 65°N with the use of geopotential height gradients on the 500 hPa level (Z500), and was applied to ERA-Interim and the mentioned RCM data between 1981 and 2010. Detected blockings centers were spatially attributed to three sectors, which have been shown to display distinctive impacts on TAS and PR during blocking episodes. As a reference for TAS and PR we used 86 weather stations across Europe from the ECA&D dataset. Our results indicate, that little improvement can be expected in the representation of Z500 fields by the RCMs. Most of them show less blocking than the driving data, while blocking representation was most in agreement with the driving data for RCMs that have been strongly conditioned to the driving data. Further, in our idealized setting the RCMs were not able to reproduce the anomalies for TAS connected to blocking. Moreover, using the blocking index of the driving data could be considered correct, because the representation of TAS and PR for falsely detected blocking and non-blocking days in the RCMs did not deviate strongly.

Structural characterization of nonactive site, TrkA-selective kinase inhibitors

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

Su, Hua-Poo; Rickert, Keith; Burlein, Christine

Current therapies for chronic pain can have insufficient efficacy and lead to side effects, necessitating research of novel targets against pain. Although originally identified as an oncogene, Tropomyosin-related kinase A (TrkA) is linked to pain and elevated levels of NGF (the ligand for TrkA) are associated with chronic pain. Antibodies that block TrkA interaction with its ligand, NGF, are in clinical trials for pain relief. Here, we describe the identification of TrkA-specific inhibitors and the structural basis for their selectivity over other Trk family kinases. The X-ray structures reveal a binding site outside the kinase active site that uses residuesmore » from the kinase domain and the juxtamembrane region. Three modes of binding with the juxtamembrane region are characterized through a series of ligand-bound complexes. The structures indicate a critical pharmacophore on the compounds that leads to the distinct binding modes. The mode of interaction can allow TrkA selectivity over TrkB and TrkC or promiscuous, pan-Trk inhibition. This finding highlights the difficulty in characterizing the structure-activity relationship of a chemical series in the absence of structural information because of substantial differences in the interacting residues. These structures illustrate the flexibility of binding to sequences outside of—but adjacent to—the kinase domain of TrkA. This knowledge allows development of compounds with specificity for TrkA or the family of Trk proteins.« less

Asymmetric block copolymer membranes with ultrahigh porosity and hierarchical pore structure by plain solvent evaporation.

PubMed

Yu, H; Qiu, X; Behzad, A R; Musteata, V; Smilgies, D-M; Nunes, S P; Peinemann, K-V

2016-10-04

Membranes with a hierarchical porous structure could be manufactured from a block copolymer blend by pure solvent evaporation. Uniform pores in a 30 nm thin skin layer supported by a macroporous structure were formed. This new process is attractive for membrane production because of its simplicity and the lack of liquid waste.

Functionalized coronenes: synthesis, solid structure, and properties.

PubMed

Wu, Di; Zhang, Hua; Liang, Jinhua; Ge, Haojie; Chi, Chunyan; Wu, Jishan; Liu, Sheng Hua; Yin, Jun

2012-12-21

The construction of coronenes using simple building blocks is a challenging task. In this work, triphenylene was used as a building block to construct functionalized coronenes, and their solid structures and optoelectronic properties were investigated. The single crystal structures showed that coronenes have different packing motifs. Their good solubility and photostability make them potential solution-processable candidates for organic devices.

Coding the Assembly of Polyoxotungstates with a Programmable Reaction System.

PubMed

Ruiz de la Oliva, Andreu; Sans, Victor; Miras, Haralampos N; Long, De-Liang; Cronin, Leroy

2017-05-01

Chemical transformations are normally conducted in batch or flow mode, thereby allowing the chemistry to be temporally or spatially controlled, but these approaches are not normally combined dynamically. However, the investigation of the underlying chemistry masked by the self-assembly processes that often occur in one-pot reactions and exploitation of the potential of complex chemical systems requires control in both time and space. Additionally, maintaining the intermediate constituents of a self-assembled system "off equilibrium" and utilizing them dynamically at specific time intervals provide access to building blocks that cannot coexist under one-pot conditions and ultimately to the formation of new clusters. Herein, we implement the concept of a programmable networked reaction system, allowing us to connect discrete "one-pot" reactions that produce the building block{W 11 O 38 } ≡ {W 11 } under different conditions and control, in real time, the assembly of a series of polyoxometalate clusters {W 12 O 42 } ≡ {W 12 }, {W 22 O 74 } ≡ {W 22 } 1a, {W 34 O 116 } ≡ {W 34 } 2a, and {W 36 O 120 } ≡ {W 36 } 3a, using pH and ultraviolet-visible monitoring. The programmable networked reaction system reveals that is possible to assemble a range of different clusters using {W 11 }-based building blocks, demonstrating the relationship between the clusters within the family of iso-polyoxotungstates, with the final structural motif being entirely dependent on the building block libraries generated in each separate reaction space within the network. In total, this approach led to the isolation of five distinct inorganic clusters using a "fixed" set of reagents and using a fully automated sequence code, rather than five entirely different reaction protocols. As such, this approach allows us to discover, record, and implement complex one-pot reaction syntheses in a more general way, increasing the yield and reproducibility and potentially giving access to nonspecialists.

Erythro-9-(2-hydroxy-3-nonyl)adenine (EHNA) blocks differentiation and maintains the expression of pluripotency markers in human embryonic stem cells.

PubMed

Burton, Peter; Adams, David R; Abraham, Achamma; Allcock, Robert W; Jiang, Zhong; McCahill, Angela; Gilmour, Jane; McAbney, John; Kaupisch, Alexandra; Kane, Nicole M; Baillie, George S; Baker, Andrew H; Milligan, Graeme; Houslay, Miles D; Mountford, Joanne C

2010-12-15

hESCs (human embryonic stem cells) have enormous potential for use in pharmaceutical development and therapeutics; however, to realize this potential, there is a requirement for simple and reproducible cell culture methods that provide adequate numbers of cells of suitable quality. We have discovered a novel way of blocking the spontaneous differentiation of hESCs in the absence of exogenous cytokines by supplementing feeder-free conditions with EHNA [erythro-9-(2-hydroxy-3-nonyl)adenine], an established inhibitor of ADA (adenosine deaminase) and cyclic nucleotide PDE2 (phosphodiesterase 2). hESCs maintained in feeder-free conditions with EHNA for more than ten passages showed no reduction in hESC-associated markers including NANOG, POU5F1 (POU domain class 5 transcription factor 1, also known as Oct-4) and SSEA4 (stage-specific embryonic antigen 4) compared with cells maintained in feeder-free conditions containing bFGF (basic fibroblast growth factor). Spontaneous differentiation was reversibly suppressed by the addition of EHNA, but, upon removing EHNA, hESC populations underwent efficient spontaneous, multi-lineage and directed differentiation. EHNA also acts as a strong blocker of directed neuronal differentiation. Chemically distinct inhibitors of ADA and PDE2 lacked the capacity of EHNA to suppress hESC differentiation, suggesting that the effect is not driven by inhibition of either ADA or PDE2. Preliminary structure-activity relationship analysis found the differentiation-blocking properties of EHNA to reside in a pharmacophore comprising a close adenine mimetic with an extended hydrophobic substituent in the 8- or 9-position. We conclude that EHNA and simple 9-alkyladenines can block directed neuronal and spontaneous differentiation in the absence of exogenous cytokine addition, and may provide a useful replacement for bFGF in large-scale or cGMP-compliant processes.

Coding the Assembly of Polyoxotungstates with a Programmable Reaction System

PubMed Central

2017-01-01

Chemical transformations are normally conducted in batch or flow mode, thereby allowing the chemistry to be temporally or spatially controlled, but these approaches are not normally combined dynamically. However, the investigation of the underlying chemistry masked by the self-assembly processes that often occur in one-pot reactions and exploitation of the potential of complex chemical systems requires control in both time and space. Additionally, maintaining the intermediate constituents of a self-assembled system “off equilibrium” and utilizing them dynamically at specific time intervals provide access to building blocks that cannot coexist under one-pot conditions and ultimately to the formation of new clusters. Herein, we implement the concept of a programmable networked reaction system, allowing us to connect discrete “one-pot” reactions that produce the building block{W11O38} ≡ {W11} under different conditions and control, in real time, the assembly of a series of polyoxometalate clusters {W12O42} ≡ {W12}, {W22O74} ≡ {W22} 1a, {W34O116} ≡ {W34} 2a, and {W36O120} ≡ {W36} 3a, using pH and ultraviolet–visible monitoring. The programmable networked reaction system reveals that is possible to assemble a range of different clusters using {W11}-based building blocks, demonstrating the relationship between the clusters within the family of iso-polyoxotungstates, with the final structural motif being entirely dependent on the building block libraries generated in each separate reaction space within the network. In total, this approach led to the isolation of five distinct inorganic clusters using a “fixed” set of reagents and using a fully automated sequence code, rather than five entirely different reaction protocols. As such, this approach allows us to discover, record, and implement complex one-pot reaction syntheses in a more general way, increasing the yield and reproducibility and potentially giving access to nonspecialists. PMID:28414229

Markov prior-based block-matching algorithm for superdimension reconstruction of porous media

NASA Astrophysics Data System (ADS)

Li, Yang; He, Xiaohai; Teng, Qizhi; Feng, Junxi; Wu, Xiaohong

2018-04-01

A superdimension reconstruction algorithm is used for the reconstruction of three-dimensional (3D) structures of a porous medium based on a single two-dimensional image. The algorithm borrows the concepts of "blocks," "learning," and "dictionary" from learning-based superresolution reconstruction and applies them to the 3D reconstruction of a porous medium. In the neighborhood-matching process of the conventional superdimension reconstruction algorithm, the Euclidean distance is used as a criterion, although it may not really reflect the structural correlation between adjacent blocks in an actual situation. Hence, in this study, regular items are adopted as prior knowledge in the reconstruction process, and a Markov prior-based block-matching algorithm for superdimension reconstruction is developed for more accurate reconstruction. The algorithm simultaneously takes into consideration the probabilistic relationship between the already reconstructed blocks in three different perpendicular directions (x , y , and z ) and the block to be reconstructed, and the maximum value of the probability product of the blocks to be reconstructed (as found in the dictionary for the three directions) is adopted as the basis for the final block selection. Using this approach, the problem of an imprecise spatial structure caused by a point simulation can be overcome. The problem of artifacts in the reconstructed structure is also addressed through the addition of hard data and by neighborhood matching. To verify the improved reconstruction accuracy of the proposed method, the statistical and morphological features of the results from the proposed method and traditional superdimension reconstruction method are compared with those of the target system. The proposed superdimension reconstruction algorithm is confirmed to enable a more accurate reconstruction of the target system while also eliminating artifacts.

Revitalizing problem based learning: student and tutor attitudes towards a structured tutorial.

PubMed

Espey, Eve; Ogburn, Tony; Kalishman, Summers; Zsemlye, Meggan; Cosgrove, Ellen

2007-03-01

The pre-clinical curriculum at the University of New Mexico School of Medicine is a hybrid model that includes small group, problem-based learning (PBL) tutorials and didactic lectures. A structured tutorial format was piloted for the human sexuality/reproduction organ system block for the PBL component. The objective of this study was to compare the acceptability of the structured format and its effectiveness with that of a traditional PBL tutorial. Students were surveyed after the renal/endocrinology block of 2004 (traditional tutorial format) and after the human sexuality/reproduction block of 2004 (structured tutorial format) (n = 70). Survey questions covered the quality of learning and of tutorial. Students (n = 132) and tutors (n = 24) who participated in human sexuality/reproduction in 2004 and 2005 were surveyed for attitudes about the structured tutorial overall and specific components. Means of responses were compared using t-tests. Students indicated that the structured tutorial format supported a greater improvement in their basic science and clinical knowledge and their ability to evaluate information (p < 0.05). The majority of students and tutors recommended the structured format for tutorials in other blocks. We demonstrated the acceptability of a structured tutorial format to students and faculty. Faculty members perceived greater depth of learning and participation by the students.

Simultaneous conduction over the fast and slow pathways during induction of atrioventricular nodal reentrant arrhythmia with a rate of less than 100 bpm and infra-His block after radiofrequency ablation of the slow pathway.

PubMed

Amasyalı, Basri; Köktürk, Bülent; Otomo, Kiyoshi; Köse, Sedat

2011-04-01

Atrioventricular nodal reentrant tachycardia (AVNRT) is the most common form of paroxysmal regular supraventricular tachycardia in adults. It is typically induced with an anterograde block over the fast pathway (FP) and conduction over the slow pathway (SP), with subsequent retrograde conduction over the FP. Rarely, a simultaneous conduction of a premature atrial complex occurs over the FP and SP to induce AVNRT and is called "one for two phenomenon". We present a 46-year-old woman with atrioventricular nodal rhythm with a rate of 95 beats per minute with distinct electrophysiological characteristics showing simultaneous conduction over the FP and SP during induction of tachycardia and an infra-His block after radiofrequency ablation of the SP.

Changes of hydrodynamic parameters on mountain stream bed within the block ramp influence and possibility of their use for integrated river management

NASA Astrophysics Data System (ADS)

Radecki-Pawlik, Artur; Plesiński, Karol

2016-04-01

In modern river management practices and philosophy one can notice coming more into use ecological friendly hydraulic structures. Those, which are especially needed for river training works, as far as expectation of Water Framework Directive is concerned, are block ramps which are hydraulic structures working similar to riffles known very well from fluvial geomorphology studies and are natural features in streams and rivers. What is important well designed block ramps do not stop fish and invertebrates against migrating, provide natural and esthetical view being built within the river channel, still working as hydraulic engineering structures and might be used in river management in different river ecosystems. The main aim of the research was to describe changes of values of hydrodynamics parameters upstream and downstream of the block ramps and to find out their influence on hydrodynamics of the stream. The study was undertaken on the Porębianka River in the Gorce Mountains, Polish Carpathians. Observed hydrodynamic parameters within the reach of the block ramps depend on the location of measuring point and the influence of individual part of the structure. We concluded that: 1. Hydrodynamic parameters close to block ramps depend on the location of the measurement points in relation to particular elements of the structure; 2. The highest value of velocities don't cause the highest force values, which acting on the bed of the watercourse, because they are rather related to the water level of the channel; 3. The values of mean velocities, shear velocities and shear stresses were similar upstream and downstream the block ramps, which means that the structures stabilize the river bed. This study was performed within the scope of the Science Activity money from Ministry of High Education and Young Scientist's Activity Money of Department of Hydraulics Engineering and Geotechnique, University of Agriculture, Cracow, Poland

Olefinic Thermoplastic Elastomer Gels: Combining Polymer Crystallization and Microphase Separation in a Selective Solvent

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

Armstrong, Daniel P.; Mineart, Kenneth P.; Lee, Byeongdu

Since selectively swollen thermoplastic elastomer gels (TPEGs) afford a wide range of beneficial properties that open new doors to developing elastomer-based technologies, in this study we examine the unique structure-property behavior of TPEGs composed of olefinic block copolymers (OBCs). Unlike their styrenic counterparts typically possessing two chemically different blocks, this class of multiblock copolymers consists of linear polyethylene hard blocks and poly(ethylene-co-α-octene) soft blocks, in which case, microphase separation between the hard and the soft blocks is accompanied by crystallization of the hard blocks. We prepare olefinic TPEGs (OTPEGs) through the incorporation of a primarily aliphatic oil that selectively swellsmore » the soft block and investigate the resultant morphological features through the use of polarized light microscopy and small-/wideangle X-ray scattering. These features are correlated with thermal and mechanical property measurements from calorimetry, rheology, and extensiometry to elucidate the roles of crystallization and self-assembly on gel characteristics and establish useful structure-property relationships.« less

Olefinic Thermoplastic Elastomer Gels: Combining Polymer Crystallization and Microphase Separation in a Selective Solvent

DOE PAGES

Armstrong, Daniel P.; Mineart, Kenneth P.; Lee, Byeongdu; ...

