Information Structure, Grammar and Strategy in Discourse

ERIC Educational Resources Information Center

Stevens, Jon

2013-01-01

This dissertation examines two information-structural phenomena, Givenness and Focus, from the perspective of both syntax and pragmatics. Evidence from English, German and other languages suggests a "split" analysis of information structure--the notions of Focus and Givenness, often thought to be closely related, exist independently at…

Effects of Catalytic Action and Ligand Binding on Conformational Ensembles of Adenylate Kinase.

PubMed

Onuk, Emre; Badger, John; Wang, Yu Jing; Bardhan, Jaydeep; Chishti, Yasmin; Akcakaya, Murat; Brooks, Dana H; Erdogmus, Deniz; Minh, David D L; Makowski, Lee

2017-08-29

Crystal structures of adenylate kinase (AdK) from Escherichia coli capture two states: an "open" conformation (apo) obtained in the absence of ligands and a "closed" conformation in which ligands are bound. Other AdK crystal structures suggest intermediate conformations that may lie on the transition pathway between these two states. To characterize the transition from open to closed states in solution, X-ray solution scattering data were collected from AdK in the apo form and with progressively increasing concentrations of five different ligands. Scattering data from apo AdK are consistent with scattering predicted from the crystal structure of AdK in the open conformation. In contrast, data from AdK samples saturated with Ap5A do not agree with that calculated from AdK in the closed conformation. Using cluster analysis of available structures, we selected representative structures in five conformational states: open, partially open, intermediate, partially closed, and closed. We used these structures to estimate the relative abundances of these states for each experimental condition. X-ray solution scattering data obtained from AdK with AMP are dominated by scattering from AdK in the open conformation. For AdK in the presence of high concentrations of ATP and ADP, the conformational ensemble shifts to a mixture of partially open and closed states. Even when AdK is saturated with Ap5A, a significant proportion of AdK remains in a partially open conformation. These results are consistent with an induced-fit model in which the transition of AdK from an open state to a closed state is initiated by ATP binding.

Probing RNA tertiary structure: interhelical crosslinking of the hammerhead ribozyme.

PubMed Central

Sigurdsson, S T; Tuschl, T; Eckstein, F

1995-01-01

Distinct structural models for the hammerhead ribozyme derived from single-crystal X-ray diffraction and fluorescence resonance energy transfer (FRET) measurements have been compared. Both models predict the same overall geometry, a wishbone shape with helices II and III nearly colinear and helix I positioned close to helix II. However, the relative orientations of helices I and II are different. To establish whether one of the models represents a kinetically active structure, a new crosslinking procedure was developed in which helices I and II of hammerhead ribozymes were disulfide-crosslinked via the 2' positions of specific sugar residues. Crosslinking residues on helices I and II that are close according to the X-ray structure did not appreciably reduce the catalytic efficiency. In contrast, crosslinking residues closely situated according to the FRET model dramatically reduced the cleavage rate by at least three orders of magnitude. These correlations between catalytic efficiencies and spatial proximities are consistent with the X-ray structure. PMID:7489517

New Convex and Spherical Structures of Bare Boron Clusters

NASA Astrophysics Data System (ADS)

Boustani, Ihsan

1997-10-01

New stable structures of bare boron clusters can easily be obtained and constructed with the help of an "Aufbau Principle" suggested by a systematicab initioHF-SCF and direct CI study. It is concluded that boron cluster formation can be established by elemental units of pentagonal and hexagonal pyramids. New convex and small spherical clusters different from the classical known forms of boron crystal structures are obtained by a combination of both basic units. Convex structures simulate boron surfaces which can be considered as segments of open or closed spheres. Both convex clusters B16and B46have energies close to those of their conjugate quasi-planar clusters, which are relatively stable and can be considered to act as a calibration mark. The closed spherical clusters B12, B22, B32, and B42are less stable than the corresponding conjugated quasi-planar structures. As a consequence, highly stable spherical boron clusters can systematically be predicted when their conjugate quasi-planar clusters are determined and energies are compared.

The influence of food abundance, food dispersion and habitat structure on territory selection and size of an Afrotropical terrestrial insectivore

USGS Publications Warehouse

Stanley, Thomas R.; Newmark, William D.

2015-01-01

Most tropical insectivorous birds, unlike their temperate counterparts, hold and defend a feeding and breeding territory year-around. However, our understanding of ecological factors influencing territory selection and size in tropical insectivores is limited. Here we examine three prominent hypotheses relating food abundance, food dispersion (spatial arrangement of food items), and habitat structure to territoriality in the Usambara Thrush Turdus roehli. We first compared leaf-litter macro-invertebrate abundance and dispersion, and habitat structure between territories and random sites. We then examined the relation between these same ecological factors and territory size. Invertebrate abundance and dispersion were sparsely and evenly distributed across our study system and did not vary between territories and random sites. In contrast, habitat structure did vary between territories and random sites indicating the Usambara Thrush selects territories with open understorey and closed overstorey habitat. Invertebrate abundance and dispersion within territories of the Usambara Thrush were not associated with habitat structure. We believe the most likely explanation for the Usambara Thrush’s preference for open understorey and closed overstorey habitat relates to foraging behavior. Using information-theoretic model selection we found that invertebrate abundance was the highest-ranked predictor of territory size and was inversely related, consistent with food value theory of territoriality.

The Relations Among Inhibition and Interference Control Functions: A Latent-Variable Analysis

ERIC Educational Resources Information Center

Friedman, Naomi P.; Miyake, Akira

2004-01-01

This study used data from 220 adults to examine the relations among 3 inhibition-related functions. Confirmatory factor analysis suggested that Prepotent Response Inhibition and Resistance to Distractor Interference were closely related, but both were unrelated to Resistance to Proactive Interference. Structural equation modeling, which combined…

Community structure of planktonic methane-oxidizing bacteria in a subtropical reservoir characterized by dominance of phylotype closely related to nitrite reducer

NASA Astrophysics Data System (ADS)

Kojima, Hisaya; Tokizawa, Riho; Kogure, Kouhei; Kobayashi, Yuki; Itoh, Masayuki; Shiah, Fuh-Kwo; Okuda, Noboru; Fukui, Manabu

2014-07-01

Methane-oxidizing bacteria (MOB) gain energy from the oxidation of methane and may play important roles in freshwater ecosystems. In this study, the community structure of planktonic MOB was investigated in a subtropical reservoir. Bacterial community structure was investigated through the analysis of the 16S rRNA gene. Three groups of phylogenetically distinct MOB were detected in the clone libraries of polymerase chain reaction products obtained with universal primers. The groups belonged to the class Gammaproteobacteria, the class Alphaproteobacteria, and the candidate phylum NC10. The last group, which consists of close relatives of the nitrite reducer `Candidatus Methylomirabilis oxyfera', was frequently detected in the clone libraries of deep-water environments. The presence of 3 groups of MOB in deep water was also shown by a cloning analysis of the pmoA gene encoding particulate methane monooxygenase. The dominance of `M. oxyfera'-like organisms in deep water was confirmed by catalyzed reporter deposition-fluorescence in situ hybridization, in which cells stained with a specific probe accounted for 16% of total microbial cells. This is the first study to demonstrate that close relatives of the nitrite reducer can be major component of planktonic MOB community which may affect carbon flow in aquatic ecosystems.

Structures in general relativity

NASA Astrophysics Data System (ADS)

Tieu, Steven

Structures within general relativity are examined. The differences between man-made structures and those predicted by the Einstein differential equations are very subtle. Exotic structures such as the Godel Universe and the Gott cosmic string are examined with emphasis on closed time-like curves. Newtonian models are seen to also have an exotic aspect in that a vast halo consisting of unknown matter dominates the galaxy. We introduce a model for galaxies based on a general relativity framework with the goal of excluding such artifacts from the system while describing the flat-rotation curves. Structures within this model were speculated to be exotic but after close scrutiny, their nature is shown to be benign. Numerical approaches are applied to model four galaxies: The Milky Way, NGC 3031, NGC 3198 and NGC 7331. Density and mass are deduced from these models and compared to the Newtonian models. Within the visible/HI region, there is 30% reduction in total mass. Extending the model to 10 times beyond the HI region using various fall-off scenerios, it is shown that there is only modest increase of the accumulated mass. In comparison to the Newtonian approach to galactic dynamics, the massive halos are not required to account for the flat velocity profiles.

Relating indices of knowledge structure coherence and accuracy to skill-based performance: Is there utility in using a combination of indices?

PubMed

Schuelke, Matthew J; Day, Eric Anthony; McEntire, Lauren E; Boatman, Jazmine Espejo; Wang, Xiaoqian; Kowollik, Vanessa; Boatman, Paul R

2009-07-01

The authors examined the relative criterion-related validity of knowledge structure coherence and two accuracy-based indices (closeness and correlation) as well as the utility of using a combination of knowledge structure indices in the prediction of skill acquisition and transfer. Findings from an aggregation of 5 independent samples (N = 958) whose participants underwent training on a complex computer simulation indicated that coherence and the accuracy-based indices yielded comparable zero-order predictive validities. Support for the incremental validity of using a combination of indices was mixed; the most, albeit small, gain came in pairing coherence and closeness when predicting transfer. After controlling for baseline skill, general mental ability, and declarative knowledge, only coherence explained a statistically significant amount of unique variance in transfer. Overall, the results suggested that the different indices largely overlap in their representation of knowledge organization, but that coherence better reflects adaptable aspects of knowledge organization important to skill transfer.

Informational temperature concept and the nature of self-organization

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

Lin, Shu-Kun

1996-12-31

Self-organization phenomena are spontaneous processes. Their behavior should be governed by the second law of thermodynamics. The dissipative structure theory of the Prigogine school of thermodynamics claims that {open_quotes}order out of chaos{close_quotes} through {open_quotes}self-organization{close_quotes} and challenges the validity of the second law of thermodynamics. Unfortunately this theory is questionable. Therefore we have to reconsider the related fundamental theoretical problems. Informational entropy (S) and information (I) are related by S = S{sub max} - I, where S{sub max} is the maximum informational entropy. This conforms with the broadly accepted definition that entropy is the information loss. As informational entropy concept hasmore » been proved to be useful, it will be convenient to define an informational temperature, T{sub I}. This can be related to energy E and the informational entropy S. Information registration is a process of {Delta}I > 0, or {Delta}S < 0, and involves the energetically excited states ({Delta}E > 0). Therefore, T{sub I} is negative, and has the opposite sign of the conventional thermodynamic temperature, T. This concept is useful for clarifying the concepts of {open_quotes}order{close_quotes} and {open_quotes}disorder{close_quotes} of static structures and characterizing many typical information loss processes of self-organization.« less

[Identification and analysis of Corydalis boweri, Meconopsis horridula and their close related species of the same genus by using ITS2 DNA barcode].

PubMed

Dou, Rong-kun; Bi, Zhen-fei; Bai, Rui-xue; Ren, Yao-yao; Tan, Rui; Song, Liang-ke; Li, Di-qiang; Mao, Can-quan

2015-04-01

The study is aimed to ensure the quality and safety of medicinal plants by using ITS2 DNA barcode technology to identify Corydalis boweri, Meconopsis horridula and their close related species. The DNA of 13 herb samples including C. boweri and M. horridula from Lhasa of Tibet was extracted, ITS PCR were amplified and sequenced. Both assembled and web downloaded 71 ITS2 sequences were removed of 5. 8S and 28S. Multiple sequence alignment was completed and the intraspecific and interspecific genetic distances were calculated by MEGA 5.0, while the neighbor-joining phylogenetic trees were constructed. We also predicted the ITS2 secondary structure of C. boweri, M. horridula and their close related species. The results showed that ITS2 as DNA barcode was able to identify C. boweri, M. horridula as well as well as their close related species effectively. The established based on ITS2 barcode method provides the regular and safe detection technology for identification of C. boweri, M. horridula and their close related species, adulterants and counterfeits, in order to ensure their quality control, safe medication, reasonable development and utilization.

Vibronic Wavepackets and Energy Transfer in Cryptophyte Light-Harvesting Complexes.

PubMed

Jumper, Chanelle C; van Stokkum, Ivo H M; Mirkovic, Tihana; Scholes, Gregory D

2018-06-21

Determining the key features of high-efficiency photosynthetic energy transfer remains an ongoing task. Recently, there has been evidence for the role of vibronic coherence in linking donor and acceptor states to redistribute oscillator strength for enhanced energy transfer. To gain further insights into the interplay between vibronic wavepackets and energy-transfer dynamics, we systematically compare four structurally related phycobiliproteins from cryptophyte algae by broad-band pump-probe spectroscopy and extend a parametric model based on global analysis to include vibrational wavepacket characterization. The four phycobiliproteins isolated from cryptophyte algae are two "open" structures and two "closed" structures. The closed structures exhibit strong exciton coupling in the central dimer. The dominant energy-transfer pathway occurs on the subpicosecond timescale across the largest energy gap in each of the proteins, from central to peripheral chromophores. All proteins exhibit a strong 1585 cm -1 coherent oscillation whose relative amplitude, a measure of vibronic intensity borrowing from resonance between donor and acceptor states, scales with both energy-transfer rates and damping rates. Central exciton splitting may aid in bringing the vibronically linked donor and acceptor states into better resonance resulting in the observed doubled rate in the closed structures. Several excited-state vibrational wavepackets persist on timescales relevant to energy transfer, highlighting the importance of further investigation of the interplay between electronic coupling and nuclear degrees of freedom in studies on high-efficiency photosynthesis.

First insights into a type II toxin-antitoxin system from the clinical isolate Mycobacterium sp. MHSD3, similar to epsilon/zeta systems.

PubMed

Jaén-Luchoro, Daniel; Aliaga-Lozano, Francisco; Gomila, Rosa Maria; Gomila, Margarita; Salvà-Serra, Francisco; Lalucat, Jorge; Bennasar-Figueras, Antoni

2017-01-01

A putative type II toxin-antitoxin (TA) system was found in the clinical isolate Mycobacterium sp. MHSD3, a strain closely related to Mycobacterium chelonae. Further analyses of the protein sequences of the two genes revealed the presence of domains related to a TA system. BLAST analyses indicated the presence of closely related proteins in the genomes of other recently published M. chelonae strains. The functionality of both elements of the TA system was demonstrated when expressed in Escherichia coli cells, and the predicted structure of the toxin is very similar to those of well-known zeta-toxins, leading to the definition of a type II TA system similar to epsilon/zeta TA systems in strains that are closely related to M. chelonae.

Quantization of wave equations and hermitian structures in partial differential varieties

PubMed Central

Paneitz, S. M.; Segal, I. E.

1980-01-01

Sufficiently close to 0, the solution variety of a nonlinear relativistic wave equation—e.g., of the form □ϕ + m2ϕ + gϕp = 0—admits a canonical Lorentz-invariant hermitian structure, uniquely determined by the consideration that the action of the differential scattering transformation in each tangent space be unitary. Similar results apply to linear time-dependent equations or to equations in a curved asymptotically flat space-time. A close relation of the Riemannian structure to the determination of vacuum expectation values is developed and illustrated by an explicit determination of a perturbative 2-point function for the case of interaction arising from curvature. The theory underlying these developments is in part a generalization of that of M. G. Krein and collaborators concerning stability of differential equations in Hilbert space and in part a precise relation between the unitarization of given symplectic linear actions and their full probabilistic quantization. The unique causal structure in the infinite symplectic group is instrumental in these developments. PMID:16592923

Ganymede - close up photos

NASA Technical Reports Server (NTRS)

1979-01-01

Two close-up photos of Ganymede, largest of Jupiter's 13 moons, were obtained on July 8 by Voyager 2 from 86,000 miles (top) and 192,000 miles. They show different views of the largest block of dark, heavily cratered terrain seen on the giant moon. The bottom image shows objects three to four miles across; has a resolution of about 1.5 miles. The light, linear stripes recurring across the dark region resemble the outer rings of the large ring structure on Callisto. If these features are in fact related to an ancient ring structure formed by a large impact, their small curvature suggests that the original structure was even larger than one seen on Callisto. There is no apparent trace now of the center of this suggested structure, which must have been destroyed by the resurfacing evident over most of Ganymede in the grooved terrain. Another interpretation is that these features are not impact-related rings but are internally produced fractures crossing the dark terrain, similar to the grooved bands.

Photographer : JPL Range : top- 86,000 miles bottom- 192,000 mi. These two close-ups of Ganymede,

NASA Technical Reports Server (NTRS)

1979-01-01

Photographer : JPL Range : top- 86,000 miles bottom- 192,000 mi. These two close-ups of Ganymede, the largest of Jupiter's 13 moons, show different views of the largest block of dark, heavily cratered terrain. The bottom image shows objects 3 or 4 miles across, with resolution of about 1.5 miles. The light, linear stripes recurring across the dark region resemble the outer rings of the large ring structure around Callisto. If these features are related to an ancient ring structure formed by a large impact, their small curvature suggests that the original structure was even larger than one seen on Callisto. There is no apparent trace now of the center of this suggested structure, which must have been destroyed by the resurfacing evident over most of Ganymede in the grooved terrain. Another interpretation is that these features are not impact-related rings, but rather internally produced fractures crossing the dark terrain, similiar to the grooved bands.

Geologic and mineral and water resources investigations in western Colorado using ERTS-1 data

NASA Technical Reports Server (NTRS)

Knepper, D. H. (Principal Investigator)

1974-01-01

The author has identified the following significant results. Most of the geologic information in ERTS-1 imagery can be extracted from bulk processed black and white transparencies by a skilled interpreter using standard photogeologic techniques. In central and western Colorado, the detectability of lithologic contacts on ERTS-1 imagery is closely related to the time of year the imagery was acquired. Geologic structures are the most readily extractable type of geologic information contained in ERTS images. Major tectonic features and associated minor structures can be rapidly mapped, allowing the geologic setting of a large region to be quickly accessed. Trends of geologic structures in younger sedimentary appear to strongly parallel linear trends in older metamorphic and igneous basement terrain. Linears and color anomalies mapped from ERTS imagery are closely related to loci of known mineralization in the Colorado mineral belt.

Structure and topology of three-dimensional hydrocarbon polymers.

PubMed

Kondrin, Mikhail V; Lebed, Yulia B; Brazhkin, Vadim V

2016-08-01

A new family of three-dimensional hydrocarbon polymers which are more energetically favorable than benzene is proposed. Although structurally these polymers are closely related to well known diamond and lonsdaleite carbon structures, using topological arguments we demonstrate that they have no known structural analogs. Topological considerations also give some indication of possible methods of synthesis. Taking into account their exceptional optical, structural and mechanical properties these polymers might have interesting applications.

Investigating the structure of a vortex flow in the closed polygonal containers

NASA Astrophysics Data System (ADS)

Podolskaya, I. Yu; Bakakin, G. V.; Naumov, I. V.

2018-03-01

The structure of confined vortex flow generated by a rotating lid in a closed container with polygonal cross-section geometry (eight, six and five angles) has been investigated numerically for different height/radius aspect ratios h from 3.0 to 4.5 and for Reynold numbers ranging from 1500 to 3000. The critical Reynolds numbers at which the flow becomes unsteady were determined numerically by STAR-CCM+ computational fluid dynamics software for pentagonal and hexagonal cross-section configurations. The obtained results were compared with the flow structure in the closed cylindrical container. The boundary of a nonstationarity in polygonal containers is found to shift to the region of smaller aspect ratio and smaller Reynolds numbers with a decrease in the number of angles in the cross-section of the container relative to the boundary in a cylindrical container. It is additionally established that the structure of the flow in the near-axis region remains similar to the vortex structure in the cylinder, therefore the shape of the container does not influence the near-axis region.