2016-11-01

Since selectively swollen thermoplastic elastomer gels (TPEGs) afford a wide range of beneficial properties that open new doors to developing elastomer-based technologies, in this study we examine the unique structure-property behavior of TPEGs composed of olefinic block copolymers (OBCs). Unlike their styrenic counterparts typically possessing two chemically different blocks, this class of multiblock copolymers consists of linear polyethylene hard blocks and poly(ethylene-co-α-octene) soft blocks, in which case, microphase separation between the hard and the soft blocks is accompanied by crystallization of the hard blocks. We prepare olefinic TPEGs (OTPEGs) through the incorporation of a primarily aliphatic oil that selectively swellsmore » the soft block and investigate the resultant morphological features through the use of polarized light microscopy and small-/wideangle X-ray scattering. These features are correlated with thermal and mechanical property measurements from calorimetry, rheology, and extensiometry to elucidate the roles of crystallization and self-assembly on gel characteristics and establish useful structure-property relationships.« less

Emplacement mechanisms of contrasting debris avalanches at Volcán Mombacho (Nicaragua), provided by structural and facies analysis

NASA Astrophysics Data System (ADS)

Shea, Thomas; van Wyk de Vries, Benjamin; Pilato, Martín

2008-07-01

We study the lithology, structure, and emplacement of two debris-avalanche deposits (DADs) with contrasting origins and materials from the Quaternary-Holocene Mombacho Volcano, Nicaragua. A clear comparison is possible because both DADs were emplaced onto similar nearly flat (3° slope) topography with no apparent barrier to transport. This lack of confinement allows us to study, in nature, the perfect case scenario of a freely spreading avalanche. In addition, there is good evidence that no substratum was incorporated in the events during flow, so facies changes are related only to internal dynamics. Mombacho shows evidence of at least three large flank collapses, producing the two well-preserved debris avalanches of this study; one on its northern flank, “Las Isletas,” directed northeast, and the other on its southern flank, “El Crater,” directed south. Other south-eastern features indicate that the debris-avalanche corresponding to the third collapse (La Danta) occurred before Las Isletas and El Crater events. The materials involved in each event were similar, except in their alteration state and in the amount of substrata initially included in the collapse. While “El Crater” avalanche shows no signs of substratum involvement and has characteristics of a hydrothermal weakening-related collapse, the “Las Isletas” avalanche involves significant substratum and was generated by gravity spreading-related failure. The latter avalanche may have interacted with Lake Nicaragua during transport, in which case its run-out could have been modified. Through a detailed morphological and structural description of the Mombacho avalanches, we provide two contrasting examples of non-eruptive volcanic flank collapse. We show that, remarkably, even with two distinct collapse mechanisms, the debris avalanches developed the same gross stratigraphy of a coarse layer above a fine layer. This fine layer provided a low friction basal slide layer. Whereas DAD layering and the run-outs are roughly similar, the distribution of structures is different and related to lithology: Las Isletas has clear proximal faults replaced distally by inter-hummock depressions where basal unit zones are exhumed, whereas El Crater has faults throughout, but the basal layer is hidden in the distal zone. Hummocky forms depend on material type, with steep hummocks being formed of coherent lava units, and low hummocks by matrix-rich units. In both avalanches, extensional structures predominate; the upper layers exclusively underwent longitudinal and lateral extension. This is consistent with evidence of only small amounts of block-to-block interactions during bulk horizontal spreading. The base of the moving mass accommodated transport by large amounts of simple shear. We suggest that contractional structures and inter-block collisions seen in many other avalanches are artifacts related to topographic confinement.

The Crustal and Mantle Velocity Structure in Central Asia from 3D Travel Time Tomography

DTIC Science & Technology

2010-09-01

the Turan plate, and the Tarim block. This geologically and tectonically complicated area is also one of the most seismically active regions in the...Asia features large blocks such as the Indian plate, the Afghan block, the Turan plate, and the Tarim block. This geologically and tectonically

Encoders for block-circulant LDPC codes

NASA Technical Reports Server (NTRS)

Divsalar, Dariush (Inventor); Abbasfar, Aliazam (Inventor); Jones, Christopher R. (Inventor); Dolinar, Samuel J. (Inventor); Thorpe, Jeremy C. (Inventor); Andrews, Kenneth S. (Inventor); Yao, Kung (Inventor)

2009-01-01

Methods and apparatus to encode message input symbols in accordance with an accumulate-repeat-accumulate code with repetition three or four are disclosed. Block circulant matrices are used. A first method and apparatus make use of the block-circulant structure of the parity check matrix. A second method and apparatus use block-circulant generator matrices.

Ultrasound guidance in regional anesthesia: state of the art review through challenging clinical scenarios

PubMed Central

Sites, Brian D; Antonakakis, John G

2009-01-01

Ultrasound guided regional anesthesia (UGRA) for peripheral nerve blockade is becoming increasingly popular. The advantage of ultrasound technology is that it affords the anesthesiologist the real time ability to visualize neural structures, needle advancement, and local anesthetic spread. Recent data suggest that UGRA generates improved success rates and reductions in performance times in comparison to traditional approaches. Further, the use of ultrasound technology in peripheral nerve blocks has provided insight into needle–nerve interactions, revealing distinct limitations of nerve stimulator techniques. Given that UGRA requires a unique set of skills, formal standards and guidelines are currently being developed by leadership societies in order to foster education and training. This review article, in a case vignette format, highlights important techniques, concepts, and limitations regarding the use of ultrasound to facilitate regional anesthesia. Clinically relevant aspects of ultrasound physics are also discussed. PMID:22915860

The Sun is Condensed Matter and has a Real Surface

NASA Astrophysics Data System (ADS)

Robitaille, Pierre-Marie

2014-03-01

The idea that the Sun was a gaseous in nature was born from 1858-65. At that time, a group of men, including Herbert Spencer, Father Angelo Secchi, Warren de la Rue, Balfour Stewart, and Benjamin Loewy, advanced that the Sun was a ball of gas. In 1865, Hervé Faye was the first to argue that the solar surface was merely an illusion. Dismissing all signs to the contrary, solar physics has promoted this idea to the present day, as manifested by the Standard Solar Model. In this work, overwhelming observational evidence will be presented that the Sun does indeed possess a distinct surface (see P.M. Robitaille, Forty Lines of Evidence for Condensed Matter -- The Sun on Trial: Liquid Metallic Hydrogen as a Solar Building Block, Progress in Physics, 2013, v. 4, 90-143). Our telescopes and satellites are sampling real structures on the surface of the Sun.

Use of satellite pictures for determining major shield fractures relevant for ore prospecting, northern Finland

NASA Technical Reports Server (NTRS)

Tuominen, H. V.; Aarnisalo, J. (Principal Investigator)

1976-01-01

The author has identified the following significant results. A combined analysis of LANDSAT 1 imagery, aeromagnetic and other maps, and aerial photos has revealed a dense network of bedrock fractures in northern Finland. They form several fracturing zones, which obviously represent surficial manifestations of major fractures. The fractures follow, in general, the eight main trends of crustal shear characteristics of the Baltic Shield, but show distinct deviations from them in detail. The major fracture zones divide the bedrock into a mosaic of polygonal blocks, which in many cases coincide with the main rock units of the area and are characterized by different patterns of internal fracturing. Known mineralizations show a tendency to concentrate along the fracture zones. Optical filtering of original LANDSAT images might provide a rapid tool for the analysis of major structural trends in extensive areas such as shields or entire continents.

Intracellular uptake of macromolecules by brain lymphatic endothelial cells during zebrafish embryonic development.

PubMed

van Lessen, Max; Shibata-Germanos, Shannon; van Impel, Andreas; Hawkins, Thomas A; Rihel, Jason; Schulte-Merker, Stefan

2017-05-12

The lymphatic system controls fluid homeostasis and the clearance of macromolecules from interstitial compartments. In mammals brain lymphatics were only recently discovered, with significant implications for physiology and disease. We examined zebrafish for the presence of brain lymphatics and found loosely connected endothelial cells with lymphatic molecular signature covering parts of the brain without forming endothelial tubular structures. These brain lymphatic endothelial cells (BLECs) derive from venous endothelium, are distinct from macrophages, and are sensitive to loss of Vegfc. BLECs endocytose macromolecules in a selective manner, which can be blocked by injection of mannose receptor ligands. This first report on brain lymphatic endothelial cells in a vertebrate embryo identifies cells with unique features, including the uptake of macromolecules at a single cell level. Future studies will address whether this represents an uptake mechanism that is conserved in mammals and how these cells affect functions of the embryonic and adult brain.

UNRAVELLING THE COMPONENTS OF A MULTI-THERMAL CORONAL LOOP USING MAGNETOHYDRODYNAMIC SEISMOLOGY

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

Prasad, S. Krishna; Jess, D. B.; Klimchuk, J. A.

Coronal loops, constituting the basic building blocks of the active Sun, serve as primary targets to help understand the mechanisms responsible for maintaining multi-million Kelvin temperatures in the solar and stellar coronae. Despite significant advances in observations and theory, our knowledge on the fundamental properties of these structures is limited. Here, we present unprecedented observations of accelerating slow magnetoacoustic waves along a coronal loop that show differential propagation speeds in two distinct temperature channels, revealing the multi-stranded and multithermal nature of the loop. Utilizing the observed speeds and employing nonlinear force-free magnetic field extrapolations, we derive the actual temperature variationmore » along the loop in both channels, and thus are able to resolve two individual components of the multithermal loop for the first time. The obtained positive temperature gradients indicate uniform heating along the loop, rather than isolated footpoint heating.« less

In Silico Identification of Novel APRIL Peptide Antagonists and Binding Insights by Molecular Modeling and Immunosorbent Assays.

PubMed

Silva, Joao H M da; Calmon-Hamaty, Flavia; Savino, Wilson; Hahne, Michael; Caffarena, Ernesto R

2015-01-01

The "A proliferation inducing ligand" protein (APRIL) is a cytokine over-expressed in many transformed and tumoral cells acting onto two distinct receptors of the Tumoral Necrosis Factor B cell maturation antigen (BCMA) and the transmembrane activator and calcium modulator and cyclophilin ligand interactor (TACI). We herein describe, through a detailed computational approach, the molecular interactions between TACI and its ligands APRIL and another structurally similar protein called B-cell activating factor (BAFF) by means of molecular dynamics. Dynamical analysis suggests R84 and D85 residues from TACI as possible mutation candidates, yielding increased affinity between TACI and APRIL. The association of computational simulations, site directed mutagenesis and peptide design could be a powerful tool, driving to better in vitro experiments. Our results contribute to the elucidation of APRIL signaling and help clarify the effects of blocking interaction between APRIL and its receptors through the use of particular peptides.

PIKfyve regulates melanosome biogenesis

PubMed Central

Jahid, Sohail; Sasaki, Junko; Sasaki, Takehiko; Boissy, Raymond E.; Ganesan, Anand K.

2018-01-01

PIKfyve, VAC14, and FIG4 form a complex that catalyzes the production of PI(3,5)P2, a signaling lipid implicated in process ranging from lysosome maturation to neurodegeneration. While previous studies have identified VAC14 and FIG4 mutations that lead to both neurodegeneration and coat color defects, how PIKfyve regulates melanogenesis is unknown. In this study, we sought to better understand the role of PIKfyve in melanosome biogenesis. Melanocyte-specific PIKfyve knockout mice exhibit greying of the mouse coat and the accumulation of single membrane vesicle structures in melanocytes resembling multivesicular endosomes. PIKfyve inhibition blocks melanosome maturation, the processing of the melanosome protein PMEL, and the trafficking of the melanosome protein TYRP1. Taken together, these studies identify a novel role for PIKfyve in controlling the delivery of proteins from the endosomal compartment to the melanosome, a role that is distinct from the role of PIKfyve in the reformation of lysosomes from endolysosomes. PMID:29584722

Epitope-dependent mechanisms of CD27 neutralization revealed by X-ray crystallography

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

Obmolova, Galina; Teplyakov, Alexey; Malia, Thomas J.

CD27 is a T and B cell co-stimulatory protein of the TNF receptor superfamily dependent on the availability of the TNF-like ligand CD70. Two anti-CD27 neutralizing monoclonal antibodies were obtained from mouse hybridoma and subsequently humanized and optimized for binding the target. The two antibodies are similar in terms of their CD27-binding affinity and ability to block NF-κB signaling, however their clearance rates in monkeys are very different. The pharmacokinetics profiles could be epitope dependent. To identify the epitopes, we determined the crystal structure of the ternary complex between CD27 and the Fab fragments of these non-competing antibodies. The structuremore » reveals the binding modes of the antibodies suggesting that their mechanisms of action are distinctly different and provides a possible explanation of the in vivo data.« less

Classification of self-assembling protein nanoparticle architectures for applications in vaccine design

NASA Astrophysics Data System (ADS)

Indelicato, G.; Burkhard, P.; Twarock, R.

2017-04-01

We introduce here a mathematical procedure for the structural classification of a specific class of self-assembling protein nanoparticles (SAPNs) that are used as a platform for repetitive antigen display systems. These SAPNs have distinctive geometries as a consequence of the fact that their peptide building blocks are formed from two linked coiled coils that are designed to assemble into trimeric and pentameric clusters. This allows a mathematical description of particle architectures in terms of bipartite (3,5)-regular graphs. Exploiting the relation with fullerene graphs, we provide a complete atlas of SAPN morphologies. The classification enables a detailed understanding of the spectrum of possible particle geometries that can arise in the self-assembly process. Moreover, it provides a toolkit for a systematic exploitation of SAPNs in bioengineering in the context of vaccine design, predicting the density of B-cell epitopes on the SAPN surface, which is critical for a strong humoral immune response.

Drug delivery systems based on nucleic acid nanostructures.

PubMed

de Vries, Jan Willem; Zhang, Feng; Herrmann, Andreas

2013-12-10

The field of DNA nanotechnology has progressed rapidly in recent years and hence a large variety of 1D-, 2D- and 3D DNA nanostructures with various sizes, geometries and shapes is readily accessible. DNA-based nanoobjects are fabricated by straight forward design and self-assembly processes allowing the exact positioning of functional moieties and the integration of other materials. At the same time some of these nanosystems are characterized by a low toxicity profile. As a consequence, the use of these architectures in a biomedical context has been explored. In this review the progress and possibilities of pristine nucleic acid nanostructures and DNA hybrid materials for drug delivery will be discussed. For the latter class of structures, a distinction is made between carriers with an inorganic core composed of gold or silica and amphiphilic DNA block copolymers that exhibit a soft hydrophobic interior. Copyright © 2013 Elsevier B.V. All rights reserved.

Composition of clusters and building blocks in amylopectins from maize mutants deficient in starch synthase III.

PubMed

Zhu, Fan; Bertoft, Eric; Seetharaman, Koushik

2013-12-18

Branches in amylopectin are distributed along the backbone. Units of the branches are building blocks (smaller) and clusters (larger) based on the distance between branches. In this study, composition of clusters and building blocks of amylopectins from dull1 maize mutants deficient in starch synthase III (SSIII) with a common genetic background (W64A) were characterized and compared with the wild type. Clusters were produced from amylopectins by partial hydrolysis using α-amylase of Bacillus amyloliquefaciens and were subsequently treated with phosphorylase a and β-amylase to produce φ,β-limit dextrins. Clusters were further extensively hydrolyzed with the α-amylase to produce building blocks. Structures of clusters and building blocks were analyzed by diverse chromatographic techniques. The results showed that the dull1 mutation resulted in larger clusters with more singly branched building blocks. The average cluster contained ~5.4 blocks in dull1 mutants and ~4.2 blocks in the wild type. The results are compared with previous results from SSIII-deficient amo1 barley and suggest fundamental differences in the cluster structures.

Credit BG. Southeast and northeast facades of concrete block structure ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Credit BG. Southeast and northeast facades of concrete block structure built in the late 1960s. It is now used to store miscellaneous equipment - Edwards Air Force Base, North Base, Liquid Oxygen Storage Facility, Second Street, Boron, Kern County, CA

Tick Talk: Block Tick Bites and Lyme Disease

MedlinePlus

... Subscribe May 2014 Print this issue Tick Talk Block Tick Bites and Lyme Disease En español Send ... Health Researchers Examine the Structure of Zika Virus Block the Buzzing, Bites, and Bumps Wise Choices To ...

A METHOD FOR USING BLOCKED AND EVENT-RELATED FMRI DATA TO STUDY “RESTING STATE” FUNCTIONAL CONNECTIVITY

PubMed Central

Fair, Damien A.; Schlaggar, Bradley L.; Cohen B.A., Alexander L.; Miezin, Francis M.; Dosenbach, Nico U.F.; Wenger, Kristin K.; Fox, Michael D.; Snyder, Abraham Z.; Raichle, Marcus E.; Petersen, Steven E.

2007-01-01

Resting state functional connectivity MRI (fcMRI) has become a particularly useful tool for studying regional relationships in typical and atypical populations. Because many investigators have already obtained large datasets of task related fMRI, the ability to use this existing task data for resting state fcMRI is of considerable interest. Two classes of datasets could potentially be modified to emulate resting state data. These datasets include: 1) “interleaved” resting blocks from blocked or mixed blocked/event-related sets, and 2) residual timecourses from event-related sets that lack rest blocks. Using correlation analysis, we compared the functional connectivity of resting epochs taken from a mixed blocked/event-related design fMRI data set and the residuals derived from event-related data with standard continuous resting state data to determine which class of data can best emulate resting state data. We show that despite some differences, the functional connectivity for the interleaved resting periods taken from blocked designs is both qualitatively and quantitatively very similar to that of “continuous” resting state data. In contrast, despite being qualitatively similar to “continuous” resting state data, residuals derived from event-related design data had several distinct quantitative differences. These results suggest that the interleaved resting state data such as those taken from blocked or mixed blocked/event-related fMRI designs are well-suited for resting state functional connectivity analyses. Although using event-related data residuals for resting state functional connectivity may still be useful, results should be interpreted with care. PMID:17239622

Total synthesis of TMG-chitotriomycin based on an automated electrochemical assembly of a disaccharide building block.

PubMed

Isoda, Yuta; Sasaki, Norihiko; Kitamura, Kei; Takahashi, Shuji; Manmode, Sujit; Takeda-Okuda, Naoko; Tamura, Jun-Ichi; Nokami, Toshiki; Itoh, Toshiyuki

2017-01-01

The total synthesis of TMG-chitotriomycin using an automated electrochemical synthesizer for the assembly of carbohydrate building blocks is demonstrated. We have successfully prepared a precursor of TMG-chitotriomycin, which is a structurally-pure tetrasaccharide with typical protecting groups, through the methodology of automated electrochemical solution-phase synthesis developed by us. The synthesis of structurally well-defined TMG-chitotriomycin has been accomplished in 10-steps from a disaccharide building block.

Synchrony between sensory and cognitive networks is associated with subclinical variation in autistic traits

PubMed Central

Young, Jacob S.; Smith, David V.; Coutlee, Christopher G.; Huettel, Scott A.

2015-01-01

Individuals with autistic spectrum disorders exhibit distinct personality traits linked to attentional, social, and affective functions, and those traits are expressed with varying levels of severity in the neurotypical and subclinical population. Variation in autistic traits has been linked to reduced functional and structural connectivity (i.e., underconnectivity, or reduced synchrony) with neural networks modulated by attentional, social, and affective functions. Yet, it remains unclear whether reduced synchrony between these neural networks contributes to autistic traits. To investigate this issue, we used functional magnetic resonance imaging to record brain activation while neurotypical participants who varied in their subclinical scores on the Autism-Spectrum Quotient (AQ) viewed alternating blocks of social and nonsocial stimuli (i.e., images of faces and of landscape scenes). We used independent component analysis (ICA) combined with a spatiotemporal regression to quantify synchrony between neural networks. Our results indicated that decreased synchrony between the executive control network (ECN) and a face-scene network (FSN) predicted higher scores on the AQ. This relationship was not explained by individual differences in head motion, preferences for faces, or personality variables related to social cognition. Our findings build on clinical reports by demonstrating that reduced synchrony between distinct neural networks contributes to a range of subclinical autistic traits. PMID:25852527

Rapid self-assembly of block copolymers to photonic crystals

DOEpatents

Xia, Yan; Sveinbjornsson, Benjamin R; Grubbs, Robert H; Weitekamp, Raymond; Miyake, Garret M; Atwater, Harry A; Piunova, Victoria; Daeffler, Christopher Scot; Hong, Sung Woo; Gu, Weiyin; Russell, Thomas P.

2016-07-05

The invention provides a class of copolymers having useful properties, including brush block copolymers, wedge-type block copolymers and hybrid wedge and polymer block copolymers. In an embodiment, for example, block copolymers of the invention incorporate chemically different blocks comprising polymer size chain groups and/or wedge groups that significantly inhibit chain entanglement, thereby enhancing molecular self-assembly processes for generating a range of supramolecular structures, such as periodic nanostructures and microstructures. The present invention also provides useful methods of making and using copolymers, including block copolymers.

Identification and Characterization of Influenza Virus Entry Inhibitors through Dual Myxovirus High-Throughput Screening.

PubMed

Weisshaar, Marco; Cox, Robert; Morehouse, Zachary; Kumar Kyasa, Shiva; Yan, Dan; Oberacker, Phil; Mao, Shuli; Golden, Jennifer E; Lowen, Anice C; Natchus, Michael G; Plemper, Richard K

2016-08-15

Influenza A virus (IAV) infections cause major morbidity and mortality, generating an urgent need for novel antiviral therapeutics. We recently established a dual myxovirus high-throughput screening protocol that combines a fully replication-competent IAV-WSN strain and a respiratory syncytial virus reporter strain for the simultaneous identification of IAV-specific, paramyxovirus-specific, and broad-spectrum inhibitors. In the present study, this protocol was applied to a screening campaign to assess a diverse chemical library with over 142,000 entries. Focusing on IAV-specific hits, we obtained a hit rate of 0.03% after cytotoxicity testing and counterscreening. Three chemically distinct hit classes with nanomolar potency and favorable cytotoxicity profiles were selected. Time-of-addition, minigenome, and viral entry studies demonstrated that these classes block hemagglutinin (HA)-mediated membrane fusion. Antiviral activity extends to an isolate from the 2009 pandemic and, in one case, another group 1 subtype. Target identification through biolayer interferometry confirmed binding of all hit compounds to HA. Resistance profiling revealed two distinct escape mechanisms: primary resistance, associated with reduced compound binding, and secondary resistance, associated with unaltered binding. Secondary resistance was mediated, unusually, through two different pairs of cooperative mutations, each combining a mutation eliminating the membrane-proximal stalk N-glycan with a membrane-distal change in HA1 or HA2. Chemical synthesis of an analog library combined with in silico docking extracted a docking pose for the hit classes. Chemical interrogation spotlights IAV HA as a major druggable target for small-molecule inhibition. Our study identifies novel chemical scaffolds with high developmental potential, outlines diverse routes of IAV escape from entry inhibition, and establishes a path toward structure-aided lead development. This study is one of the first to apply a fully replication-competent third-generation IAV reporter strain to a large-scale high-throughput screen (HTS) drug discovery campaign, allowing multicycle infection and screening in physiologically relevant human respiratory cells. A large number of potential druggable targets was thus chemically interrogated, but mechanistic characterization, positive target identification, and resistance profiling demonstrated that three chemically promising and structurally distinct hit classes selected for further analysis all block HA-mediated membrane fusion. Viral escape from inhibition could be achieved through primary and secondary resistance mechanisms. In silico docking predicted compound binding to a microdomain located at the membrane-distal site of the prefusion HA stalk that was also previously suggested as a target site for chemically unrelated HA inhibitors. This study identifies an unexpected chemodominance of the HA stalk microdomain for small-molecule inhibitors in IAV inhibitor screening campaigns and highlights a novel mechanism of cooperative resistance to IAV entry blockers. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Identification and Characterization of Influenza Virus Entry Inhibitors through Dual Myxovirus High-Throughput Screening

PubMed Central

Weisshaar, Marco; Cox, Robert; Morehouse, Zachary; Kumar Kyasa, Shiva; Yan, Dan; Oberacker, Phil; Mao, Shuli; Lowen, Anice C.; Natchus, Michael G.

2016-01-01

ABSTRACT Influenza A virus (IAV) infections cause major morbidity and mortality, generating an urgent need for novel antiviral therapeutics. We recently established a dual myxovirus high-throughput screening protocol that combines a fully replication-competent IAV-WSN strain and a respiratory syncytial virus reporter strain for the simultaneous identification of IAV-specific, paramyxovirus-specific, and broad-spectrum inhibitors. In the present study, this protocol was applied to a screening campaign to assess a diverse chemical library with over 142,000 entries. Focusing on IAV-specific hits, we obtained a hit rate of 0.03% after cytotoxicity testing and counterscreening. Three chemically distinct hit classes with nanomolar potency and favorable cytotoxicity profiles were selected. Time-of-addition, minigenome, and viral entry studies demonstrated that these classes block hemagglutinin (HA)-mediated membrane fusion. Antiviral activity extends to an isolate from the 2009 pandemic and, in one case, another group 1 subtype. Target identification through biolayer interferometry confirmed binding of all hit compounds to HA. Resistance profiling revealed two distinct escape mechanisms: primary resistance, associated with reduced compound binding, and secondary resistance, associated with unaltered binding. Secondary resistance was mediated, unusually, through two different pairs of cooperative mutations, each combining a mutation eliminating the membrane-proximal stalk N-glycan with a membrane-distal change in HA1 or HA2. Chemical synthesis of an analog library combined with in silico docking extracted a docking pose for the hit classes. Chemical interrogation spotlights IAV HA as a major druggable target for small-molecule inhibition. Our study identifies novel chemical scaffolds with high developmental potential, outlines diverse routes of IAV escape from entry inhibition, and establishes a path toward structure-aided lead development. IMPORTANCE This study is one of the first to apply a fully replication-competent third-generation IAV reporter strain to a large-scale high-throughput screen (HTS) drug discovery campaign, allowing multicycle infection and screening in physiologically relevant human respiratory cells. A large number of potential druggable targets was thus chemically interrogated, but mechanistic characterization, positive target identification, and resistance profiling demonstrated that three chemically promising and structurally distinct hit classes selected for further analysis all block HA-mediated membrane fusion. Viral escape from inhibition could be achieved through primary and secondary resistance mechanisms. In silico docking predicted compound binding to a microdomain located at the membrane-distal site of the prefusion HA stalk that was also previously suggested as a target site for chemically unrelated HA inhibitors. This study identifies an unexpected chemodominance of the HA stalk microdomain for small-molecule inhibitors in IAV inhibitor screening campaigns and highlights a novel mechanism of cooperative resistance to IAV entry blockers. PMID:27252534

Strategic retrieval processing and the impact of knowing when a memory was first created.

PubMed

Roberts, J S; Tsivilis, D; Mayes, A R

2014-04-01

Retrieval orientation refers to a process where participants strategically alter how a memory cue is processed in response to different task demands. In the present study we explored whether retrieval orientation is influenced by knowing when an old stimulus was first encoded. Participants completed separate remember/know test blocks for old items from a recent delay (40min) and old items from a remote delay (48h). Manipulations at encoding ensured that performance levels were matched between these two blocks, thus avoiding confounds with differences in retrieval effort. Importantly, a third test block comprised old items from both delays randomly intermixed. As the nature of the old items varies unpredictably in the mixed block, it should not be possibly to adopt a specific retrieval orientation and the mixed block therefore acts as a control condition. Participants saw the words "mixed," "recent" or "remote" prior to each test block. Comparing ERPs from the recent and remote blocks permitted an investigation of whether participants alter their retrieval orientation in response to the specific length of the retention interval. Comparing ERPs from the pure (recent and remote) test blocks to ERPs from the mixed block permitted an investigation of whether delay information per se led to differences in retrieval strategy. Analysis of the ERP data found no differences between the recent and remote blocks. However, ERPs from these pure blocks were significantly less positive than ERPs from the mixed block from 200ms towards the end of the epoch. The findings suggest that the delay information was useful in a general sense and encouraged retrieval strategies distinct from those engaged in the mixed block. We speculate that such strategies might relate to whether or not the retrieval search is specific and constrained and/or whether processes that serve to reinstate the original encoding context are engaged. Copyright © 2014 Elsevier Inc. All rights reserved.

The Impact of Individual Differences, Types of Model and Social Settings on Block Building Performance among Chinese Preschoolers

PubMed Central

Tian, Mi; Deng, Zhu; Meng, Zhaokun; Li, Rui; Zhang, Zhiyi; Qi, Wenhui; Wang, Rui; Yin, Tingting; Ji, Menghui

2018-01-01

Children’s block building performances are used as indicators of other abilities in multiple domains. In the current study, we examined individual differences, types of model and social settings as influences on children’s block building performance. Chinese preschoolers (N = 180) participated in a block building activity in a natural setting, and performance was assessed with multiple measures in order to identify a range of specific skills. Using scores generated across these measures, three dependent variables were analyzed: block building skills, structural balance and structural features. An overall MANOVA showed that there were significant main effects of gender and grade level across most measures. Types of model showed no significant effect in children’s block building. There was a significant main effect of social settings on structural features, with the best performance in the 5-member group, followed by individual and then the 10-member block building. These findings suggest that boys performed better than girls in block building activity. Block building performance increased significantly from 1st to 2nd year of preschool, but not from second to third. The preschoolers created more representational constructions when presented with a model made of wooden rather than with a picture. There was partial evidence that children performed better when working with peers in a small group than when working alone or working in a large group. It is suggested that future study should examine other modalities rather than the visual one, diversify the samples and adopt a longitudinal investigation. PMID:29441031

Evidence of formation of site-selective inclusion complexation between beta-cyclodextrin and poly(ethylene oxide)-block-poly(propylene oxide)- block-poly(ethylene oxide) copolymers.