Stabilizing the hexagonal close packed structure of hard spheres with polymers: Phase diagram, structure, and dynamics

NASA Astrophysics Data System (ADS)

Edison, John R.; Dasgupta, Tonnishtha; Dijkstra, Marjolein

2016-08-01

We study the phase behaviour of a binary mixture of colloidal hard spheres and freely jointed chains of beads using Monte Carlo simulations. Recently Panagiotopoulos and co-workers predicted [Nat. Commun. 5, 4472 (2014)] that the hexagonal close packed (HCP) structure of hard spheres can be stabilized in such a mixture due to the interplay between polymer and the void structure in the crystal phase. Their predictions were based on estimates of the free-energy penalty for adding a single hard polymer chain in the HCP and the competing face centered cubic (FCC) phase. Here we calculate the phase diagram using free-energy calculations of the full binary mixture and find a broad fluid-solid coexistence region and a metastable gas-liquid coexistence region. For the colloid-monomer size ratio considered in this work, we find that the HCP phase is only stable in a small window at relatively high polymer reservoir packing fractions, where the coexisting HCP phase is nearly close packed. Additionally we investigate the structure and dynamic behaviour of these mixtures.

Stability Criteria of Fullerene-like Nanoparticles: Comparing V₂O5 to Layered Metal Dichalcogenides and Dihalides.

PubMed

Levi, Roi; Bar-Sadan, Maya; Albu-Yaron, Ana; Popovitz-Biro, Ronit; Houben, Lothar; Prior, Yehiam; Tenne, Reshef

2010-08-18

Numerous examples of closed-cage nanostructures, such as nested fullerene-like nanoparticles and nanotubes, formed by the folding of materials with layered structure are known. These compounds include WS₂, NiCl₂, CdCl₂, Cs₂O, and recently V₂O₅. Layered materials, whose chemical bonds are highly ionic in character, possess relatively stiff layers, which cannot be evenly folded. Thus, stress-relief generally results in faceted nanostructures seamed by edge-defects. V₂O₅, is a metal oxide compound with a layered structure. The study of the seams in nearly perfect inorganic "fullerene-like" hollow V₂O 5 nanoparticles (NIF-V₂O₅) synthesized by pulsed laser ablation (PLA), is discussed in the present work. The relation between the formation mechanism and the seams between facets is examined. The formation mechanism of the NIF-V₂O 5 is discussed in comparison to fullerene-like structures of other layered materials, like IF structures of MoS₂, CdCl₂, and Cs₂O. The criteria for the perfect seaming of such hollow closed structures are highlighted.

The nuclear higher-order structure defined by the set of topological relationships between DNA and the nuclear matrix is species-specific in hepatocytes.

PubMed

Silva-Santiago, Evangelina; Pardo, Juan Pablo; Hernández-Muñoz, Rolando; Aranda-Anzaldo, Armando

2017-01-15

During the interphase the nuclear DNA of metazoan cells is organized in supercoiled loops anchored to constituents of a nuclear substructure or compartment known as the nuclear matrix. The stable interactions between DNA and the nuclear matrix (NM) correspond to a set of topological relationships that define a nuclear higher-order structure (NHOS). Current evidence suggests that the NHOS is cell-type-specific. Biophysical evidence and theoretical models suggest that thermodynamic and structural constraints drive the actualization of DNA-NM interactions. However, if the topological relationships between DNA and the NM were the subject of any biological constraint with functional significance then they must be adaptive and thus be positively selected by natural selection and they should be reasonably conserved, at least within closely related species. We carried out a coarse-grained, comparative evaluation of the DNA-NM topological relationships in primary hepatocytes from two closely related mammals: rat and mouse, by determining the relative position to the NM of a limited set of target sequences corresponding to highly-conserved genomic regions that also represent a sample of distinct chromosome territories within the interphase nucleus. Our results indicate that the pattern of topological relationships between DNA and the NM is not conserved between the hepatocytes of the two closely related species, suggesting that the NHOS, like the karyotype, is species-specific. Copyright © 2016 Elsevier B.V. All rights reserved.

Numerical modelling of closed-cell aluminium foam under dynamic loading

NASA Astrophysics Data System (ADS)

Hazell, Paul; Kader, M. A.; Islam, M. A.; Escobedo, J. P.; Saadatfar, M.

2015-06-01

Closed-cell aluminium foams are extensively used in aerospace and automobile industries. The understanding of their behaviour under impact loading conditions is extremely important since impact problems are directly related to design of these engineering structures. This research investigates the response of a closed-cell aluminium foam (CYMAT) subjected to dynamic loading using the finite element software ABAQUS/explicit. The aim of this research is to numerically investigate the material and structural properties of closed-cell aluminium foam under impact loading conditions with interest in shock propagation and its effects on cell wall deformation. A μ-CT based 3D foam geometry is developed to simulate the local cell collapse behaviours. A number of numerical techniques are applied for modelling the crush behaviour of aluminium foam to obtain the more accurate results. The simulation results are compared with experimental data. Comparison of the results shows a good correlation between the experimental results and numerical predictions.

Improvement of open and semi-open core wall system in tall buildings by closing of the core section in the last story

NASA Astrophysics Data System (ADS)

Kheyroddin, A.; Abdollahzadeh, D.; Mastali, M.

2014-09-01

Increasing number of tall buildings in urban population caused development of tall building structures. One of the main lateral load resistant systems is core wall system in high-rise buildings. Core wall system has two important behavioral aspects where the first aspect is related to reduce the lateral displacement by the core bending resistance and the second is governed by increasing of the torsional resistance and core warping of buildings. In this study, the effects of closed section core in the last story have been considered on the behavior of models. Regarding this, all analyses were performed by ETABS 9.2.v software (Wilson and Habibullah). Considering (a) drift and rotation of the core over height of buildings, (b) total and warping stress in the core body, (c) shear in beams due to warping stress, (d) effect of closing last story on period of models in various modes, (e) relative displacement between walls in the core system and (f) site effects in far and near field of fault by UBC97 spectra on base shear coefficient showed that the bimoment in open core is negative in the last quarter of building and it is similar to wall-frame structures. Furthermore, analytical results revealed that closed section core in the last story improves behavior of the last quarter of structure height, since closing of core section in the last story does not have significant effect on reducing base shear value in near and far field of active faults.

Wing scale ultrastructure underlying convergent and divergent iridescent colours in mimetic Heliconius butterflies.

PubMed

Parnell, Andrew J; Bradford, James E; Curran, Emma V; Washington, Adam L; Adams, Gracie; Brien, Melanie N; Burg, Stephanie L; Morochz, Carlos; Fairclough, J Patrick A; Vukusic, Pete; Martin, Simon J; Doak, Scott; Nadeau, Nicola J

2018-04-01

Iridescence is an optical phenomenon whereby colour changes with the illumination and viewing angle. It can be produced by thin film interference or diffraction. Iridescent optical structures are fairly common in nature, but relatively little is known about their production or evolution. Here we describe the structures responsible for producing blue-green iridescent colour in Heliconius butterflies. Overall the wing scale structures of iridescent and non-iridescent Heliconius species are very similar, both having longitudinal ridges joined by cross-ribs. However, iridescent scales have ridges composed of layered lamellae, which act as multilayer reflectors. Differences in brightness between species can be explained by the extent of overlap of the lamellae and their curvature as well as the density of ridges on the scale. Heliconius are well known for their Müllerian mimicry. We find that iridescent structural colour is not closely matched between co-mimetic species. Differences appear less pronounced in models of Heliconius vision than models of avian vision, suggesting that they are not driven by selection to avoid heterospecific courtship by co-mimics. Ridge profiles appear to evolve relatively slowly, being similar between closely related taxa, while ridge density evolves faster and is similar between distantly related co-mimics. © 2018 The Authors.

Wing scale ultrastructure underlying convergent and divergent iridescent colours in mimetic Heliconius butterflies

PubMed Central

Bradford, James E.; Curran, Emma V.; Washington, Adam L.; Adams, Gracie; Brien, Melanie N.; Burg, Stephanie L.; Morochz, Carlos; Fairclough, J. Patrick A.; Vukusic, Pete; Martin, Simon J.; Doak, Scott

2018-01-01

Iridescence is an optical phenomenon whereby colour changes with the illumination and viewing angle. It can be produced by thin film interference or diffraction. Iridescent optical structures are fairly common in nature, but relatively little is known about their production or evolution. Here we describe the structures responsible for producing blue-green iridescent colour in Heliconius butterflies. Overall the wing scale structures of iridescent and non-iridescent Heliconius species are very similar, both having longitudinal ridges joined by cross-ribs. However, iridescent scales have ridges composed of layered lamellae, which act as multilayer reflectors. Differences in brightness between species can be explained by the extent of overlap of the lamellae and their curvature as well as the density of ridges on the scale. Heliconius are well known for their Müllerian mimicry. We find that iridescent structural colour is not closely matched between co-mimetic species. Differences appear less pronounced in models of Heliconius vision than models of avian vision, suggesting that they are not driven by selection to avoid heterospecific courtship by co-mimics. Ridge profiles appear to evolve relatively slowly, being similar between closely related taxa, while ridge density evolves faster and is similar between distantly related co-mimics. PMID:29669892

Structural divergence among genomes of closely related baculoviruses and its implications for baculovirus evolution

USDA-ARS?s Scientific Manuscript database

Baculoviruses are members of a large, well-characterized family of dsDNA viruses that have been identified from insects of the orders Lepidoptera, Hymenoptera, and Diptera. Baculovirus genomes from different virus species generally exhibit a considerable degree of structural diversity. However, so...

24 CFR 3285.802 - Structural interconnection of multi-section homes.

Code of Federal Regulations, 2011 CFR

2011-04-01

...-section homes. 3285.802 Section 3285.802 Housing and Urban Development Regulations Relating to Housing and..., DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT MODEL MANUFACTURED HOME INSTALLATION STANDARDS Exterior and Interior Close-Up § 3285.802 Structural interconnection of multi-section homes. (a) For multi-section homes...

24 CFR 3285.802 - Structural interconnection of multi-section homes.

Code of Federal Regulations, 2010 CFR

2010-04-01

...-section homes. 3285.802 Section 3285.802 Housing and Urban Development Regulations Relating to Housing and..., DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT MODEL MANUFACTURED HOME INSTALLATION STANDARDS Exterior and Interior Close-Up § 3285.802 Structural interconnection of multi-section homes. (a) For multi-section homes...

24 CFR 3285.802 - Structural interconnection of multi-section homes.

Code of Federal Regulations, 2013 CFR

2013-04-01

...-section homes. 3285.802 Section 3285.802 Housing and Urban Development Regulations Relating to Housing and..., DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT MODEL MANUFACTURED HOME INSTALLATION STANDARDS Exterior and Interior Close-Up § 3285.802 Structural interconnection of multi-section homes. (a) For multi-section homes...