PubMed

Tsai, Chi-Chun; Zhang, Wen-Bin; Wang, Chien-Lung; Van Horn, Ryan M; Graham, Matthew J; Huang, Jing; Chen, Yongming; Guo, Mingming; Cheng, Stephen Z D

2010-05-28

A series of inclusion complexes of poly(ethylene oxide)-block-poly(propylene oxide)-block-poly(ethylene oxide) (PEO-b-PPO-b-PEO) with beta-cyclodextrin (beta-CD) was prepared. Their formation, structure, and dynamics were investigated by solution two-dimensional rotating-frame Overhauser effect spectroscopy (2D ROESY) and one-dimensional (1D) and 2D solid-state (13)C NMR. The inclusion complexes between the PEO-b-PPO-b-PEO copolymers and the beta-CDs were formed in aqueous solution and detected by 2D ROESY. The high efficiency of cross polarization and spin diffusion experiments in (13)C solid-state NMR showed that the mobility of the PPO blocks dramatically decreases after beta-CD complexation, indicating that they are selectively incorporated onto the PPO blocks. The hydrophobic cavities of beta-CD restrict the PPO block mobility, which is evidence of the formation of inclusion complexes in the solid state. The 2D wide-line separation NMR experiments suggested that beta-CDs only thread onto the PPO blocks while forming the inclusion complexes. The stoichiometry of inclusion complexes was studied using (1)H NMR, and a 3:1 (PO unit to beta-CD) was found for all inclusion complexes, which indicated that the number of threaded beta-CDs was only dependent on the molecular weight of the PPO blocks. 1D wide angle x-ray diffraction studies demonstrated that the beta-CD in the inclusion complex formed a channel-like structure that is different from the pure beta-CD crystal structure.

Evidence of formation of site-selective inclusion complexation between β-cyclodextrin and poly(ethylene oxide)-block-poly(propylene oxide)- block-poly(ethylene oxide) copolymers

NASA Astrophysics Data System (ADS)

Tsai, Chi-Chun; Zhang, Wen-Bin; Wang, Chien-Lung; Van Horn, Ryan M.; Graham, Matthew J.; Huang, Jing; Chen, Yongming; Guo, Mingming; Cheng, Stephen Z. D.

2010-05-01

A series of inclusion complexes of poly(ethylene oxide)-block-poly(propylene oxide)-block-poly(ethylene oxide) (PEO-b-PPO-b-PEO) with β-cyclodextrin (β-CD) was prepared. Their formation, structure, and dynamics were investigated by solution two-dimensional rotating-frame Overhauser effect spectroscopy (2D ROESY) and one-dimensional (1D) and 2D solid-state C13 NMR. The inclusion complexes between the PEO-b-PPO-b-PEO copolymers and the β-CDs were formed in aqueous solution and detected by 2D ROESY. The high efficiency of cross polarization and spin diffusion experiments in C13 solid-state NMR showed that the mobility of the PPO blocks dramatically decreases after β-CD complexation, indicating that they are selectively incorporated onto the PPO blocks. The hydrophobic cavities of β-CD restrict the PPO block mobility, which is evidence of the formation of inclusion complexes in the solid state. The 2D wide-line separation NMR experiments suggested that β-CDs only thread onto the PPO blocks while forming the inclusion complexes. The stoichiometry of inclusion complexes was studied using H1 NMR, and a 3:1 (PO unit to β-CD) was found for all inclusion complexes, which indicated that the number of threaded β-CDs was only dependent on the molecular weight of the PPO blocks. 1D wide angle x-ray diffraction studies demonstrated that the β-CD in the inclusion complex formed a channel-like structure that is different from the pure β-CD crystal structure.

Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities.

PubMed

Zgadzaj, Rafal; Garrido-Oter, Ruben; Jensen, Dorthe Bodker; Koprivova, Anna; Schulze-Lefert, Paul; Radutoiu, Simona

2016-12-06

Lotus japonicus has been used for decades as a model legume to study the establishment of binary symbiotic relationships with nitrogen-fixing rhizobia that trigger root nodule organogenesis for bacterial accommodation. Using community profiling of 16S rRNA gene amplicons, we reveal that in Lotus, distinctive nodule- and root-inhabiting communities are established by parallel, rather than consecutive, selection of bacteria from the rhizosphere and root compartments. Comparative analyses of wild-type (WT) and symbiotic mutants in Nod factor receptor5 (nfr5), Nodule inception (nin) and Lotus histidine kinase1 (lhk1) genes identified a previously unsuspected role of the nodulation pathway in the establishment of different bacterial assemblages in the root and rhizosphere. We found that the loss of nitrogen-fixing symbiosis dramatically alters community structure in the latter two compartments, affecting at least 14 bacterial orders. The differential plant growth phenotypes seen between WT and the symbiotic mutants in nonsupplemented soil were retained under nitrogen-supplemented conditions that blocked the formation of functional nodules in WT, whereas the symbiosis-impaired mutants maintain an altered community structure in the nitrogen-supplemented soil. This finding provides strong evidence that the root-associated community shift in the symbiotic mutants is a direct consequence of the disabled symbiosis pathway rather than an indirect effect resulting from abolished symbiotic nitrogen fixation. Our findings imply a role of the legume host in selecting a broad taxonomic range of root-associated bacteria that, in addition to rhizobia, likely contribute to plant growth and ecological performance.

Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities

PubMed Central

Zgadzaj, Rafal; Garrido-Oter, Ruben; Jensen, Dorthe Bodker; Koprivova, Anna; Schulze-Lefert, Paul; Radutoiu, Simona

2016-01-01

Lotus japonicus has been used for decades as a model legume to study the establishment of binary symbiotic relationships with nitrogen-fixing rhizobia that trigger root nodule organogenesis for bacterial accommodation. Using community profiling of 16S rRNA gene amplicons, we reveal that in Lotus, distinctive nodule- and root-inhabiting communities are established by parallel, rather than consecutive, selection of bacteria from the rhizosphere and root compartments. Comparative analyses of wild-type (WT) and symbiotic mutants in Nod factor receptor5 (nfr5), Nodule inception (nin) and Lotus histidine kinase1 (lhk1) genes identified a previously unsuspected role of the nodulation pathway in the establishment of different bacterial assemblages in the root and rhizosphere. We found that the loss of nitrogen-fixing symbiosis dramatically alters community structure in the latter two compartments, affecting at least 14 bacterial orders. The differential plant growth phenotypes seen between WT and the symbiotic mutants in nonsupplemented soil were retained under nitrogen-supplemented conditions that blocked the formation of functional nodules in WT, whereas the symbiosis-impaired mutants maintain an altered community structure in the nitrogen-supplemented soil. This finding provides strong evidence that the root-associated community shift in the symbiotic mutants is a direct consequence of the disabled symbiosis pathway rather than an indirect effect resulting from abolished symbiotic nitrogen fixation. Our findings imply a role of the legume host in selecting a broad taxonomic range of root-associated bacteria that, in addition to rhizobia, likely contribute to plant growth and ecological performance. PMID:27864511

Hierarchical structure and dynamics of oligocarbonate-functionalized PEG block copolymer gels

NASA Astrophysics Data System (ADS)

Prabhu, Vivek; Wei, Guangmin; Ali, Samim; Venkataraman, Shrinivas; Yang, Yi Yan; Hedrick, James

Hierarchical, self-assembled block copolymers in aqueous solutions provide advanced materials for biomaterial applications. Recent advancements in the synthesis of aliphatic polycarbonates have shown nontraditional micellar and hierarchical structures driven by the supramolecular assembly of the carbonate block functionality that includes cholesterol, vitamin D, and fluorene. This presentation shall describe the supramolecular assembly structure and dynamics observed by static and dynamic light scattering, small-angle neutron scattering and transmission electron microscopy in a model pi-pi stacking driven fluorene system. The combination of real-space and reciprocal space methods to develop appropriate models that quantify the structure from the micelle to transient gel network will be discussed. 1) Biomedical Research Council, Agency for Science, Technology and Research, Singapore, 2) NIST Materials Genome Initiative.

Analysis of the impact of crude oil price fluctuations on China's stock market in different periods-Based on time series network model

NASA Astrophysics Data System (ADS)

An, Yang; Sun, Mei; Gao, Cuixia; Han, Dun; Li, Xiuming

2018-02-01

This paper studies the influence of Brent oil price fluctuations on the stock prices of China's two distinct blocks, namely, the petrochemical block and the electric equipment and new energy block, applying the Shannon entropy of information theory. The co-movement trend of crude oil price and stock prices is divided into different fluctuation patterns with the coarse-graining method. Then, the bivariate time series network model is established for the two blocks stock in five different periods. By joint analysis of the network-oriented metrics, the key modes and underlying evolutionary mechanisms were identified. The results show that the both networks have different fluctuation characteristics in different periods. Their co-movement patterns are clustered in some key modes and conversion intermediaries. The study not only reveals the lag effect of crude oil price fluctuations on the stock in Chinese industry blocks but also verifies the necessity of research on special periods, and suggests that the government should use different energy policies to stabilize market volatility in different periods. A new way is provided to study the unidirectional influence between multiple variables or complex time series.

Multivariate analysis of subsurface radiometric data in Rongsohkham area, East Khasi Hills district, Meghalaya (India): implication on uranium exploration.

PubMed

Kukreti, B M; Pandey, Pradeep; Singh, R V

2012-08-01

Non-coring based exploratory drilling was under taken in the sedimentary environment of Rangsohkham block, East Khasi Hills district to examine the eastern extension of existing uranium resources located at Domiasiat and Wakhyn in the Mahadek basin of Meghalaya (India). Although radiometric survey and radiometric analysis of surface grab/channel samples in the block indicate high uranium content but the gamma ray logging results of exploratory boreholes in the block, did not obtain the expected results. To understand this abrupt discontinuity between the two sets of data (surface and subsurface) multivariate statistical analysis of primordial radioactive elements (K(40), U(238) and Th(232)) was performed using the concept of representative subsurface samples, drawn from the randomly selected 11 boreholes of this block. The study was performed to a high confidence level (99%), and results are discussed for assessing the U and Th behavior in the block. Results not only confirm the continuation of three distinct geological formations in the area but also the uranium bearing potential in the Mahadek sandstone of the eastern part of Mahadek Basin. Copyright © 2012 Elsevier Ltd. All rights reserved.

The Capricorn Orogen Passive source Array (COPA) in Western Australia

NASA Astrophysics Data System (ADS)

Gessner, K.; Yuan, H.; Murdie, R.; Dentith, M. C.; Johnson, S.; Brett, J.

2015-12-01

COPA is the passive source component of a multi-method geophysical program aimed at assessing the mineral deposits potential of the Proterozoic Capricorn Orogen. Previous results from the active source surveys, receiver functions and magnetotelluric studies show reworked orogenic crust in the orogen that contrasts with more simple crust in the neighbouring Archean cratons, suggesting progressive and punctuated collisional processes during the final amalgamation of the Western Australian craton. Previous seismic studies are all based on line deployment or single station analyses; therefore it is essential to develop 3D seismic images to test whether these observations are representative for the whole orogen. With a careful design that takes advantage of previous passive source surveys, the current long-term and short-term deployments span an area of approximately 500 x 500 km. The 36-month total deployment can guarantee enough data recording for 3D structure imaging using body wave tomography, ambient noise surface wave tomography and P- and S-wave receiver function Common Conversion Point (CCP) stacking techniques. A successive instrument loan from the ANSIR national instrument pool, provided 34 broadband seismometers that have been deployed in the western half of the orogen since March 2014. We expect approximately 40-km lateral resolution near the surface for the techniques we propose, which due to low frequency nature of earthquake waves will degrade to about 100 km near the base of the cratonic lithosphere, which is expected at depths between 200 to 250 km. Preliminary results from the first half of the COPA deployment will be presented in the light of the hypotheses that 1) distinct crustal blocks can be detected continuously throughout the orogen (using ambient noise/body wave tomography); 2) distinct lithologies are present in the crust and upper mantle across the orogen (using receiver function CCP images); and 3) crustal and lithosphere deformation along craton margins in general follows the "wedge" tectonic model (e.g. subduction of Juvenile blocks under the craton mantle as represented by craton-ward dipping sutures.

Distinct Tensile Response of Model Semi-flexible Elastomer Networks

NASA Astrophysics Data System (ADS)

Aguilera-Mercado, Bernardo M.; Cohen, Claude; Escobedo, Fernando A.

2011-03-01

Through coarse-grained molecular modeling, we study how the elastic response strongly depends upon nanostructural heterogeneities in model networks made of semi-flexible chains exhibiting both regular and realistic connectivity. Idealized regular polymer networks have been shown to display a peculiar elastic response similar to that of super-tough natural materials (e.g., organic adhesives inside abalone shells). We investigate the impact of chain stiffness, and the effect of including tri-block copolymer chains, on the network's topology and elastic response. We find in some systems a dual tensile response: a liquid-like behavior at small deformations, and a distinct saw-tooth shaped stress-strain curve at moderate to large deformations. Additionally, stiffer regular networks exhibit a marked hysteresis over loading-unloading cycles that can be deleted by heating-cooling cycles or by performing deformations along different axes. Furthermore, small variations of chain stiffness may entirely change the nature of the network's tensile response from an entropic to an enthalpic elastic regime, and micro-phase separation of different blocks within elastomer networks may significantly enhance their mechanical strength. This work was supported by the American Chemical Society.

Nanocluster building blocks of artificial square spin ice: Stray-field studies of thermal dynamics

NASA Astrophysics Data System (ADS)

Pohlit, Merlin; Porrati, Fabrizio; Huth, Michael; Ohno, Yuzo; Ohno, Hideo; Müller, Jens

2015-05-01

We present measurements of the thermal dynamics of a Co-based single building block of an artificial square spin ice fabricated by focused electron-beam-induced deposition. We employ micro-Hall magnetometry, an ultra-sensitive tool to study the stray field emanating from magnetic nanostructures, as a new technique to access the dynamical properties during the magnetization reversal of the spin-ice nanocluster. The obtained hysteresis loop exhibits distinct steps, displaying a reduction of their "coercive field" with increasing temperature. Therefore, thermally unstable states could be repetitively prepared by relatively simple temperature and field protocols allowing one to investigate the statistics of their switching behavior within experimentally accessible timescales. For a selected switching event, we find a strong reduction of the so-prepared states' "survival time" with increasing temperature and magnetic field. Besides the possibility to control the lifetime of selected switching events at will, we find evidence for a more complex behavior caused by the special spin ice arrangement of the macrospins, i.e., that the magnetic reversal statistically follows distinct "paths" most likely driven by thermal perturbation.

Block-structured grids for complex aerodynamic configurations: Current status

NASA Technical Reports Server (NTRS)

Vatsa, Veer N.; Sanetrik, Mark D.; Parlette, Edward B.

1995-01-01

The status of CFD methods based on the use of block-structured grids for analyzing viscous flows over complex configurations is examined. The objective of the present study is to make a realistic assessment of the usability of such grids for routine computations typically encountered in the aerospace industry. It is recognized at the very outset that the total turnaround time, from the moment the configuration is identified until the computational results have been obtained and postprocessed, is more important than just the computational time. Pertinent examples will be cited to demonstrate the feasibility of solving flow over practical configurations of current interest on block-structured grids.

Lightweight Structures

NASA Technical Reports Server (NTRS)

Whittenberger, J. Daniel

2001-01-01

Present structural concepts for hot static structures are conventional "sheet & stringer" or truss core construction. More weight-efficient concepts such as honeycomb and lattice block are being investigated, in combination with both conventional superalloys and TiAl. Development efforts for components made from TiAl sheet are centered on lower cost methods for sheet and foil production, plus alloy development for higher temperature capability. A low-cost casting technology recently developed for aluminum and steel lattice blocks has demonstrated the required higher strength and stiffness, with weight efficiency approach- ing honeycombs. The current effort is based on extending the temperature capability by developing lattice block materials made from IN-718 and Mar-M247.