Structural Determinants of the Closed KCa3.1 Channel Pore in Relation to Channel Gating: Results from a Substituted Cysteine Accessibility Analysis

PubMed Central

Klein, Hélène; Garneau, Line; Banderali, Umberto; Simoes, Manuel; Parent, Lucie; Sauvé, Rémy

2007-01-01

In this work we address the question of the KCa3.1 channel pore structure in the closed configuration in relation to the contribution of the C-terminal end of the S6 segments to the Ca2+-dependent gating process. Our results based on SCAM (substituted cysteine accessibility method) experiments first demonstrate that the S6 transmembrane segment of the open KCa3.1 channel contains two distinct functional domains delimited by V282 with MTSEA and MTSET binding leading to a total channel inhibition at positions V275, T278, and V282 and to a steep channel activation at positions A283 and A286. The rates of modification by MTSEA (diameter 4.6 Å) of the 275C (central cavity) and 286C residues (S6 C-terminal end) for the closed channel configuration were found to differ by less than sevenfold, whereas experiments performed with the larger MTSET reagent (diameter 5.8 Å) resulted in modification rates 103–104 faster for cysteines at 286 compared with 275. Consistent with these results, the modification rates of the cavity lining 275C residue by MTSEA, Et-Hg+, and Ag+ appeared poorly state dependent, whereas modification rates by MTSET were 103 faster for the open than the closed configuration. A SCAM analysis of the channel inner vestibule in the closed state revealed in addition that cysteine residues at 286 were accessible to MTS reagents as large as MTS-PtrEA, a result supported by the observation that binding of MTSET to cysteines at positions 283 or 286 could neither sterically nor electrostatically block the access of MTSEA to the closed channel cavity (275C). It follows that the closed KCa3.1 structure can hardly be accountable by an inverted teepee-like structure as described for KcsA, but is better represented by a narrow passage centered at V282 (equivalent to V474 in Shaker) connecting the channel central cavity to the cytosolic medium. This passage would not be however restrictive to the diffusion of small reagents such as MTSEA, Et-Hg+, and Ag+, arguing against the C-terminal end of S6 forming an obstructive barrier to the diffusion of K+ ions for the closed channel configuration. PMID:17353352

Electronic structure contributions to reactivity in xanthine oxidase family enzymes.

PubMed

Stein, Benjamin W; Kirk, Martin L

2015-03-01

We review the xanthine oxidase (XO) family of pyranopterin molybdenum enzymes with a specific emphasis on electronic structure contributions to reactivity. In addition to xanthine and aldehyde oxidoreductases, which catalyze the two-electron oxidation of aromatic heterocycles and aldehyde substrates, this mini-review highlights recent work on the closely related carbon monoxide dehydrogenase (CODH) that catalyzes the oxidation of CO using a unique Mo-Cu heterobimetallic active site. A primary focus of this mini-review relates to how spectroscopy and computational methods have been used to develop an understanding of critical relationships between geometric structure, electronic structure, and catalytic function.

Are artificial opals non-close-packed fcc structures?

NASA Astrophysics Data System (ADS)

García-Santamaría, F.; Braun, P. V.

2007-06-01

The authors report a simple experimental method to accurately measure the volume fraction of artificial opals. The results are modeled using several methods, and they find that some of the most common yield very inaccurate results. Both finite size and substrate effects play an important role in calculations of the volume fraction. The experimental results show that the interstitial pore volume is 4%-15% larger than expected for close-packed structures. Consequently, calculations performed in previous work relating the amount of material synthesized in the opal interstices with the optical properties may need revision, especially in the case of high refractive index materials.

Prolongation structures of nonlinear evolution equations. II

NASA Technical Reports Server (NTRS)

Estabrook, F. B.; Wahlquist, H. D.

1976-01-01

The prolongation structure of a closed ideal of exterior differential forms is further discussed, and its use illustrated by application to an ideal (in six dimensions) representing the cubically nonlinear Schroedinger equation. The prolongation structure in this case is explicitly given, and recurrence relations derived which support the conjecture that the structure is open - i.e., does not terminate as a set of structure relations of a finite-dimensional Lie group. We introduce the use of multiple pseudopotentials to generate multiple Baecklund transformation, and derive the double Baecklund transformation. This symmetric transformation concisely expresses the (usually conjectured) theorem of permutability, which must consequently apply to all solutions irrespective of asymptotic constraints.

Category Membership and Semantic Coding in the Cerebral Hemispheres.

PubMed

Turner, Casey E; Kellogg, Ronald T

2016-01-01

Although a gradient of category membership seems to form the internal structure of semantic categories, it is unclear whether the 2 hemispheres of the brain differ in terms of this gradient. The 2 experiments reported here examined this empirical question and explored alternative theoretical interpretations. Participants viewed category names centrally and determined whether a closely related or distantly related word presented to either the left visual field/right hemisphere (LVF/RH) or the right visual field/left hemisphere (RVF/LH) was a member of the category. Distantly related words were categorized more slowly in the LVF/RH relative to the RVF/LH, with no difference for words close to the prototype. The finding resolved past mixed results showing an unambiguous typicality effect for both visual field presentations. Furthermore, we examined items near the fuzzy border that were sometimes rejected as nonmembers of the category and found both hemispheres use the same category boundary. In Experiment 2, we presented 2 target words to be categorized, with the expectation of augmenting the speed advantage for the RVF/LH if the 2 hemispheres differ structurally. Instead the results showed a weakening of the hemispheric difference, arguing against a structural in favor of a processing explanation.

On non-homogeneous tachyon condensation in closed string theory

NASA Astrophysics Data System (ADS)

Giribet, Gaston; Rado, Laura

2017-08-01

Lorentzian continuation of the Sine-Liouville model describes non-homogeneous rolling closed string tachyon. Via T-duality, this relates to the gauged H + 3 Wess-Zumino-Witten model at subcritical level. This model is exactly solvable. We give a closed formula for the 3-point correlation functions for the model at level k within the range 0 < k < 2, which relates to the analogous quantity for k > 2 in a similar way as how the Harlow-Maltz-Witten 3-point function of timelike Liouville field theory relates to the analytic continuation of the Dorn-Otto-Zamolodchikov-Zamolodchikov structure constants: we find that the ratio between both 3-point functions can be written in terms of quotients of Jacobi's θ-functions, while their product exhibits remarkable cancellations and eventually factorizes. Our formula is consistent with previous proposals made in the literature.

Crystal structure of hexagonal MnAl(4).

PubMed

Pauling, L

1987-06-01

A structure is proposed for the hexagonal form of MnAl(4), with a(H) = 28.4 A and c(H) = 12.43 A, on the basis of a high-resolution electron micrograph and comparison with crystals of known structures. The proposed structure involves seven 104-atom complexes of 20 Friauf polyhedra, sharing some atoms with one another. It is closely related to the 23.36-A cubic structure of MnAl(4) and to the 14.19-A cubic structure of Mg(32)(Al,Zn)(49).

Linkage between mantle and crustal structures and its bearing on inherited structures in northwestern Scotland

USGS Publications Warehouse

Snyder, D.B.; England, R.W.; McBride, J.H.

1997-01-01

Deep seismic reflection profiles in Scotland reveal mantle structures beneath a crust with a polyphase tectonic history that resulted in several generations of structures. Continuum mechanics suggests that coeval mantle and crustal structures must be kinematically linked. Inherited structures imply relative ages for the reflectors, ages that can be placed into the context of the geological history of the near-surface rocks of northern Scotland. Thus, some mantle reflectors are assigned Triassic ages related to the opening of the West Orkney and related marginal basins of the Atlantic Ocean. Other mantle reflectors are cut by late Caledonian structures associated with the Great Glen Fault Zone and therefore older than c. 400 Ma. Many of these structures also track the late Precambrian margin of Laurentia and may be related to either the opening (900-600 Ma) or closing (500-400 Ma) of the Iapetus Ocean. Some reflective structures may also be attributed to 1800-1700 Ma Laxfordian deformation that was part of a global-scale orogenic belt.

Does Closeness to Someone Who Is Gay, Lesbian, or Bisexual Influence Etiology Beliefs About Homosexuality?

PubMed

Chonody, Jill M; Kavanagh, Phillip S; Woodford, Michael R

2016-12-01

Research suggests that contact with sexual minorities and etiology beliefs regarding the origins of homosexuality are associated with antigay bias; however, factors related to etiology beliefs have received little empirical attention. Our primary research question is: Does closeness to someone who is gay, lesbian, or bisexual influence etiology beliefs? Students (n = 851) from four U.S. universities completed an anonymous survey, and regression results indicated that contact and closeness were not significantly associated with etiology beliefs. Because both contact and relationship closeness were associated with antigay attitudes, and closeness demonstrated the largest effect, we tested three alternative structural equation models to determine if contact and closeness mediated etiology beliefs. Results suggested that contact and the degree of closeness are indirectly associated with students' etiology beliefs through antigay bias.

Siphonophores and the Deep Scattering Layer.

PubMed

Barham, E G

1963-05-17

Bathyscaphe dives in the San Diego Trough have revealed a close spatial relation between siphonophores and the deep scattering layer as recorded by precision depth recording echo-sounders. Measurements of gas bubbles within the flotation structures of Nanomia bijuga captured in a closing net in an ascended scattering layer indicate that these are very close to the resonant size for 12-kcy/sec sound. Because such organisms are capable of making prolonged vertical migrations, and are widespread geographically, they are very probably the major cause of stratified zones of scattering throughout the oceans of the world.

Closed-form solutions for linear regulator design of mechanical systems including optimal weighting matrix selection

NASA Technical Reports Server (NTRS)

Hanks, Brantley R.; Skelton, Robert E.

1991-01-01

Vibration in modern structural and mechanical systems can be reduced in amplitude by increasing stiffness, redistributing stiffness and mass, and/or adding damping if design techniques are available to do so. Linear Quadratic Regulator (LQR) theory in modern multivariable control design, attacks the general dissipative elastic system design problem in a global formulation. The optimal design, however, allows electronic connections and phase relations which are not physically practical or possible in passive structural-mechanical devices. The restriction of LQR solutions (to the Algebraic Riccati Equation) to design spaces which can be implemented as passive structural members and/or dampers is addressed. A general closed-form solution to the optimal free-decay control problem is presented which is tailored for structural-mechanical system. The solution includes, as subsets, special cases such as the Rayleigh Dissipation Function and total energy. Weighting matrix selection is a constrained choice among several parameters to obtain desired physical relationships. The closed-form solution is also applicable to active control design for systems where perfect, collocated actuator-sensor pairs exist.

Using Concrete & Representational Experiences to Understand the Structure of DNA: A Four-Step Instructional Framework

ERIC Educational Resources Information Center

Harrell, Pamela Esprivalo; Richards, Debbie; Collins, James; Taylor, Sarah

2005-01-01

A description of learning experience that uses a four-step instrumentational framework involving concrete and representational experiences to promote conceptual understanding of abstract biological concepts by a series of closely-related activities is presented. The students are introduced to the structure and implications of DNA using four…

Structural and genetic relationships of closely related O-antigens of Cronobacter spp. and Escherichia coli: C. sakazakii G2594 (serotype O4)/E. coli O103 and C. malonaticus G3864 (serotype O1)/E. coli O29.

PubMed

Shashkov, Alexander S; Wang, Min; Turdymuratov, Eldar M; Hu, Shaohui; Arbatsky, Nikolay P; Guo, Xi; Wang, Lei; Knirel, Yuriy A

2015-03-02

O-Antigen (O-polysaccharide) variation is the basis for bacterial serotyping and is important in bacterial virulence and niche adaptation. In this work, we present structural and genetic evidences for close relationships between the O-antigens of the Cronobacter spp. and Escherichia coli. Cronobacter sakazakii G2594 (serotype O4) and Cronobacter malonaticus G3864 (serotype O1) are structurally related to those of E. coli O103 and O29, respectively, and some other members of the Enterobacteriaceae family differing in the patterns of lateral glucosylation (C. sakazakii G2594) or O-acetylation (C. malonaticus G3864). The O-antigen gene clusters of the corresponding Cronobacter and E. coli strains contain the same genes with high-level similarity, and the structural differences within both O-antigen pairs were suggested to be due to modification genes carried by prophages. Copyright © 2014 Elsevier Ltd. All rights reserved.

JSEP fellowship

NASA Astrophysics Data System (ADS)

Goodman, Alvin M.; Powers, Edward J.

1993-06-01

In this dissertation, the precision of molecular-beam epitaxy (MBE) is taken advantage of in order to grow semiconductor reflectors, microcavities, and quantum wells for studies of vertical-cavity surface-emitting lasers (VCSEL's) and the coupling between reflectors and the spatially localized dipoles of semiconductor quantum wells. The design of the structures and the choice of epitaxial growth parameters used for the structures are discussed in detail. Experimental techniques and results are discussed which relate to studies that advance the optoelectronics technology and our understanding of fundamental physics. MBE is used to grow epitaxial structures in which a QW is precisely placed either in close proximity to a DBR, or near the surface of the epitaxial layer, so that a highly reflective mirror can be placed in close proximity to the QW.

Structural and functional analysis of the finished genome of the recently isolated toxic Anabaena sp. WA102.

PubMed

Brown, Nathan M; Mueller, Ryan S; Shepardson, Jonathan W; Landry, Zachary C; Morré, Jeffrey T; Maier, Claudia S; Hardy, F Joan; Dreher, Theo W

2016-06-13

Very few closed genomes of the cyanobacteria that commonly produce toxic blooms in lakes and reservoirs are available, limiting our understanding of the properties of these organisms. A new anatoxin-a-producing member of the Nostocaceae, Anabaena sp. WA102, was isolated from a freshwater lake in Washington State, USA, in 2013 and maintained in non-axenic culture. The Anabaena sp. WA102 5.7 Mbp genome assembly has been closed with long-read, single-molecule sequencing and separately a draft genome assembly has been produced with short-read sequencing technology. The closed and draft genome assemblies are compared, showing a correlation between long repeats in the genome and the many gaps in the short-read assembly. Anabaena sp. WA102 encodes anatoxin-a biosynthetic genes, as does its close relative Anabaena sp. AL93 (also introduced in this study). These strains are distinguished by differences in the genes for light-harvesting phycobilins, with Anabaena sp. AL93 possessing a phycoerythrocyanin operon. Biologically relevant structural variants in the Anabaena sp. WA102 genome were detected only by long-read sequencing: a tandem triplication of the anaBCD promoter region in the anatoxin-a synthase gene cluster (not triplicated in Anabaena sp. AL93) and a 5-kbp deletion variant present in two-thirds of the population. The genome has a large number of mobile elements (160). Strikingly, there was no synteny with the genome of its nearest fully assembled relative, Anabaena sp. 90. Structural and functional genome analyses indicate that Anabaena sp. WA102 has a flexible genome. Genome closure, which can be readily achieved with long-read sequencing, reveals large scale (e.g., gene order) and local structural features that should be considered in understanding genome evolution and function.

Rigid closed-cell polyimide foams for aircraft applications and foam-in-place technology

NASA Technical Reports Server (NTRS)

Gagliani, J.; Straub, P.; Gagliani, J., Jr.

1983-01-01

Significant accomplishments generated are summarized. Testing of closed cell foams, which has resulted in the characterization of compositions which produce rigid foams for use in galley structure applications is reported. It is shown that the density, compressive strength and shear strength of the foams are directly related to the concentrations of the microballoons. The same properties are also directly related to the resin loading. Prototype samples of rigid closed cell foams meeting the requirements of the program were submitted. Investigation of the apparatus to produce polyimide foams using foam in place techniques, resulted in the selection of a spray gun apparatus, capable to deliver a mixture of microballoons and resin binder on substrates which cures to yield a closed cell foam. It is found that the adhesion of the foam on aluminum, titanium and steel substrates is satisfactory. It is concluded that the material meets the mechanical and thermal requirements of the program.

Stability Criteria of Fullerene-like Nanoparticles: Comparing V2O5 to Layered Metal Dichalcogenides and Dihalides

PubMed Central

Levi, Roi; Bar-Sadan, Maya; Albu-Yaron, Ana; Popovitz-Biro, Ronit; Houben, Lothar; Prior, Yehiam; Tenne, Reshef

2010-01-01

Numerous examples of closed-cage nanostructures, such as nested fullerene-like nanoparticles and nanotubes, formed by the folding of materials with layered structure are known. These compounds include WS2, NiCl2, CdCl2, Cs2O, and recently V2O5. Layered materials, whose chemical bonds are highly ionic in character, possess relatively stiff layers, which cannot be evenly folded. Thus, stress-relief generally results in faceted nanostructures seamed by edge-defects. V2O5, is a metal oxide compound with a layered structure. The study of the seams in nearly perfect inorganic "fullerene-like" hollow V2O5 nanoparticles (NIF-V2O5) synthesized by pulsed laser ablation (PLA), is discussed in the present work. The relation between the formation mechanism and the seams between facets is examined. The formation mechanism of the NIF-V2O5 is discussed in comparison to fullerene-like structures of other layered materials, like IF structures of MoS2, CdCl2, and Cs2O. The criteria for the perfect seaming of such hollow closed structures are highlighted. PMID:28883335

The effect of Gossypolone on the growth and development of Helicoverpa zea (Boddie)

USDA-ARS?s Scientific Manuscript database

The pigment glands of the cotton plant (Gossypium) produce a group of structurally related terpenoid aldehydes that protect the plant from herbivorous insects. Of these terpenoids, the most extensively studied is gossypol. Gossypolone, a compound closely related to gossypol, has been reported in t...

The gamut of alkoxy radicals

NASA Astrophysics Data System (ADS)

Box, Harold C.; Budzinski, Edwin E.; Freund, Harold G.

1984-12-01

It is shown that various radicals exhibiting diverse ESR and ENDOR spectral characteristics are nonetheless a closely related family of alkoxy radicals. The relationship is established by correlating the g tensor with crystal structure and by relating dihedral angles inferred from proton hyperfine couplings to dihedral angles inferred from the g tensor and crystal structure. The analysis also serves to demonstrate that an ESR absorption observed in x-irradiated single crystals of uridine 5'-monophosphate is due to an alkoxy radical.

What is worse? A hierarchy of family-related risk factors predicting alcohol use in adolescence.

PubMed

Kuntsche, Emmanuel N; Kuendig, Hervé

2006-01-01

The aim of the present study was to determine if family structure, perception of excessive drinking in the family, and family bonding hold a graduated importance in predicting adolescent alcohol use and their association with peers who drink excessively. Three nested linear structural models were calculated separately for frequent and excessive drinking, based on a sample of 3,127 eighth and ninth graders in Switzerland (mean age 15.3, SD 0.8) surveyed in spring 2002 in the context of the "Health Behavior in School-Aged Children (HBSC)" study. The results confirm that the perception of excessive drinking in the family is more closely related to both frequent and excessive drinking than family structure, and family bonding is more closely related than drinking perception. Adjusting for both socio-demographic variables and the association with peers who drink excessively only slightly changed the results. To predict an association with the latter, family structure was more important than the perception of drinking, but family bonding remained the predominant predictor. The results stress the graduated importance of family-related risk factors: by listening to their children's worries, by spending their free time with them, and by providing help when needed, parents might have the possibility to actively minimize the risk of frequent and excessive drinking regardless of whether they are frequent excessive drinkers or live without a partner.

Temperature maxima in stable two-dimensional shock waves

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

Kum, O.; Hoover, W.G.; Hoover, C.G.

1997-07-01

We use molecular dynamics to study the structure of moderately strong shock waves in dense two-dimensional fluids, using Lucy{close_quote}s pair potential. The stationary profiles show relatively broad temperature maxima, for both the longitudinal and the average kinetic temperatures, just as does Mott-Smith{close_quote}s model for strong shock waves in dilute three-dimensional gases. {copyright} {ital 1997} {ital The American Physical Society}

Quantifying side-chain conformational variations in protein structure

PubMed Central

Miao, Zhichao; Cao, Yang

2016-01-01

Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs. PMID:27845406

Quantifying side-chain conformational variations in protein structure

NASA Astrophysics Data System (ADS)

Miao, Zhichao; Cao, Yang

2016-11-01

Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs.