[The role of gap junction communication in metastatic B16 melanoma in C57BL mice].

PubMed

Fëdorov, E S; Manikhas, G M; Petrishchëv, N N; Dubina, M V

2006-01-01

The study is concerned with the effects of non-specific blocking gap junction communication with oleamide as well as genesis and spreading of melanoma B16 metastases to the lung in mice C57B1. The blocking exerted no distinct influence on primary tumorigenesis but had a marked effect on metastatic spread. Oleamide treatment during tumor growth led to an increase in area covered by metastases. A correlation was established between metastatic frequency and dosage: 1 mg/kg was followed by an upsurge in frequency of secondary lung tumors while 10 mg/kg--by a drop.

Total synthesis of TMG-chitotriomycin based on an automated electrochemical assembly of a disaccharide building block

PubMed Central

Isoda, Yuta; Sasaki, Norihiko; Kitamura, Kei; Takahashi, Shuji; Manmode, Sujit; Takeda-Okuda, Naoko; Tamura, Jun-ichi

2017-01-01

The total synthesis of TMG-chitotriomycin using an automated electrochemical synthesizer for the assembly of carbohydrate building blocks is demonstrated. We have successfully prepared a precursor of TMG-chitotriomycin, which is a structurally-pure tetrasaccharide with typical protecting groups, through the methodology of automated electrochemical solution-phase synthesis developed by us. The synthesis of structurally well-defined TMG-chitotriomycin has been accomplished in 10-steps from a disaccharide building block. PMID:28684973

Highly ordered gold nanotubes using thiols at a cleavable block copolymer interface.

PubMed

Ryu, Ja-Hyoung; Park, Soojin; Kim, Bokyung; Klaikherd, Akamol; Russell, Thomas P; Thayumanavan, S

2009-07-29

We have prepared functionalized nanoporous thin films from a polystyrene-block-polyethylene oxide block copolymer, which was made cleavable due to the intervening disulfide bond. The cleavage reaction of the disulfide bond leaves behind free thiol groups inside the nanopores of polystyrene thin film. This nanoporous thin film can be used as a template for generating gold nanoring structures. This strategy can provide a facile method to form a highly ordered array of biopolymer or metal-polymer composite structures.

31. Detail of Southeast Light lens and roof structure of ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

31. Detail of Southeast Light lens and roof structure of light gallery, 1985. Taken day after Hurricane Gloria, courtesy of Gerald F. Abbott and Block Island Historical Society. - Block Island Southeast Light, Spring Street & Mohegan Trail at Mohegan Bluffs, New Shoreham, Washington County, RI

Seismic responses and controlling factors of Miocene deepwater gravity-flow deposits in Block A, Lower Congo Basin

NASA Astrophysics Data System (ADS)

Wang, Linlin; Wang, Zhenqi; Yu, Shui; Ngia, Ngong Roger

2016-08-01

The Miocene deepwater gravity-flow sedimentary system in Block A of the southwestern part of the Lower Congo Basin was identified and interpreted using high-resolution 3-D seismic, drilling and logging data to reveal development characteristics and main controlling factors. Five types of deepwater gravity-flow sedimentary units have been identified in the Miocene section of Block A, including mass transport, deepwater channel, levee, abandoned channel and sedimentary lobe deposits. Each type of sedimentary unit has distinct external features, internal structures and lateral characteristics in seismic profiles. Mass transport deposits (MTDs) in particular correspond to chaotic low-amplitude reflections in contact with mutants on both sides. The cross section of deepwater channel deposits in the seismic profile is in U- or V-shape. The channel deposits change in ascending order from low-amplitude, poor-continuity, chaotic filling reflections at the bottom, to high-amplitude, moderate to poor continuity, chaotic or sub-parallel reflections in the middle section and to moderate-weak amplitude, good continuity, parallel or sub-parallel reflections in the upper section. The sedimentary lobes are laterally lobate, which corresponds to high-amplitude, good-continuity, moundy reflection signatures in the seismic profile. Due to sediment flux, faults, and inherited terrain, few mass transport deposits occur in the northeastern part of the study area. The front of MTDs is mainly composed of channel-levee complex deposits, while abandoned-channel and lobe-deposits are usually developed in high-curvature channel sections and the channel terminals, respectively. The distribution of deepwater channel, levee, abandoned channel and sedimentary lobe deposits is predominantly controlled by relative sea level fluctuations and to a lesser extent by tectonism and inherited terrain.

NUCLEAR REACTORS

DOEpatents

Long, E.; Ashby, J.W.

1958-09-16

ABS>A graphite moderator structure is presented for a nuclear reactor compriscd of an assembly of similarly orientated prismatic graphite blocks arranged on spaced longitudinal axes lying in common planes wherein the planes of the walls of the blocks are positioned so as to be twisted reintive to the planes of said axes so thatthe unlmpeded dtrect paths in direction wholly across the walls of the blocks are limited to the width of the blocks plus spacing between the blocks.

Assemblies and methods for mitigating effects of reactor pressure vessel expansion

DOEpatents

Challberg, Roy C.; Gou, Perng-Fei; Chu, Cherk Lam; Oliver, Robert P.

1999-01-01

Support assemblies for allowing RPV radial expansion while simultaneously limiting horizontal, vertical, and azimuthal movement of the RPV within a nuclear reactor are described. In one embodiment, the support assembly includes a support block and a guide block. The support block includes a first portion and a second portion, and the first portion is rigidly coupled to the RPV adjacent the first portion. The guide block is rigidly coupled to a reactor pressure vessel support structure and includes a channel sized to receive the second portion of the support block. The second portion of the support block is positioned in the guide block channel to movably couple the guide block to the support block.

Assemblies and methods for mitigating effects of reactor pressure vessel expansion

DOEpatents

Challberg, R.C.; Gou, P.F.; Chu, C.L.; Oliver, R.P.

1999-07-27

Support assemblies for allowing RPV radial expansion while simultaneously limiting horizontal, vertical, and azimuthal movement of the RPV within a nuclear reactor are described. In one embodiment, the support assembly includes a support block and a guide block. The support block includes a first portion and a second portion, and the first portion is rigidly coupled to the RPV adjacent the first portion. The guide block is rigidly coupled to a reactor pressure vessel support structure and includes a channel sized to receive the second portion of the support block. The second portion of the support block is positioned in the guide block channel to movably couple the guide block to the support block. 6 figs.

Structure-Preserving Smoothing of Biomedical Images

NASA Astrophysics Data System (ADS)

Gil, Debora; Hernàndez-Sabaté, Aura; Burnat, Mireia; Jansen, Steven; Martínez-Villalta, Jordi

Smoothing of biomedical images should preserve gray-level transitions between adjacent tissues, while restoring contours consistent with anatomical structures. Anisotropic diffusion operators are based on image appearance discontinuities (either local or contextual) and might fail at weak inter-tissue transitions. Meanwhile, the output of block-wise and morphological operations is prone to present a block structure due to the shape and size of the considered pixel neighborhood.

2016 Summer Series - Kenneth Cheung: Building Blocks for Aerospace Structures

NASA Image and Video Library

2016-06-16

Strong, ultra-lightweight materials are expected to play a key role in the design of future aircraft and space vehicles. Lower structural mass leads to improved performance, maneuverability, efficiency, range and payload capacity. Dr. Kenneth Cheung is developing cellular composite building blocks, or digital materials, to create transformable aerostructures. In his presentation, Dr. Cheung will discuss the implications of the digital materials and morphing structures.

Express saccades in distinct populations: east, west, and in-between.

PubMed

Knox, Paul C; Wolohan, Felicity D A; Helmy, Mai S

2017-12-01

Express saccades are low latency (80-130 ms), visually guided saccades. While their occurrence is encouraged by the use of gap tasks (the fixation target is extinguished 200 ms prior to the saccade target appearing) and suppressed by the use of overlap tasks (the fixation target remains present when the saccade target appears), there are some healthy, adult participants, "express saccade makers" (ESMs), who persist in generating high proportions (> 30%) of express saccades in overlap conditions. These participants are encountered much more frequently in Chinese participant groups than amongst the Caucasian participants tested to date. What is not known is whether this high number of ESMs is only a feature of Chinese participant groups. More broadly, there are few comparative studies of saccade behaviour across large participant groups drawn from different populations. We, therefore, tested an independent group of 70 healthy adult Egyptian participants, using the same equipment and procedures as employed in the previous studies. Each participant was exposed to two blocks of 200 gap, and two blocks of 200 overlap trials, with block order counterbalanced. Results from the Schwartz Value Survey were used to confirm that this group of participants was culturally distinct from the Chinese and Caucasian (white British) groups tested previously. Fourteen percent (10/70) of this new group were ESMs, and the pattern of latency distribution in these ESMs was identical to that identified in the other participant groups, with a prominent peak in the express latency range in overlap conditions. Overall, we identified three modes in the distribution of saccade latency in overlap conditions, the timing of which (express peak at 110 ms, subsequent peaks at 160 and 210 ms) were strikingly consistent with our previous observations. That these behavioural patterns of saccade latency are observed consistently in large participant groups, drawn from geographically, ethnically, and culturally distinct populations, suggests that they relate to the underlying architecture of the saccade system.

Assembly of the Pamirs: Age and origin of magmatic belts from the southern Tien Shan to the southern Pamirs and their relation to Tibet

USGS Publications Warehouse

Schwab, M.; Ratschbacher, L.; Siebel, W.; McWilliams, M.; Minaev, V.; Lutkov, V.; Chen, F.; Stanek, K.; Nelson, B.; Frisch, W.; Wooden, J.L.

2004-01-01

Magmatic rocks and depositional setting of associated volcaniclastic strata along a north-south traverse spanning the southern Tien Shan and eastern Pamirs of Kyrgyzstan and Tajikistan constrain the tectonics of the Pamirs and Tibet. The northern Pamirs and northwestern Tibet contain the north facing Kunlun suture, the south facing Jinsha suture, and the intervening Carboniferous to Triassic Karakul-Mazar subduction accretion system; the latter is correlated with the Songpan-Garze-Hoh Xi system of Tibet. The Kunlun arc is a composite early Paleozoic to late Paleozoic-Triassic arc. Arc formation in the Pamirs is characterized by ???370-320 Ma volcanism that probably continued until the Triassic. The cryptic Tanymas suture of the southern northern Pamirs is part of the Jinsha suture. A massive ??????227 Ma batholith stitches the Karakul-Mazar complex in the Pamirs. There are striking similarities between the Qiangtang block in the Pamirs and Tibet. Like Tibet, the regional structure of the Pamirs is an anticlinorium that includes the Muskol and Sares domes. Like Tibet, the metamorphic rocks in these domes are equivalents to the Karakul-Mazar-Songpan-Garze system. Granitoids intruding the Qiangtang block yield ???200-230 Ma ages in the Pamirs and in central Tibet. The stratigraphy of the eastern Pshart area in the Pamirs is similar to the Bangong-Nujiang suture zone in the Amdo region of eastern central Tibet, but a Triassic ocean basin sequence is preserved in the Pamirs. Arc-type granitoids that intruded into the eastern Pshart oceanic-basin-arc sequence (???190-160 Ma) and granitoids that cut the southern Qiangtang block (???170-160 Ma) constitute the Rushan-Pshart arc. Cretaceous plutons that intruded the central and southern Pamirs record a long-lasting magmatic history. Their zircons and those from late Miocene xenoliths show that the most distinct magmatic events were Cambro-Ordovician (???410-575 Ma), Triassic (???210-250 Ma; likely due to subduction along the Jinsha suture), Middle Jurassic (???147-195 Ma; subduction along Rushan-Pshart suture), and mainly Cretaceous. Middle and Late Cretaceous magmatism may reflect arc activity in Asia prior to the accretion of the Karakoram block and flat-slab subduction along the Shyok suture north of the Kohistan-Ladakh arc, respectively. Before India and Asia collided, the Pamir region from the Indus-Yarlung to the Jinsha suture was an Andean-style plate margin. Our analysis suggests a relatively simple crustal structure for the Pamirs and Tibet. From the Kunlun arc in the north to the southern Qiangtang block in the south the Pamirs and Tibet likely have a dominantly sedimentary crust, characterized by Karakul-Mazar-Songpan-Garze accretionary wedge rocks. The crust south of the southern Qiangtang block is likely of granodioritic composition, reflecting long-lived subduction, arc formation, and Cretaceous-Cenozoic underthrusting. Copyright 2004 by the American Geophysical Union.

Structure and Dynamics Ionic Block co-Polymer Melts: Computational Study

NASA Astrophysics Data System (ADS)

Aryal, Dipak; Perahia, Dvora; Grest, Gary S.

Tethering ionomer blocks into co-polymers enables engineering of polymeric systems designed to encompass transport while controlling structure. Here the structure and dynamics of symmetric pentablock copolymers melts are probed by fully atomistic molecular dynamics simulations. The center block consists of randomly sulfonated polystyrene with sulfonation fractions f = 0 to 0.55 tethered to a hydrogenated polyisoprene (PI), end caped with poly(t-butyl styrene). We find that melts with f = 0.15 and 0.30 consist of isolated ionic clusters whereas melts with f = 0.55 exhibit a long-range percolating ionic network. Similar to polystyrene sulfonate, a small number of ionic clusters slow the mobility of the center of mass of the co-polymer, however, formation of the ionic clusters is slower and they are often intertwined with PI segments. Surprisingly, the segmental dynamics of the other blocks are also affected. NSF DMR-1611136; NERSC; Palmetto Cluster Clemson University; Kraton Polymers US, LLC.

Emergent mechanics of biological structures

PubMed Central

Dumont, Sophie; Prakash, Manu

2014-01-01

Mechanical force organizes life at all scales, from molecules to cells and tissues. Although we have made remarkable progress unraveling the mechanics of life's individual building blocks, our understanding of how they give rise to the mechanics of larger-scale biological structures is still poor. Unlike the engineered macroscopic structures that we commonly build, biological structures are dynamic and self-organize: they sculpt themselves and change their own architecture, and they have structural building blocks that generate force and constantly come on and off. A description of such structures defies current traditional mechanical frameworks. It requires approaches that account for active force-generating parts and for the formation of spatial and temporal patterns utilizing a diverse array of building blocks. In this Perspective, we term this framework “emergent mechanics.” Through examples at molecular, cellular, and tissue scales, we highlight challenges and opportunities in quantitatively understanding the emergent mechanics of biological structures and the need for new conceptual frameworks and experimental tools on the way ahead. PMID:25368421

Elfin: An algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks.

PubMed

Yeh, Chun-Ting; Brunette, T J; Baker, David; McIntosh-Smith, Simon; Parmeggiani, Fabio

2018-02-01

Computational protein design methods have enabled the design of novel protein structures, but they are often still limited to small proteins and symmetric systems. To expand the size of designable proteins while controlling the overall structure, we developed Elfin, a genetic algorithm for the design of novel proteins with custom shapes using structural building blocks derived from experimentally verified repeat proteins. By combining building blocks with compatible interfaces, it is possible to rapidly build non-symmetric large structures (>1000 amino acids) that match three-dimensional geometric descriptions provided by the user. A run time of about 20min on a laptop computer for a 3000 amino acid structure makes Elfin accessible to users with limited computational resources. Protein structures with controlled geometry will allow the systematic study of the effect of spatial arrangement of enzymes and signaling molecules, and provide new scaffolds for functional nanomaterials. Copyright © 2017 Elsevier Inc. All rights reserved.