Quantifying side-chain conformational variations in protein structure.

PubMed

Miao, Zhichao; Cao, Yang

2016-11-15

Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs.

gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances.

PubMed

Domazet-Lošo, Mirjana; Domazet-Lošo, Tomislav

2016-01-01

Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of complete prokaryotic genomes. As an alternative, alignment-free solutions are more efficient, but cannot map (align) a query to subject genomes. To address this problem, we have developed gmos (Genome MOsaic Structure), a new program that determines the mosaic structure of query genomes when compared to a set of closely related subject genomes. The program first computes local alignments between query and subject genomes and then reconstructs the query mosaic structure by choosing the best local alignment for each query region. To accomplish the analysis quickly, the program mostly relies on pairwise alignments and constructs multiple sequence alignments over short overlapping subject regions only when necessary. This fine-tuned implementation achieves an efficiency comparable to an alignment-free tool. The program performs well for simulated and real data sets of closely related genomes and can be used for fast recombination detection; for instance, when a new prokaryotic pathogen is discovered. As an example, gmos was used to detect genome mosaicism in a pathogenic Enterococcus faecium strain compared to seven closely related genomes. The analysis took less than two minutes on a single 2.1 GHz processor. The output is available in fasta format and can be visualized using an accessory program, gmosDraw (freely available with gmos).

gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances

PubMed Central

Domazet-Lošo, Mirjana; Domazet-Lošo, Tomislav

2016-01-01

Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of complete prokaryotic genomes. As an alternative, alignment-free solutions are more efficient, but cannot map (align) a query to subject genomes. To address this problem, we have developed gmos (Genome MOsaic Structure), a new program that determines the mosaic structure of query genomes when compared to a set of closely related subject genomes. The program first computes local alignments between query and subject genomes and then reconstructs the query mosaic structure by choosing the best local alignment for each query region. To accomplish the analysis quickly, the program mostly relies on pairwise alignments and constructs multiple sequence alignments over short overlapping subject regions only when necessary. This fine-tuned implementation achieves an efficiency comparable to an alignment-free tool. The program performs well for simulated and real data sets of closely related genomes and can be used for fast recombination detection; for instance, when a new prokaryotic pathogen is discovered. As an example, gmos was used to detect genome mosaicism in a pathogenic Enterococcus faecium strain compared to seven closely related genomes. The analysis took less than two minutes on a single 2.1 GHz processor. The output is available in fasta format and can be visualized using an accessory program, gmosDraw (freely available with gmos). PMID:27846272

Electronic Structure Contributions to Reactivity in Xanthine Oxidase Family Enzymes

PubMed Central

Stein, Benjamin W.; Kirk, Martin L.

2016-01-01

We review the xanthine oxidase (XO) family of pyranopterin molybdenum enzymes with a specific emphasis on electronic structure contributions to reactivity. In addition to xanthine and aldehyde oxidoreductases, which catalyze the 2-electron oxidation of aromatic heterocycles and aldehyde substrates, this mini-review highlights recent work on the closely related carbon monoxide dehydrogenase (CODH) that catalyzes the oxidation of CO using a unique Mo-Cu heterobimetallic active site. A primary focus of this mini-review relates to how spectroscopy and computational methods have been used to develop an understanding of critical relationships between geometric structure, electronic structure, and catalytic function. PMID:25425163

Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes

PubMed Central

Lorenzi, Hernan; Khan, Asis; Behnke, Michael S.; Namasivayam, Sivaranjani; Swapna, Lakshmipuram S.; Hadjithomas, Michalis; Karamycheva, Svetlana; Pinney, Deborah; Brunk, Brian P.; Ajioka, James W.; Ajzenberg, Daniel; Boothroyd, John C.; Boyle, Jon P.; Dardé, Marie L.; Diaz-Miranda, Maria A.; Dubey, Jitender P.; Fritz, Heather M.; Gennari, Solange M.; Gregory, Brian D.; Kim, Kami; Saeij, Jeroen P. J.; Su, Chunlei; White, Michael W.; Zhu, Xing-Quan; Howe, Daniel K.; Rosenthal, Benjamin M.; Grigg, Michael E.; Parkinson, John; Liu, Liang; Kissinger, Jessica C.; Roos, David S.; David Sibley, L

2016-01-01

Toxoplasma gondii is among the most prevalent parasites worldwide, infecting many wild and domestic animals and causing zoonotic infections in humans. T. gondii differs substantially in its broad distribution from closely related parasites that typically have narrow, specialized host ranges. To elucidate the genetic basis for these differences, we compared the genomes of 62 globally distributed T. gondii isolates to several closely related coccidian parasites. Our findings reveal that tandem amplification and diversification of secretory pathogenesis determinants is the primary feature that distinguishes the closely related genomes of these biologically diverse parasites. We further show that the unusual population structure of T. gondii is characterized by clade-specific inheritance of large conserved haploblocks that are significantly enriched in tandemly clustered secretory pathogenesis determinants. The shared inheritance of these conserved haploblocks, which show a different ancestry than the genome as a whole, may thus influence transmission, host range and pathogenicity. PMID:26738725

Comparative analysis of chloroplast genomes of the genus Citrus and its close relatives.

PubMed

Liu, Xiaogang; Wu, Hongkun; Luo, Yan; Xi, Wanpeng; Zhou, Zhiqin

2017-01-01

The genus Citrus and its close relatives are economically and nutritionally important fruit trees. However, the huge controversy over the phylogeny of key wild species, as well as the genetic relationship between the cultivated species and their putative wild progenitors, remains unresolved. Comparative analyses of chloroplast (cp) genomes have been useful in resolving various phylogenetic issues. Thus far, the cp genomes of only two Citrus species have been sequenced. In this study, we sequenced six complete cp genomes, four belonging to the genus Citrus, and two belonging to the genera Fortunella and Poncirus, respectively. These newly sequenced genomes together with the two publicly available were used for comparative analyses of the genus Citrus and its close relatives. All eight cp genomes share similar basic structure, gene order and gene content. Phylogenetic analyses supported the monophyly of the three genera in the order Sapindales within the major clade Malvidae.

Sibling death and death fear in relation to depressive symptomatology in older adults.

PubMed

Cicirelli, Victor G

2009-01-01

Previously overlooked factors in elders' depressive symptomatology were examined, including death fear, sibling death, and sibling closeness. Participants were 150 elders (61 men, 89 women) aged 65-97 years with at least one sibling. Measures were proportion of deceased siblings, sibling closeness, the Death Fear Subscale of the Death Attitude Profile-Revised, and the Center for Epidemiological Studies-Depression scale (20-item adult form). Age and education were exogenous variables in a structural equation model. Death fear, sibling closeness, and proportion of dead siblings were directly related to depression, with path coefficients of .42, -.24, and .13, respectively. Proportion of dead siblings had indirect effects on depression, as did age and education. Depressive symptomatology in old age is influenced by death fear related to sibling death as well as by poor relationships with them; it must be understood within a situational context including death fear and sibling relationships.

Comparing population structure as inferred from genealogical versus genetic information.

PubMed

Colonna, Vincenza; Nutile, Teresa; Ferrucci, Ronald R; Fardella, Giulio; Aversano, Mario; Barbujani, Guido; Ciullo, Marina

2009-12-01

Algorithms for inferring population structure from genetic data (ie, population assignment methods) have shown to effectively recognize genetic clusters in human populations. However, their performance in identifying groups of genealogically related individuals, especially in scanty-differentiated populations, has not been tested empirically thus far. For this study, we had access to both genealogical and genetic data from two closely related, isolated villages in southern Italy. We found that nearly all living individuals were included in a single pedigree, with multiple inbreeding loops. Despite F(st) between villages being a low 0.008, genetic clustering analysis identified two clusters roughly corresponding to the two villages. Average kinship between individuals (estimated from genealogies) increased at increasing values of group membership (estimated from the genetic data), showing that the observed genetic clusters represent individuals who are more closely related to each other than to random members of the population. Further, average kinship within clusters and F(st) between clusters increases with increasingly stringent membership threshold requirements. We conclude that a limited number of genetic markers is sufficient to detect structuring, and that the results of genetic analyses faithfully mirror the structuring inferred from detailed analyses of population genealogies, even when F(st) values are low, as in the case of the two villages. We then estimate the impact of observed levels of population structure on association studies using simulated data.

Comparing population structure as inferred from genealogical versus genetic information

PubMed Central

Colonna, Vincenza; Nutile, Teresa; Ferrucci, Ronald R; Fardella, Giulio; Aversano, Mario; Barbujani, Guido; Ciullo, Marina

2009-01-01

Algorithms for inferring population structure from genetic data (ie, population assignment methods) have shown to effectively recognize genetic clusters in human populations. However, their performance in identifying groups of genealogically related individuals, especially in scanty-differentiated populations, has not been tested empirically thus far. For this study, we had access to both genealogical and genetic data from two closely related, isolated villages in southern Italy. We found that nearly all living individuals were included in a single pedigree, with multiple inbreeding loops. Despite Fst between villages being a low 0.008, genetic clustering analysis identified two clusters roughly corresponding to the two villages. Average kinship between individuals (estimated from genealogies) increased at increasing values of group membership (estimated from the genetic data), showing that the observed genetic clusters represent individuals who are more closely related to each other than to random members of the population. Further, average kinship within clusters and Fst between clusters increases with increasingly stringent membership threshold requirements. We conclude that a limited number of genetic markers is sufficient to detect structuring, and that the results of genetic analyses faithfully mirror the structuring inferred from detailed analyses of population genealogies, even when Fst values are low, as in the case of the two villages. We then estimate the impact of observed levels of population structure on association studies using simulated data. PMID:19550436

Electronic shell structure in Ga12 icosahedra and the relation to the bulk forms of gallium.