Hierarchically Ordered Nanopatterns for Spatial Control of Biomolecules

PubMed Central

2015-01-01

The development and study of a benchtop, high-throughput, and inexpensive fabrication strategy to obtain hierarchical patterns of biomolecules with sub-50 nm resolution is presented. A diblock copolymer of polystyrene-b-poly(ethylene oxide), PS-b-PEO, is synthesized with biotin capping the PEO block and 4-bromostyrene copolymerized within the polystyrene block at 5 wt %. These two handles allow thin films of the block copolymer to be postfunctionalized with biotinylated biomolecules of interest and to obtain micropatterns of nanoscale-ordered films via photolithography. The design of this single polymer further allows access to two distinct superficial nanopatterns (lines and dots), where the PEO cylinders are oriented parallel or perpendicular to the substrate. Moreover, we present a strategy to obtain hierarchical mixed morphologies: a thin-film coating of cylinders both parallel and perpendicular to the substrate can be obtained by tuning the solvent annealing and irradiation conditions. PMID:25363506

Convulsions may alter the specificity of kappa-opiate receptors.

PubMed

Mansour, A; Valenstein, E S

1986-06-01

Morphine, a mu-opiate agonist, and ethylketazocine, a kappa-opiate agonist, produce distinct behavioral, pharmacologic, and biochemical effects. In the mouse, large doses of morphine produce convulsions that are usually lethal and that cannot be blocked by naltrexone, whereas ethylketazocine produces nonlethal clonic convulsions that can be blocked by naltrexone. Moreover, mice made tolerant to morphine failed to show cross-tolerance to ethylketazocine, suggesting that the convulsions induced by these drugs are not mediated via a common opioid mechanism. Following a series of electroconvulsive shocks, both morphine and ethylketazocine produced clonic convulsions that were not lethal and that could be blocked by naltrexone. Furthermore, electroconvulsive shock-treated animals made tolerant to morphine-induced convulsions showed cross-tolerance to ethylketazocine. These data suggest that electroconvulsive shock may alter kappa-opioid systems in such a way as to allow mu-agonists to be functional at these sites.

Hierarchically Ordered Nanopatterns for Spatial Control of Biomolecules

DOE PAGES

Tran, Helen; Ronaldson, Kacey; Bailey, Nevette A.; ...

2014-11-04

We present the development and study of a benchtop, high-throughput, and inexpensive fabrication strategy to obtain hierarchical patterns of biomolecules with sub-50 nm resolution. A diblock copolymer of polystyrene-b-poly(ethylene oxide), PS-b-PEO, is synthesized with biotin capping the PEO block and 4-bromostyrene copolymerized within the polystyrene block at 5 wt %. These two handles allow thin films of the block copolymer to be postfunctionalized with biotinylated biomolecules of interest and to obtain micropatterns of nanoscale-ordered films via photolithography. The design of this single polymer further allows access to two distinct superficial nanopatterns (lines and dots), where the PEO cylinders are orientedmore » parallel or perpendicular to the substrate. Moreover, we present a strategy to obtain hierarchical mixed morphologies: a thin-film coating of cylinders both parallel and perpendicular to the substrate can be obtained by tuning the solvent annealing and irradiation conditions.« less

A simulation for gravity fine structure recovery from low-low GRAVSAT SST data

NASA Technical Reports Server (NTRS)

Estes, R. H.; Lancaster, E. R.

1976-01-01

Covariance error analysis techniques were applied to investigate estimation strategies for the low-low SST mission for accurate local recovery of gravitational fine structure, considering the aliasing effects of unsolved for parameters. A 5 degree by 5 degree surface density block representation of the high order geopotential was utilized with the drag-free low-low GRAVSAT configuration in a circular polar orbit at 250 km altitude. Recovery of local sets of density blocks from long data arcs was found not to be feasible due to strong aliasing effects. The error analysis for the recovery of local sets of density blocks using independent short data arcs demonstrated that the estimation strategy of simultaneously estimating a local set of blocks covered by data and two "buffer layers" of blocks not covered by data greatly reduced aliasing errors.

Similar bowtie structures and distinct largest strong components are identified in the transcriptional regulatory networks of Arabidopsis thaliana during photomorphogenesis and heat shock.

PubMed

Luo, Shitao; Zhang, Fengming; Ruan, Yingfei; Li, Jie; Zhang, Zheng; Sun, Yan; Deng, Shixiong; Peng, Rui

2018-06-01

Photomorphogenesis and heat shock are critical biological processes of plants. A recent research constructed the transcriptional regulatory networks (TRNs) of Arabidopsis thaliana during these processes using DNase-seq. In this study, by strong decomposition, we revealed that each of these TRNs can be represented as a similar bowtie structure with only one non-trivial and distinct strong component. We further identified distinct patterns of variation of a few light-related genes in these bowtie structures during photomorphogenesis. These results suggest that bowtie structure may be a common property of TRNs of plants, and distinct variation patterns of genes in bowtie structures of TRNs during biological processes may reflect distinct functions. Overall, our study provides an insight into the molecular mechanisms underlying photomorphogenesis and heat shock, and emphasizes the necessity to investigate the strong connectivity structures while studying TRNs. Copyright © 2018 Elsevier B.V. All rights reserved.

Sub-seafloor acoustic characterization of seamounts near the Ogasawara Fracture Zone in the western Pacific using chirp (3-7 kHz) subbottom profiles

USGS Publications Warehouse

Lee, T.-G.; Hein, J.R.; Lee, Kenneth; Moon, J.-W.; Ko, Y.-T.

2005-01-01

A detailed analysis of chirp (3-7 kHz) subbottom profiles and bathymetry was performed on data collected from seamounts near the Ogasawara Fracture Zone (OFZ) in the western Pacific. The OFZ, which is a 150 km wide rift zone showing 600 km of right-lateral movement in a NW-SE direction, is unique among the fracture zones of the Pacific in that it includes many old seamounts (e.g., Magellan Seamounts and seamounts on Dutton Ridge). Sub-seafloor acoustic echoes on the seamounts are classified into nine specific types based on the nature and continuity of the echoes, subbottom structure, and morphology of the seafloor: (1) distinct echoes (types I-1, I-2, I-3), (2) indistinct echoes (types II-1, II-2, II-3), and (3) hyperbolic echoes (types III-1, III-2, III-3). Type I-2 pelagic sediments, characterized by thin and intermittent coverage, were probably deposited in topographically sheltered areas when bottom currents were strong, whereas type I-1 pelagic sediments accumulated during continuous and widespread sedimentation. Development of seamount flank rift zones in the OFZ may have been influenced by preexisting structures in the transform fracture zone at the time of volcanism, whereas those on Ita Mai Tai seamount in the Pigafetta Basin originated solely by edifice-building processes. Flank rift zones that formed by dike intrusions and eruptions played an important role in mass wasting. Mass-wasting processes included block faulting or block slides around the summit margin, sliding/slumping, debris flows, and turbidites, which may have been triggered by faulting, volcanism, dike injection, and weathering during various stages in the evolution of the seamounts. ?? 2005 Elsevier Ltd. All rights reserved.

Divalent ions are potential permeating blockers of the non-selective NaK ion channel: combined QM and MD based investigations.

PubMed

Sadhu, Biswajit; Sundararajan, Mahesh; Bandyopadhyay, Tusar

2017-10-18

The bacterial NaK ion channel is distinctly different from other known ion channels due to its inherent non-selective feature. One of the unexplored and rather interesting features is its ability to permeate divalent metal ions (such as Ca 2+ and Ba 2+ ) and not monovalent alkali metal ions. Several intriguing questions about the energetics and structural aspects still remain unanswered. For instance, what causes Ca 2+ to permeate as well as block the selectivity filter (SF) of the NaK ion channel and act as a "permeating blocker"? How and at what energetic cost does another chemical congener, Sr 2+ , as well as Ba 2+ , a potent blocker of the K + ion channel, permeate through the SF of the NaK ion channel? Finally, how do their translocation energetics differ from those of monovalent ions such as K + ? Here, in an attempt to address these outstanding issues, we elucidate the structure, binding and selectivity of divalent ions (Ca 2+ , Sr 2+ and Ba 2+ ) as they permeate through the SF of the NaK ion channel using all-atom molecular dynamics simulations and density functional theory based calculations. We unveil mechanistic insight into this translocation event using well-tempered metadynamics simulations in a polarizable environment using the mean-field model of water and incorporating electronic continuum corrections for ions via charge rescaling. The results show that, akin to K + coordination, Sr 2+ and Ba 2+ bind at the SF in a very similar fashion and remain octa-coordinated at all sites. Interestingly, differing from its local hydration structure, Ca 2+ interacts with eight carbonyls to remain at the middle of the S3 site. Furthermore, the binding of divalent metals at SF binding sites is more favorable than the binding of K + . However, their permeation through the extracellular entrance faces a considerably higher energetic barrier compared to that for K + , which eventually manifests their inherent blocking feature.

Biopolymers Containing Unnatural Building Blocks

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

Schultz, Peter G.

2013-06-30

Although the main chain structure of polymers has a profound effect on their materials properties, the side groups can also have dramatic effects on their properties including conductivity, liquid crystallinity, hydrophobicity, elasticity and biodegradability. Unfortunately control over the side chain structure of polymers remains a challenge – it is difficult to control the sequence of chain elongation when mixtures of monomers are polymerized, and postpolymerization side chain modification is made difficult by polymer effects on side chain reactivity. In contrast, the mRNA templated synthesis of polypeptides on the ribosome affords absolute control over the primary sequence of the twenty aminomore » acid monomers. Moreover, the length of the biopolymer is precisely controlled as are sites of crosslinking. However, whereas synthetic polymers can be synthesized from monomers with a wide range of chemically defined structures, ribosomal biosynthesis is largely limited to the 20 canonical amino acids. For many applications in material sciences, additional building blocks would be desirable, for example, amino acids containing metallocene, photoactive, and halogenated side chains. To overcome this natural constraint we have developed a method that allows unnatural amino acids, beyond the common twenty, to be genetically encoded in response to nonsense or frameshift codons in bacteria, yeast and mammalian cells with high fidelity and good yields. Here we have developed methods that allow identical or distinct noncanonical amino acids to be incorporated at multiple sites in a polypeptide chain, potentially leading to a new class of templated biopolymers. We have also developed improved methods for genetically encoding unnatural amino acids. In addition, we have genetically encoded new amino acids with novel physical and chemical properties that allow selective modification of proteins with synthetic agents. Finally, we have evolved new metal-ion binding sites in proteins using a novel metal-ion binding amino acid, which may facilitate our ability to generate new protein based sensors and catalysts.« less

Mutations in yeast proliferating cell nuclear antigen define distinct sites for interaction with DNA polymerase delta and DNA polymerase epsilon.

PubMed Central

Eissenberg, J C; Ayyagari, R; Gomes, X V; Burgers, P M

1997-01-01

The importance of the interdomain connector loop and of the carboxy-terminal domain of Saccharomyces cerevisiae proliferating cell nuclear antigen (PCNA) for functional interaction with DNA polymerases delta (Poldelta) and epsilon (Pol epsilon) was investigated by site-directed mutagenesis. Two alleles, pol30-79 (IL126,128AA) in the interdomain connector loop and pol30-90 (PK252,253AA) near the carboxy terminus, caused growth defects and elevated sensitivity to DNA-damaging agents. These two mutants also had elevated rates of spontaneous mutations. The mutator phenotype of pol30-90 was due to partially defective mismatch repair in the mutant. In vitro, the mutant PCNAs showed defects in DNA synthesis. Interestingly, the pol30-79 mutant PCNA (pcna-79) was most defective in replication with Poldelta, whereas pcna-90 was defective in replication with Pol epsilon. Protein-protein interaction studies showed that pcna-79 and pcna-90 failed to interact with Pol delta and Pol epsilon, respectively. In addition, pcna-90 was defective in interaction with the FEN-1 endo-exonuclease (RTH1 product). A loss of interaction between pcna-79 and the smallest subunit of Poldelta, the POL32 gene product, implicates this interaction in the observed defect with the polymerase. Neither PCNA mutant showed a defect in the interaction with replication factor C or in loading by this complex. Processivity of DNA synthesis by the mutant holoenzyme containing pcna-79 was unaffected on poly(dA) x oligo(dT) but was dramatically reduced on a natural template with secondary structure. A stem-loop structure with a 20-bp stem formed a virtually complete block for the holoenzyme containing pcna-79 but posed only a minor pause site for wild-type holoenzyme, indicating a function of the POL32 gene product in allowing replication past structural blocks. PMID:9343398

BST2/Tetherin Inhibition of Alphavirus Exit

PubMed Central

Ooi, Yaw Shin; Dubé, Mathieu; Kielian, Margaret

2015-01-01

Alphaviruses such as chikungunya virus (CHIKV) and Semliki Forest virus (SFV) are small enveloped RNA viruses that bud from the plasma membrane. Tetherin/BST2 is an interferon-induced host membrane protein that inhibits the release of many enveloped viruses via direct tethering of budded particles to the cell surface. Alphaviruses have highly organized structures and exclude host membrane proteins from the site of budding, suggesting that their release might be insensitive to tetherin inhibition. Here, we demonstrated that exogenously-expressed tetherin efficiently inhibited the release of SFV and CHIKV particles from host cells without affecting virus entry and infection. Alphavirus release was also inhibited by the endogenous levels of tetherin in HeLa cells. While rubella virus (RuV) and dengue virus (DENV) have structural similarities to alphaviruses, tetherin inhibited the release of RuV but not DENV. We found that two recently identified tetherin isoforms differing in length at the N-terminus exhibited distinct capabilities in restricting alphavirus release. SFV exit was efficiently inhibited by the long isoform but not the short isoform of tetherin, while both isoforms inhibited vesicular stomatitis virus exit. Thus, in spite of the organized structure of the virus particle, tetherin specifically blocks alphavirus release and shows an interesting isoform requirement. PMID:25912717

A synoptic and dynamical characterization of wave-train and blocking cold surge over East Asia

NASA Astrophysics Data System (ADS)

Park, Tae-Won; Ho, Chang-Hoi; Deng, Yi

2014-08-01

Through an agglomerative hierarchical clustering method, cold surges over East Asia are classified into two distinct types based on the spatial pattern of the geopotential height anomalies at 300 hPa. One is the wave-train type that is associated with developing large-scale waves across the Eurasian continent. The other is the blocking type whose occurrence accompanies subarctic blocking. During the wave-train cold surge, growing baroclinic waves induce a southeastward expansion of the Siberian High and strong northerly winds over East Asia. Blocking cold surge, on the other hand, is associated with a southward expansion of the Siberian High and northeasterly winds inherent to a height dipole consisting of the subarctic blocking and the East Asian coastal trough. The blocking cold surge tends to be more intense and last longer compared to the wave-train type. The wave-train cold surge is associated with the formation of a negative upper tropospheric height anomaly southeast of Greenland approximately 12 days before the surge occurrence. Further analysis of isentropic potential vorticity reveals that this height anomaly could originate from the lower stratosphere over the North Atlantic. Cold surge of the blocking type occurs with an amplifying positive geopotential and a negative potential vorticity anomaly over the Arctic and the northern Eurasia in stratosphere. These anomalies resemble the stratospheric signature of a negative phase of the Arctic Oscillation. This stratospheric feature is further demonstrated by the observation that the blocking type cold surge occurs more often when the Arctic Oscillation is in its negative phase.