PubMed

Schebarchov, D; Gaston, N

2012-07-28

The electronic structure of known cluster compounds with a cage-like icosahedral Ga(12) centre is studied by first-principles theoretical methods, based on density functional theory. We consider these hollow metalloid nanostructures in the context of the polymorphism of the bulk, and identify a close relation to the α phase of gallium. This previously unrecognised connection is established using the electron localisation function, which reveals the ubiquitous presence of radially-pointing covalent bonds around the Ga(12) centre--analogous to the covalent bonds between buckled deltahedral planes in α-Ga. Furthermore, we find prominent superatom shell structure in these clusters, despite their hollow icosahedral motif and the presence of covalent bonds. The exact nature of the electronic shell structure is contrasted with simple electron shell models based on jellium, and we demonstrate how the interplay between gallium dimerisation, ligand- and crystal-field effects can alter the splitting of the partially filled 1F shell. Finally, in the unique compound where the Ga(12) centre is bridged by six phosphorus ligands, the electronic structure most closely resembles that of δ-Ga and there are no well-defined superatom orbitals. The results of this comprehensive study bring new insights into the nature of chemical bonding in metalloid gallium compounds and the relation to bulk gallium metal, and they may also guide the development of more general models for ligand-protected clusters.

MRI-based stereolithographic models of the temporomandibular joint: technical innovation.

PubMed

Undt, G; Wild, K; Reuther, G; Ewers, R

2000-10-01

A new technique of manufacturing dual-colour stereolithographic models of hard and soft tissues of the temporomandibular joint (TMJ) is presented. Sagittal T1/PD weighted magnetic resonance (MR) images of joints with and without disc displacement were obtained in the closed and open mouth positions. Individual interactive contour identification of bony structures and the articular disc followed by binary interpolation provided the data for the generation of acrylic TMJ models. Three dimensional in vivo visualization of the articular disc in relation to bony structures in the closed and open mouth positions allows a new perception of normal and pathological TMJ anatomy.

[Maxillodental anomalies and consanguineous marriages].

PubMed

Garaev, Z I

1999-01-01

Families of 549 probands and families of 123 probands with cleft lip and/or palate were examined in order to evaluate the relationship between marriages between close relatives and the incidence and structure of maxillodental diseases. Clinical and genealogical analysis of families of probands with maxillodental abnormalities and cleft lip and/or palate showed a significantly higher incidence of marriages between close relatives and an inbreeding coefficient in these families. Analysis of the population and familial incidence of maxillodental abnormalities and the inbreeding coefficient will help the physicians consulting such families more accurately evaluate the risk and improve the efficacy of prevention of such conditions.

Carotenoids Database: structures, chemical fingerprints and distribution among organisms.

PubMed

Yabuzaki, Junko

2017-01-01

To promote understanding of how organisms are related via carotenoids, either evolutionarily or symbiotically, or in food chains through natural histories, we built the Carotenoids Database. This provides chemical information on 1117 natural carotenoids with 683 source organisms. For extracting organisms closely related through the biosynthesis of carotenoids, we offer a new similarity search system 'Search similar carotenoids' using our original chemical fingerprint 'Carotenoid DB Chemical Fingerprints'. These Carotenoid DB Chemical Fingerprints describe the chemical substructure and the modification details based upon International Union of Pure and Applied Chemistry (IUPAC) semi-systematic names of the carotenoids. The fingerprints also allow (i) easier prediction of six biological functions of carotenoids: provitamin A, membrane stabilizers, odorous substances, allelochemicals, antiproliferative activity and reverse MDR activity against cancer cells, (ii) easier classification of carotenoid structures, (iii) partial and exact structure searching and (iv) easier extraction of structural isomers and stereoisomers. We believe this to be the first attempt to establish fingerprints using the IUPAC semi-systematic names. For extracting close profiled organisms, we provide a new tool 'Search similar profiled organisms'. Our current statistics show some insights into natural history: carotenoids seem to have been spread largely by bacteria, as they produce C30, C40, C45 and C50 carotenoids, with the widest range of end groups, and they share a small portion of C40 carotenoids with eukaryotes. Archaea share an even smaller portion with eukaryotes. Eukaryotes then have evolved a considerable variety of C40 carotenoids. Considering carotenoids, eukaryotes seem more closely related to bacteria than to archaea aside from 16S rRNA lineage analysis. : http://carotenoiddb.jp. © The Author(s) 2017. Published by Oxford University Press.

Carotenoids Database: structures, chemical fingerprints and distribution among organisms

PubMed Central

2017-01-01

Abstract To promote understanding of how organisms are related via carotenoids, either evolutionarily or symbiotically, or in food chains through natural histories, we built the Carotenoids Database. This provides chemical information on 1117 natural carotenoids with 683 source organisms. For extracting organisms closely related through the biosynthesis of carotenoids, we offer a new similarity search system ‘Search similar carotenoids’ using our original chemical fingerprint ‘Carotenoid DB Chemical Fingerprints’. These Carotenoid DB Chemical Fingerprints describe the chemical substructure and the modification details based upon International Union of Pure and Applied Chemistry (IUPAC) semi-systematic names of the carotenoids. The fingerprints also allow (i) easier prediction of six biological functions of carotenoids: provitamin A, membrane stabilizers, odorous substances, allelochemicals, antiproliferative activity and reverse MDR activity against cancer cells, (ii) easier classification of carotenoid structures, (iii) partial and exact structure searching and (iv) easier extraction of structural isomers and stereoisomers. We believe this to be the first attempt to establish fingerprints using the IUPAC semi-systematic names. For extracting close profiled organisms, we provide a new tool ‘Search similar profiled organisms’. Our current statistics show some insights into natural history: carotenoids seem to have been spread largely by bacteria, as they produce C30, C40, C45 and C50 carotenoids, with the widest range of end groups, and they share a small portion of C40 carotenoids with eukaryotes. Archaea share an even smaller portion with eukaryotes. Eukaryotes then have evolved a considerable variety of C40 carotenoids. Considering carotenoids, eukaryotes seem more closely related to bacteria than to archaea aside from 16S rRNA lineage analysis. Database URL: http://carotenoiddb.jp PMID:28365725

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

Cang, Zixuan; Mu, Lin; Wu, Kedi

Here, protein function and dynamics are closely related to its sequence and structure. However, prediction of protein function and dynamics from its sequence and structure is still a fundamental challenge in molecular biology. Protein classification, which is typically done through measuring the similarity between proteins based on protein sequence or physical information, serves as a crucial step toward the understanding of protein function and dynamics.

Parenting and antisocial behavior: a model of the relationship between adolescent self-disclosure, parental closeness, parental control, and adolescent antisocial behavior.

PubMed

Vieno, Alessio; Nation, Maury; Pastore, Massimiliano; Santinello, Massimo

2009-11-01

This study used data collected from a sample of 840 Italian adolescents (418 boys; M age = 12.58) and their parents (657 mothers; M age = 43.78) to explore the relations between parenting, adolescent self-disclosure, and antisocial behavior. In the hypothesized model, parenting practices (e.g., parental monitoring and control) have direct effects on parental knowledge and antisocial behavior. Parenting style (e.g., parent-child closeness), on the other hand, is directly related to adolescent self-disclosure, which in turn is positively related to parental knowledge and negatively related to adolescents' antisocial behavior. A structural equation model, which incorporated data from parents and adolescents, largely supported the hypothesized model. Gender-specific models also found some gender differences among adolescents and parents, as the hypothesized model adequately fit the subsample of mothers but not fathers. Mothers' closeness to girls predicted their knowledge of their daughters' behavior; mothers' control predicted boys' antisocial behavior.

Crystal structure of hexagonal MnAl4

PubMed Central

Pauling, Linus

1987-01-01

A structure is proposed for the hexagonal form of MnAl4, with aH = 28.4 Å and cH = 12.43 Å, on the basis of a high-resolution electron micrograph and comparison with crystals of known structures. The proposed structure involves seven 104-atom complexes of 20 Friauf polyhedra, sharing some atoms with one another. It is closely related to the 23.36-Å cubic structure of MnAl4 and to the 14.19-Å cubic structure of Mg32(Al,Zn)49. Images PMID:16593837

Floral nectary, nectar production dynamics, and floral reproductive isolation among closely related species of Pedicularis.

PubMed

Liu, Ya-Nan; Li, Yan; Yang, Fu-Sheng; Wang, Xiao-Quan

2016-02-01

Floral nectar is thought to be one of the most important rewards that attract pollinators in Pedicularis; however, few studies have examined variation of nectary structure and/or nectar secretion in the genus, particularly among closely related species. Here we investigated nectary morphology, nectar quality, and nectar production dynamics in flowers of Pedicularis section Cyathophora. We found a conical floral nectary at the base of the ovary in species of the rex-thamnophila clade. Stomata were found on the surface of the nectary, and copious starch grains were detected in the nectary tissues. In contrast, a semi-annular nectary was found in flowers of the species of the superba clade. Only a few starch grains were observed in tissues of the semi-annular nectary, and the nectar sugar concentration in these flowers was much lower than that in the flowers of the rex-thamnophila clade. Our results indicate that the floral nectary has experienced considerable morphological, structural, and functional differentiation among closely related species of Pedicularis. This could have affected nectar production, leading to a shift of the pollination mode. Our results also imply that variation of the nectary morphology and nectar production may have played an important role in the speciation of sect. Cyathophora. © 2015 Institute of Botany, Chinese Academy of Sciences.

Uncertainty relations, zero point energy and the linear canonical group

NASA Technical Reports Server (NTRS)

Sudarshan, E. C. G.

1993-01-01

The close relationship between the zero point energy, the uncertainty relations, coherent states, squeezed states, and correlated states for one mode is investigated. This group-theoretic perspective enables the parametrization and identification of their multimode generalization. In particular the generalized Schroedinger-Robertson uncertainty relations are analyzed. An elementary method of determining the canonical structure of the generalized correlated states is presented.