Nanostructured Block Copolymer Solutions and Composites: Mechanical and Structural Properties

NASA Astrophysics Data System (ADS)

Walker, Lynn

2015-03-01

Self-assembled block copolymer templates are used to control the nanoscale structure of materials that would not otherwise order in solution. In this work, we have developed a technique to use close-packed cubic and cylindrical mesophases of a thermoreversible block copolymer (PEO-PPO-PEO) to impart spatial order on dispersed nanoparticles. The thermoreversible nature of the template allows for the dispersion of particles synthesized outside the template. This feature extends the applicability of this templating method to many particle-polymer systems, including proteins, and also permits a systematic evaluation of the impact of design parameters on the structure and mechanical properties of the nanocomposites. The criteria for forming co-crystals have been characterized using small-angle scatting and the mechanical properties of these soft crystals determined. Numerous crystal structures have been reported for the block copolymer system and we have taken advantage of several to generate soft co-crystals. The result of this templating is spatially ordered nanoparticle arrays embedded within the block copolymer nanostructure. These soft materials can be shear aligned into crystals with long range order and this shear alignment is discussed. Finally, the dynamics of nanoparticles within the nanostructured material are characterized with fluorescence recovery after photobleaching (FRAP). The applications and general behavior of these nanostructured hydrogels are outlined.

Amplifying (Im)perfection: The Impact of Crystallinity in Discrete and Disperse Block Co-oligomers

PubMed Central

2017-01-01

Crystallinity is seldomly utilized as part of the microphase segregation process in ultralow-molecular-weight block copolymers. Here, we show the preparation of two types of discrete, semicrystalline block co-oligomers, comprising an amorphous oligodimethylsiloxane block and a crystalline oligo-l-lactic acid or oligomethylene block. The self-assembly of these discrete materials results in lamellar structures with unforeseen uniformity in the domain spacing. A systematic introduction of dispersity reveals the extreme sensitivity of the microphase segregation process toward chain length dispersity in the crystalline block. PMID:28994585

Amplifying (Im)perfection: The Impact of Crystallinity in Discrete and Disperse Block Co-oligomers.

PubMed

van Genabeek, Bas; Lamers, Brigitte A G; de Waal, Bas F M; van Son, Martin H C; Palmans, Anja R A; Meijer, E W

2017-10-25

Crystallinity is seldomly utilized as part of the microphase segregation process in ultralow-molecular-weight block copolymers. Here, we show the preparation of two types of discrete, semicrystalline block co-oligomers, comprising an amorphous oligodimethylsiloxane block and a crystalline oligo-l-lactic acid or oligomethylene block. The self-assembly of these discrete materials results in lamellar structures with unforeseen uniformity in the domain spacing. A systematic introduction of dispersity reveals the extreme sensitivity of the microphase segregation process toward chain length dispersity in the crystalline block.

Structural ceramics containing electric arc furnace dust.

PubMed

Stathopoulos, V N; Papandreou, A; Kanellopoulou, D; Stournaras, C J

2013-11-15

In the present work the stabilization of electric arc furnace dust EAFD waste in structural clay ceramics was investigated. EAFD was collected over eleven production days. The collected waste was characterized for its chemical composition by Flame Atomic Absorption Spectroscopy. By powder XRD the crystal structure was studied while the fineness of the material was determined by a laser particle size analyzer. The environmental characterization was carried out by testing the dust according to EN12457 standard. Zn, Pb and Cd were leaching from the sample in significant amounts. The objective of this study is to investigate the stabilization properties of EAFD/clay ceramic structures and the potential of EAFD utilization into structural ceramics production (blocks). Mixtures of clay with 2.5% and 5% EAFD content were studied by TG/DTA, XRD, SEM, EN12457 standard leaching and mechanical properties as a function of firing temperature at 850, 900 and 950 °C. All laboratory facilities maintained 20 ± 1 °C. Consequently, a pilot-scale experiment was conducted with an addition of 2.5% and 5% EAFD to the extrusion mixture for the production of blocks. During blocks manufacturing, the firing step reached 950 °C in a tunnel kiln. Laboratory heating/cooling gradients were similar to pilot scale production firing. The as produced blocks were then subjected to quality control tests, i.e. dimensions according to EN772-17, water absorbance according to EN772-6, and compressive strength according to EN772-1 standard, in laboratory facilities certified under EN17025. The data obtained showed that the incorporation of EAFD resulted in an increase of mechanical strength. Moreover, leaching tests performed according to the Europeans standards on the EAFD-block samples showed that the quantities of heavy metals leached from crushed blocks were within the regulatory limits. Thus the EAFD-blocks can be regarded as material of no environmental concern. Copyright © 2013 Elsevier B.V. All rights reserved.

Modeling of DNA local parameters predicts encrypted architectural motifs in Xenopus laevis ribosomal gene promoter.

PubMed

Roux-Rouquie, M; Marilley, M

2000-09-15

We have modeled local DNA sequence parameters to search for DNA architectural motifs involved in transcription regulation and promotion within the Xenopus laevis ribosomal gene promoter and the intergenic spacer (IGS) sequences. The IGS was found to be shaped into distinct topological domains. First, intrinsic bends split the IGS into domains of common but different helical features. Local parameters at inter-domain junctions exhibit a high variability with respect to intrinsic curvature, bendability and thermal stability. Secondly, the repeated sequence blocks of the IGS exhibit right-handed supercoiled structures which could be related to their enhancer properties. Thirdly, the gene promoter presents both inherent curvature and minor groove narrowing which may be viewed as motifs of a structural code for protein recognition and binding. Such pre-existing deformations could simply be remodeled during the binding of the transcription complex. Alternatively, these deformations could pre-shape the promoter in such a way that further remodeling is facilitated. Mutations shown to abolish promoter curvature as well as intrinsic minor groove narrowing, in a variant which maintained full transcriptional activity, bring circumstantial evidence for structurally-preorganized motifs in relation to transcription regulation and promotion. Using well documented X. laevis rDNA regulatory sequences we showed that computer modeling may be of invaluable assistance in assessing encrypted architectural motifs. The evidence of these DNA topological motifs with respect to the concept of structural code is discussed.

Petrography and zircon U-Pb isotopic study of the Bayanwulashan Complex: Constrains on the Paleoproterozoic evolution of the Alxa Block, westernmost North China Craton

NASA Astrophysics Data System (ADS)

Wu, Sujuan; Hu, Jianmin; Ren, Minghua; Gong, Wangbin; Liu, Yang; Yan, Jiyuan

2014-11-01

The Bayanwulashan Metamorphic Complex (BMC) exposes along the eastern margin of the Alxa Block, the westernmost part of the North China Craton (NCC). BMC is principally composed of metamorphic rocks with amphibole plagiogneiss, biotite plagioclase gneiss and granitic gneiss. Our research has been focused on the petrography and zircon U-Pb geochronology of the BMC to better understand the evolution of the Alxa Block and its relationship with the NCC. Evidences from field geology, petrography, and mineral chemistry indicate that two distinct metamorphic assemblages, the amphibolite and greenschist facies, had overprinted the preexisting granitic gneiss and suggest that the BMC experienced retrograde metamorphic episodes. The LA-ICP-MS zircon U-Pb ages reveal that the primary magmatic activities of BMC were at ca. 2.30-2.24 Ga and the two metamorphic events were at ca. 1.95-1.91 Ga and ca. 1.88-1.85 Ga respectively. These ages indicate that BMC initially intruded during Paleoproterozoic, not as previously suggested at Archean period. The Early Paleoproterozoic metamorphic records and the magmatic thermochronological data in BMC exhibit different evolution paths between the Alxa Block and the NCC. The Alxa Block was most likely an independent Early Paleoproterozoic terrain. Following different amalgamation processes, The Alxa Block combined with Western Block at ca. 1.95 Ga and then united with NCC at ca. 1.85 Ga.

Development of high resolution phoswich depth-of-interaction block detectors utilizing Mg co-doped new scintillators

NASA Astrophysics Data System (ADS)

Kobayashi, Takahiro; Yamamoto, Seiichi; Yeom, Jung-Yeol; Kamada, Kei; Yoshikawa, Akira

2017-12-01

To correct for parallax error in positron emission tomography (PET), phoswich depth-of-interaction (DOI) detector using multiple scintillators with different decay times is a practical approach. However not many scintillator combinations suitable for phoswich DOI detector have been reported. Ce doped Gd3Ga3Al2O12 (GFAG) is a newly developed promising scintillator for PET detector, which has high density, high light output, appropriate light emission wavelength for silicon-photomultiplier (Si-PM) and faster decay time than that of Ce doped Gd3Al2Ga3O12 (GAGG). In this study, we developed a Si-PM based phoswich DOI block detector of GFAG with GAGG crystal arrays and evaluated its performance. We assembled a GFAG block and a GAGG block and they were optically coupled in depth direction to form a phoswich detector block. The phoswich block was optically coupled to a Si-PM array with a 1 mm thick light guide. The sizes of the GFAG and GAGG pixels were 0.9 mm x 0.9 mm x 7.5 mm and they were arranged into 24 x 24 matrix with 0.1 mm thick BaSO4 as reflector. We conducted the performance evaluation for two types of configurations; GFAG block arranged in upper layer (GFAG/GAGG) and GAGG arranged in upper layer (GAGG/GFAG). The measured two dimensional position histograms of these block detectors showed good separation and pulse shape spectra produced two distinct peaks for both configurations although some difference in energy spectra were observed. These results indicate phoswich block detectors composed of GFAG and GAGG are promising for high resolution DOI PET systems.

Blocking a Redundant Cue: What does it say about preschoolers’ causal competence?

PubMed Central

Kloos, Heidi; Sloutsky, Vladimir M.

2013-01-01

The current study investigates the degree to which preschoolers can engage in causal inferences in blocking paradigm, a paradigm in which a cue is consistently linked with a target, either alone (A-T) or paired with another cue (AB-T). Unlike previous blocking studies with preschoolers, we manipulated the causal structure of the events without changing the specific contingencies. In particular, cues were said to be either potential causes (prediction condition), or they were said to be potential effects (diagnosis condition). The causally appropriate inference is to block the redundant cue B when it is a potential cause of the target, but not when it is a potential effect. Findings show a stark difference in performance between preschoolers and adults: While adults blocked the redundant cue only in the prediction condition, children blocked the redundant cue indiscriminately across both conditions. Therefore, children, but not adults ignored the causal structure of the events. These findings challenge a developmental account that attributes sophisticated machinery of causal reasoning to young children. PMID:24033577

Two innovative solutions based on fibre concrete blocks designed for building substructure

NASA Astrophysics Data System (ADS)

Pazderka, J.; Hájek, P.

2017-09-01

Using of fibers in a high-strength concrete allows reduction of the dimensions of small precast concrete elements, which opens up new ways of solution for traditional construction details in buildings. The paper presents two innovative technical solutions for building substructure: The special shaped plinth block from fibre concrete and the fibre concrete elements for new technical solution of ventilated floor. The main advantages of plinth block from fibre concrete blocks (compared with standard plinth solutions) is: easier and faster assembly, higher durability and thanks to the air cavity between the vertical part of the block, the building substructure reduced moisture level of structures under the waterproofing layer and a comprehensive solution to the final surface of building plinth as well as the surface of adjacent terrain. The ventilated floor based on fibre concrete precast blocks is an attractive structural alternative for tackling the problem of increased moisture in masonry in older buildings, lacking a functional waterproof layer in the substructure.

A new method for detection and discrimination of Pepino mosaic virus isolates using high resolution melting analysis of the triple gene block 3.

PubMed

Hasiów-Jaroszewska, Beata; Komorowska, Beata

2013-10-01

Diagnostic methods distinguished different Pepino mosaic virus (PepMV) genotypes but the methods do not detect sequence variation in particular gene segments. The necrotic and non-necrotic isolates (pathotypes) of PepMV share a 99% sequence similarity. These isolates differ from each other at one nucleotide site in the triple gene block 3. In this study, a combination of real-time reverse transcription polymerase chain reaction and high resolution melting curve analysis of triple gene block 3 was developed for simultaneous detection and differentiation of PepMV pathotypes. The triple gene block 3 region carrying a transition A → G was amplified using two primer pairs from twelve virus isolates, and was subjected to high resolution melting curve analysis. The results showed two distinct melting curve profiles related to each pathotype. The results also indicated that the high resolution melting method could readily differentiate between necrotic and non-necrotic PepMV pathotypes. Copyright © 2013 Elsevier B.V. All rights reserved.

Computational Design of High-χ Block Oligomers for Accessing 1 nm Domains.

PubMed

Chen, Qile P; Barreda, Leonel; Oquendo, Luis E; Hillmyer, Marc A; Lodge, Timothy P; Siepmann, J Ilja

2018-05-22

Molecular dynamics simulations are used to design a series of high-χ block oligomers (HCBOs) that can self-assemble into a variety of mesophases with domain sizes as small as 1 nm. The exploration of these oligomers with various chain lengths, volume fractions, and chain architectures at multiple temperatures reveals the presence of ordered lamellae, perforated lamellae, and hexagonally packed cylinders. The achieved periods are as small as 3.0 and 2.1 nm for lamellae and cylinders, respectively, which correspond to polar domains of approximately 1 nm. Interestingly, the detailed phase behavior of these oligomers is distinct from that of either solvent-free surfactants or block polymers. The simulations reveal that the behavior of these HCBOs is a product of an interplay between both "surfactant factors" (headgroup interactions, chain flexibility, and interfacial curvature) and "block polymer factors" (χ, chain length N, and volume fraction f). This insight promotes the understanding of molecular features pivotal for mesophase formation at the sub-5 nm length scale, which facilitates the design of HCBOs tailored toward particular desired morphologies.

Bone loss from Wnt inhibition mitigated by concurrent alendronate therapy.

PubMed

Madan, Babita; McDonald, Mitchell J; Foxa, Gabrielle E; Diegel, Cassandra R; Williams, Bart O; Virshup, David M

2018-01-01

Dysregulated Wnt signaling is associated with the pathogenesis of cancers, fibrosis, and vascular diseases. Inhibition of Wnt signaling has shown efficacy in various pre-clinical models of these disorders. One of the key challenges in developing targeted anti-cancer drugs is to balance efficacy with on-target toxicity. Given the crucial role Wnts play in the differentiation of osteoblasts and osteoclasts, acute inhibition of Wnt signaling is likely to affect bone homeostasis. In this study, we evaluated the skeletal effect of small molecule inhibitor of an o-acyl transferase porcupine (PORCN) that prevents Wnt signaling by blocking the secretion of all Wnts. Micro-computed tomography and histomorphometric evaluation revealed that the bones of mice treated with two structurally distinct PORCN inhibitors LGK974 and ETC-1922159 (ETC-159) had loss-of-bone volume and density within 4 weeks of exposure. This decreased bone mass was associated with a significant increase in adipocytes within the bone marrow. Notably, simultaneous administration of a clinically approved anti-resorptive, alendronate, a member of the bisphosphonate family, mitigated loss-of-bone mass seen upon ETC-159 treatment by regulating activity of osteoclasts and blocking accumulation of bone marrow adipocytes. Our results support the addition of bone protective agents when treating patients with PORCN inhibitors. Mitigation of bone toxicity can extend the therapeutic utility of Wnt pathway inhibitors.

Multivalent peptoid conjugates which overcome enzalutamide resistance in prostate cancer cells

PubMed Central

Wang, Yu; Dehigaspitiya, Dilani C.; Levine, Paul M.; Profit, Adam A.; Haugbro, Michael; Imberg-Kazdan, Keren; Logan, Susan K.; Kirshenbaum, Kent; Garabedian, Michael J.

2016-01-01

Development of resistance to anti-androgens for treating advanced prostate cancer is a growing concern, and extends to recently developed therapeutics, including enzalutamide. Therefore, new strategies to block androgen receptor (AR) function in prostate cancer are required. Here we report the characterization of a multivalent conjugate presenting two bioactive ethisterone ligands arrayed as spatially defined pendant groups on a peptoid oligomer. The conjugate, named Multivalent Peptoid Conjugate 6 (MPC6), suppressed the proliferation of multiple AR-expressing prostate cancer cell lines including those that failed to respond to enzalutamide and ARN509. The structure-activity relationships of MPC6 variants were evaluated, revealing that increased spacing between ethisterone moieties and changes in peptoid topology eliminated its anti-proliferative effect, suggesting that both ethisterone ligand presentation and scaffold characteristics contribute to MPC6 activity. Mechanistically, MPC6 blocked AR coactivator-peptide interaction, and prevented AR intermolecular interactions. Protease sensitivity assays suggested that the MPC6-bound AR induced a receptor conformation distinct from that of dihydrotestosterone- or enzalutamide-bound AR. Pharmacological studies revealed that MPC6 was metabolically stable and displayed a low plasma clearance rate. Notably, MPC6 treatment reduced tumor growth and decreased Ki67 and AR expression in mouse xenograft models of enzalutamide-resistant LNCaP-abl cells. Thus, MPC6 represents a new class of compounds with the potential to combat treatment-resistant prostate cancer. PMID:27488525

Intraoperative Consultation and Macroscopic Handling: The International Society of Urological Pathology (ISUP) Testicular Cancer Consultation Conference Recommendations.

PubMed

Verrill, Clare; Perry-Keene, Joanna; Srigley, John R; Zhou, Ming; Humphrey, Peter A; Lopez-Beltran, Antonio; Egevad, Lars; Ulbright, Thomas M; Tickoo, Satish K; Epstein, Jonathan I; Compérat, Eva; Berney, Daniel M

2018-06-01

The International Society of Urological Pathology held a conference on issues in testicular and penile pathology in Boston in March 2015, which included a presentation by the testis macroscopic features working group. The presentation focused on current published guidance for macroscopic handling of testicular tumors and retroperitoneal lymph node dissections with a summary of results from an online survey of members preceding the conference. The survey results were used to initiate discussions, but decisions on practice were made by expert consensus rather than voting. The importance of comprehensive assessment at the time of gross dissection with confirmation of findings by microscopic assessment was underscored. For example, the anatomic landmarks denoting the distinction of hilar soft tissue invasion (pT2) from spermatic cord invasion (pT3 category) can only be determined by careful macroscopic assessment in many cases. Other recommendations were to routinely sample epididymis, rete testis, hilar soft tissue, and tunica vaginalis in order to confirm macroscopic invasion of these structures or if not macroscopically evident, to exclude subtle microscopic invasion. Tumors 2 cm or less in greatest dimension should be completely embedded. If the tumor is >2 cm in greatest dimension, 10 blocks or a minimum of 1 to 2 additional blocks per centimeter should be taken (whichever is greater).

Brownian dynamics simulation of amphiphilic block copolymers with different tail lengths, comparison with theory and comicelles.

PubMed

Hafezi, Mohammad-Javad; Sharif, Farhad

2015-11-01

Study on the effect of amphiphilic copolymers structure on their self assembly is an interesting subject, with important applications in the area of drug delivery and biological system treatments. Brownian dynamics simulations were performed to study self-assembly of the linear amphiphilic block copolymers with the same hydrophilic head, but hydrophobic tails of different lengths. Critical micelle concentration (CMC), gyration radius distribution, micelle size distribution, density profiles of micelles, shape anisotropy, and dynamics of micellization were investigated as a function of tail length. Simulation results were compared with predictions from theory and simulation for mixed systems of block copolymers with long and short hydrophobic tail, reported in our previous work. Interestingly, the equilibrium structural and dynamic parameters of pure and mixed block copolymers were similarly dependant on the intrinsic/apparent hydrophobic block length. Log (CMC) was, however; proportional to the tail length and had a different behavior compared to the mixed system. The power law scaling relation of equilibrium structural parameters for amphiphilic block copolymers predicts the same dependence for similar hydrophobic tail lengths, but the power law prediction of CMC is different, which is due to its simplifying assumptions as discussed here. Copyright © 2015 Elsevier Inc. All rights reserved.

Swell Gels to Dumbbell Micelles: Construction of Materials and Nanostructure with Self-assembly

NASA Astrophysics Data System (ADS)

Pochan, Darrin

2007-03-01

Bionanotechnology, the emerging field of using biomolecular and biotechnological tools for nanostructure or nanotecnology development, provides exceptional opportunity in the design of new materials. Self-assembly of molecules is an attractive materials construction strategy due to its simplicity in application. By considering peptidic or charged synthetic polymer molecules in the bottom-up materials self-assembly design process, one can take advantage of inherently biomolecular attributes; intramolecular folding events, secondary structure, and electrostatic interactions; in addition to more traditional self-assembling molecular attributes such as amphiphilicty, to define hierarchical material structure and consequent properties. Several molecular systems will be discussed. Synthetic block copolymers with charged corona blocks can be assembled in dilute solution containing multivalent organic counterions to produce micelle structures such as toroids. These ring-like micelles are similar to the toroidal bundling of charged semiflexible biopolymers like DNA in the presence of multivalent counterions. Micelle structure can be tuned between toroids, cylinders, and disks simply by using different concentrations or molecular volumes of organic counterion. In addition, these charged blocks can consist of amino acids as monomers producing block copolypeptides. In addition to the above attributes, block copolypeptides provide the control of block secondary structure to further control self-assembly. Design strategies based on small (less than 24 amino acids) beta-hairpin peptides will be discussed. Self-assembly of the peptides is predicated on an intramolecular folding event caused by desired solution properties. Importantly, the intramolecular folding event impart a molecular-level mechanism for environmental responsiveness at the material level (e.g. infinite change in viscosity of a solution to a gel with changes in pH, ionic strength, temperature).

Study on turbulent flow and heat transfer performance of tubes with internal fins in EGR cooler

NASA Astrophysics Data System (ADS)

Liu, Lin; Ling, Xiang; Peng, Hao

2015-07-01

In this paper, flow and heat transfer performances of the tubes with internal longitudinal fins in Exhaust Gas Recirculation (EGR ) cooler were investigated by three-dimension computation and experiment . Each test tube was a single-pipe structure, without inner tube. Three-dimension computation was performed to determine the thermal characteristics difference between the two kinds of tubes, that is, the tube with an inner solid staff as a blocked structure and the tube without the blocked structure. The effects of fin width and fin height on heat transfer and flow are examined. For proving the validity of numerical method, the calculated results were compared with corresponding experimental data. The tube-side friction factor and heat transfer coefficient were examined. As a result, the maximum deviations between the numerical results and the experimental data are approximately 5.4 % for friction factor and 8.6 % for heat transfer coefficient, respectively. It is found that two types of internally finned tubes enhance significantly heat transfer. The heat transfer of the tube with blocked structure is better, while the pressure drop of the tube without blocked structure is lower. The comprehensive performance of the unblocked tube is better to applied in EGR cooler.

Modelling the role of basement block rotation and strike-slip faulting on structural pattern in the cover units of fold-and-thrust belts

NASA Astrophysics Data System (ADS)

Koyi, Hemin; Nilfouroushan, Faramarz; Hessami, Khaled

2015-04-01

A series of scaled analogue models are run to study the degree of coupling between basement block kinematics and cover deformation. In these models, rigid basal blocks were rotated about vertical axis in a "bookshelf" fashion, which caused strike-slip faulting along the blocks and, to some degrees, in the overlying cover units of loose sand. Three different combinations of cover basement deformations are modeled; cover shortening prior to basement fault movement; basement fault movement prior to shortening of cover units; and simultaneous cover shortening with basement fault movement. Model results show that the effect of basement strike-slip faults depends on the timing of their reactivation during the orogenic process. Pre- and syn-orogen basement strike-slip faults have a significant impact on the structural pattern of the cover units, whereas post-orogenic basement strike-slip faults have less influence on the thickened hinterland of the overlying fold-and-thrust belt. The interaction of basement faulting and cover shortening results in formation of rhomb features. In models with pre- and syn-orogen basement strike-slip faults, rhomb-shaped cover blocks develop as a result of shortening of the overlying cover during basement strike-slip faulting. These rhombic blocks, which have resemblance to flower structures, differ in kinematics, genesis and structural extent. They are bounded by strike-slip faults on two opposite sides and thrusts on the other two sides. In the models, rhomb-shaped cover blocks develop as a result of shortening of the overlying cover during basement strke-slip faulting. Such rhomb features are recognized in the Alborz and Zagros fold-and-thrust belts where cover units are shortened simultaneously with strike-slip faulting in the basement. Model results are also compared with geodetic results obtained from combination of all available GPS velocities in the Zagros and Alborz FTBs. Geodetic results indicate domains of clockwise and anticlockwise rotation in these two FTBs. The typical pattern of structures and their spatial distributions are used to suggest clockwise block rotation of basement blocks about vertical axes and their associated strike-slip faulting in both west-central Alborz and the southeastern part of the Zagros fold-and-thrust belt.

Periodic nanostructures from self assembled wedge-type block-copolymers

DOEpatents

Xia, Yan; Sveinbjornsson, Benjamin R.; Grubbs, Robert H.; Weitekamp, Raymond; Miyake, Garret M.; Piunova, Victoria; Daeffler, Christopher Scot

2015-06-02

The invention provides a class of wedge-type block copolymers having a plurality of chemically different blocks, at least a portion of which incorporates a wedge group-containing block providing useful properties. For example, use of one or more wedge group-containing blocks in some block copolymers of the invention significantly inhibits chain entanglement and, thus, the present block copolymers materials provide a class of polymer materials capable of efficient molecular self-assembly to generate a range of structures, such as periodic nanostructures and microstructures. Materials of the present invention include copolymers having one or more wedge group-containing blocks, and optionally for some applications copolymers also incorporating one or more polymer side group-containing blocks. The present invention also provides useful methods of making and using wedge-type block copolymers.

Motor neurons and oligodendrocytes arise from distinct cell lineages by progenitor recruitment

PubMed Central

Ravanelli, Andrew M.; Appel, Bruce

2015-01-01

During spinal cord development, ventral neural progenitor cells that express the transcription factors Olig1 and Olig2, called pMN progenitors, produce motor neurons and then oligodendrocytes. Whether motor neurons and oligodendrocytes arise from common or distinct progenitors in vivo is not known. Using zebrafish, we found that motor neurons and oligodendrocytes are produced sequentially by distinct progenitors that have distinct origins. When olig2+ cells were tracked during the peak period of motor neuron formation, most differentiated as motor neurons without further cell division. Using time-lapse imaging, we found that, as motor neurons differentiated, more dorsally positioned neuroepithelial progenitors descended to the pMN domain and initiated olig2 expression. Inhibition of Hedgehog signaling during motor neuron differentiation blocked the ventral movement of progenitors, the progressive initiation of olig2 expression, and oligodendrocyte formation. We therefore propose that the motor neuron-to-oligodendrocyte switch results from Hedgehog-mediated recruitment of glial-fated progenitors to the pMN domain subsequent to neurogenesis. PMID:26584621

Mesoscale simulation of the formation and dynamics of lipid-structured poly(ethylene oxide)-block-poly(methyl methacrylate) diblock copolymers.

PubMed

Mu, Dan; Li, Jian-Quan; Feng, Sheng-Yu

2015-05-21

Twelve poly(ethylene oxide)-block-poly(methyl methacrylate) (PEO-b-PMMA) copolymers with lipid-like structures were designed and investigated by MesoDyn simulation. Spherical and worm-like micelles as well as bicontinuous, lamellar and defected lamellar phases were obtained. A special structure, designated B2412, with two lipid structures connected by their heads, was found to undergo four stages prior to forming a spherical micelle phase. Two possible assembly mechanisms were found via thermodynamic and dynamic process analyses; namely, the fusion and fission of micelles in dynamic equilibrium during the adjustment stage. Water can be encapsulated into these micelles, which can affect their size, particularly in low concentration aqueous solutions. The assignment of weak negative charges to the hydrophilic EO blocks resulted in a clear effect on micelle size. Surprisingly, the largest effect was observed with EO blocks with -0.5 e, wherein an ordered perfect hexagonal phase was formed. The obtained results can be applied in numerous fields of study, including adsorption, catalysis, controlled release and drug delivery.

Superalloy Lattice Block Developed for Use in Lightweight, High-Temperature Structures

NASA Technical Reports Server (NTRS)

Hebsur, Mohan G.; Whittenberger, J. Daniel; Krause, David L.

2003-01-01

Successful development of advanced gas turbine engines for aircraft will require lightweight, high-temperature components. Currently titanium-aluminum- (TiAl) based alloys are envisioned for such applications because of their lower density (4 g/cm3) in comparison to superalloys (8.5 g/cm3), which have been utilized for hot turbine engine parts for over 50 years. However, a recently developed concept (lattice block) by JAMCORP, Inc., of Willmington, Massachusetts, would allow lightweight, high-temperature structures to be directly fabricated from superalloys and, thus, take advantage of their well-known, characterized properties. In its simplest state, lattice block is composed of thin ligaments arranged in a three dimensional triangulated trusslike configuration that forms a structurally rigid panel. Because lattice block can be fabricated by casting, correctly sized hardware is produced with little or no machining; thus very low cost manufacturing is possible. Together, the NASA Glenn Research Center and JAMCORP have extended their lattice block methodology for lower melting materials, such as Al alloys, to demonstrate that investment casting of superalloy lattice block is possible. This effort required advances in lattice block pattern design and assembly, higher temperature mold materials and mold fabrication technology, and foundry practice suitable for superalloys (ref. 1). Lattice block panels have been cast from two different Ni-base superalloys: IN 718, which is the most commonly utilized superalloy and retains its strength up to 650 C; and MAR M247, which possesses excellent mechanical properties to at least 1100 C. In addition to the open-cell lattice block geometry, same-sized lattice block panels containing a thin (1-mm-thick) solid face on one side have also been cast from both superalloys. The elevated-temperature mechanical properties of the open cell and face-sheeted superalloy lattice block panels are currently being examined, and the microstructure is being characterized in terms of casting defects. In addition, a small study (ref. 3) is being undertaken with GE Aircraft Engines to determine the suitability of superalloy lattice block for engine components.

The Astro-E/XRS Blocking Filter Calibration

NASA Technical Reports Server (NTRS)

Audley, Michael D.; Arnaud, Keith A.; Gendreau, Keith C.; Boyce, Kevin R.; Fleetwood, Charles M.; Kelley, Richard L.; Keski-Kuha, Ritva A.; Porter, F. Scott; Stahle, Caroline K.; Szymkowiak, Andrew E.

1999-01-01

We describe the transmission calibration of the Astro-E XRS blocking filters. The XRS instrument has five aluminized polyimide blocking filters. These filters are located at thermal stages ranging from 200 K to 60 mK. They are each about 1000 A thick. XRS will have high energy resolution which will enable it to see some of the extended fine structure around the oxygen and aluminum K edges of these filters. Thus, we are conducting a high spectral resolution calibration of the filters near these energies to resolve out extended flue structure and absorption lines.