Bud structure, position and fate generate various branching patterns along shoots of closely related Rosaceae species: a review

PubMed Central

Costes, Evelyne; Crespel, Laurent; Denoyes, Béatrice; Morel, Philippe; Demene, Marie-Noëlle; Lauri, Pierre-Eric; Wenden, Bénédicte

2014-01-01

Branching in temperate plants is closely linked to bud fates, either floral or vegetative. Here, we review how the fate of meristematic tissues contained in buds and their position along a shoot imprint specific branching patterns which differ among species. Through examples chosen in closely related species in different genera of the Rosaceae family, a panorama of patterns is apparent. Patterns depend on whether vegetative and floral buds are borne individually or together in mixed buds, develop as the shoot grows or after a rest period, and are located in axillary or terminal positions along the parent shoot. The resulting branching patterns are conserved among varieties in a given species but progressively change with the parent shoot length during plant ontogeny. They can also be modulated by agronomic and environmental conditions. The existence of various organizations in the topology and fate of meristematic tissues and their appendages in closely related species questions the between-species conservation of physiological and molecular mechanisms leading to bud outgrowth vs. quiescence and to floral induction vs. vegetative development. PMID:25520729

Automatic phylogenetic classification of bacterial beta-lactamase sequences including structural and antibiotic substrate preference information.

PubMed

Ma, Jianmin; Eisenhaber, Frank; Maurer-Stroh, Sebastian

2013-12-01

Beta lactams comprise the largest and still most effective group of antibiotics, but bacteria can gain resistance through different beta lactamases that can degrade these antibiotics. We developed a user friendly tree building web server that allows users to assign beta lactamase sequences to their respective molecular classes and subclasses. Further clinically relevant information includes if the gene is typically chromosomal or transferable through plasmids as well as listing the antibiotics which the most closely related reference sequences are known to target and cause resistance against. This web server can automatically build three phylogenetic trees: the first tree with closely related sequences from a Tachyon search against the NCBI nr database, the second tree with curated reference beta lactamase sequences, and the third tree built specifically from substrate binding pocket residues of the curated reference beta lactamase sequences. We show that the latter is better suited to recover antibiotic substrate assignments through nearest neighbor annotation transfer. The users can also choose to build a structural model for the query sequence and view the binding pocket residues of their query relative to other beta lactamases in the sequence alignment as well as in the 3D structure relative to bound antibiotics. This web server is freely available at http://blac.bii.a-star.edu.sg/.

Statistical Analysis of High-Cycle Fatigue Behavior of Friction Stir Welded AA5083-H321

DTIC Science & Technology

2011-01-01

durable structures are: (a) FSW is 111being used in a serial production of aluminum alloy -based 112ferryboat deck structures in Finland; (b) Al-Mg- Si -based...and strain-hardened/stabilized Al-Mg-Mn alloy ) are characterized by a relatively large statistical scatter. This scatter is closely related to the...associated with friction stir-welded (FSW) joints of AA5083-H321 (a solid-solution-strengthened and strain-hardened/stabilized Al-Mg-Mn alloy ) are

Analysis and application of a velocity command motor as a reaction mass actuator

NASA Technical Reports Server (NTRS)

Sulla, Jeffrey L.; Juang, Jer-Nan; Horta, Lucas G.

1990-01-01

A commercially available linear stepper motor is applied as a reaction mass (RM) actuator. With the actuator operating in the (RM) relative-velocity command mode, open-loop and closed-loop testing is performed to determine operational limits. With the actuator mounted on a simple beam structure, root strain, RM acceleration, or beam acceleration is used in the feedback loop to augment the structural damping. The RM relative position is also used as feedback to ensure that the RM remains centered.

Upstream gyrophase bunched ions - A mechanism for creation at the bow shock and the growth of velocity space structure through gyrophase mixing

NASA Technical Reports Server (NTRS)

Gurgiolo, C.; Parks, G. K.; Mauk, G. H.

1983-01-01

The conditions necessary for the production of gyrophase bunched ions at the bow shock are developed. The conditions are applied to the reflection mechanism presented by Paschmann et al. (1980), showing that when in their model a portion of the incident parallel velocity is converted into reflected perpendicular velocity, the reflected particles are gyrophase bunched. The growth of velocity space structure in the gyrophase bunched distribution through gyrophase mixing is also explored. The structure is found to be similar to that reported in diffuse and dispersed ion events. This together with the close correlation of the observation of gyrophase bunched ions with diffuse and dispersed ions has led us to speculate that these two populations may be closely related.

1,2-Diiodo-4,5-dimethyl­benzene

PubMed Central

Hathaway, Bruce A.; Kilgore, Uriah J.; Bond, Marcus R.

2009-01-01

The structure of the title compound, C8H8I2, conforms closely to the mm2 symmetry expected for the free mol­ecule and is the first reported structure of a diiodo­dimethyl­benzene. Repulsion by neighboring I atoms and the neighboring methyl groups opposite to them results in a slight elongation of the mol­ecule along the approximate twofold rotation axis that bis­ects the ring between the two I atoms. In the extended structure, the mol­ecules form inversion-related pairs which are organized in approximately hexa­gonal close-packed layers and the layers then stacked so that mol­ecules in neighboring layers abut head-to-tail in a manner that optimizes dipole–dipole inter­actions. PMID:21583089

Shear-modulated electroosmotic flow on a patterned charged surface.

PubMed

Wei, Hsien-Hung

2005-04-15

The effect of imposing shear flow on a charge-modulated electroosmotic flow is theoretically investigated. The flow structures exhibit either saddle points or closed streamlines, depending on the relative strength of an imposed shear to the applied electric field. The formation of closed streamlines could be advantageous for trapping nondiffusive particles at desired locations. Different time periodic alternating flows and their corresponding particle trajectories are also examined to assess strategies for creating efficient mixing.

The Relationship between "Theory of Mind" and Attachment-Related Anxiety and Avoidance in Italian Adolescents

ERIC Educational Resources Information Center

Hunefeldt, Thomas; Laghi, Fiorenzo; Ortu, Francesca; Belardinelli, Marta Olivetti

2013-01-01

This study examined the relationship between "theory of mind" and attachment-related anxiety and avoidance in adolescence. The "Reading the Mind in the Eyes" test and the "Experiences in Close Relationships--Relationship Structures" questionnaires were administered to 402 14-19 year-old adolescents. Contrary to…

ISEE 3 observations of low-energy proton bidirectional events and their relation to isolated interplanetary magnetic structures

NASA Technical Reports Server (NTRS)

Marsden, R. G.; Sanderson, T. R.; Tranquille, C.; Wenzel, K.-P.; Smith, E. J.

1987-01-01

The paper represents the results of a comprehensive survey of low-energy proton bidirectional anisotropies and associated transient magnetic structures as observed in the 35-1600 keV energy range on ISEE-3 during the last solar maximum. The majority of observed bidirectional flow (BDF) events (more than 70 percent) are associated with isolated magnetic structures which are postulated to be an interplanetary manifestation of coronal mass ejection (CME) events. The observed BDF events can be qualitatively grouped into five classes depending on the field signature of the related magnetic structure and the association (or lack of association) with an interplanetary shock. Concerning the topology of the CME-related magnetic structures, the observations are interpreted as being consistent with a detached bubble, comprising closed loops or tightly wound helices.

Structure and molecular mechanism of a nucleobase-cation-symport-1 family transporter.

PubMed

Weyand, Simone; Shimamura, Tatsuro; Yajima, Shunsuke; Suzuki, Shun'ichi; Mirza, Osman; Krusong, Kuakarun; Carpenter, Elisabeth P; Rutherford, Nicholas G; Hadden, Jonathan M; O'Reilly, John; Ma, Pikyee; Saidijam, Massoud; Patching, Simon G; Hope, Ryan J; Norbertczak, Halina T; Roach, Peter C J; Iwata, So; Henderson, Peter J F; Cameron, Alexander D

2008-10-31

The nucleobase-cation-symport-1 (NCS1) transporters are essential components of salvage pathways for nucleobases and related metabolites. Here, we report the 2.85-angstrom resolution structure of the NCS1 benzyl-hydantoin transporter, Mhp1, from Microbacterium liquefaciens. Mhp1 contains 12 transmembrane helices, 10 of which are arranged in two inverted repeats of five helices. The structures of the outward-facing open and substrate-bound occluded conformations were solved, showing how the outward-facing cavity closes upon binding of substrate. Comparisons with the leucine transporter LeuT(Aa) and the galactose transporter vSGLT reveal that the outward- and inward-facing cavities are symmetrically arranged on opposite sides of the membrane. The reciprocal opening and closing of these cavities is synchronized by the inverted repeat helices 3 and 8, providing the structural basis of the alternating access model for membrane transport.

The review on tessellation origami inspired folded structure

NASA Astrophysics Data System (ADS)

Chu, Chai Chen; Keong, Choong Kok

2017-10-01

Existence of folds enhances the load carrying capacity of a folded structure which makes it suitable to be used for application where large open space is required such as large span roof structures and façade. Folded structure is closely related to origami especially the tessellation origami. Tessellation origami provides a folded configuration with facetted surface as a result from repeated folding pattern. Besides that, tessellation origami has flexible folding mechanism that produced a variety of 3-dimensional folded configurations. Despite the direct relationship between fold in origami and folded structure, the idea of origami inspired folded structure is not properly reviewed in the relevant engineering field. Hence, this paper aims to present the current studies from related discipline which has direct relation with application of tessellation origami in folded structure. First, tessellation origami is properly introduced and defined. Then, the review covers the topic on the origami tessellation design suitable for folded structure, its modeling and simulation method, and existing studies and applications of origami as folded structure is presented. The paper also includes the discussion on the current issues related to each topic.

Unraveling the Origin of Structural Disorder in High Temperature Transition Al2O3: Structure of θ-Al2O3

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

Kovarik, Libor; Bowden, Mark E.; Shi, Dachuan

The crystallography of transition Al2O3 has been extensively studied in the past due to the advantageous properties of the oxide in catalytic and a range of other technological applications. However, existing crystallographic models are insufficient to describe the structure of many important Al2O3 polymorphs due to their highly disordered nature. In this work, we investigate structure and disorder in high-temperature treated transition Al2O3, and provide a structural description for θ-Al2O3 by using a suite of complementary imaging, spectroscopy and quantum calculation techniques. Contrary to current understanding, our high-resolution imaging shows that θ-Al2O3 is a disordered composite phase of at leastmore » two different end members. By correlating imaging and spectroscopy results with DFT calculations, we propose a model that describes θ-Al2O3 as a disordered intergrowth of two crystallographic variants at the unit cell level. One variant is based on β-Ga2O3, and the other on a monoclinic phase that is closely-related to δ-Al2O3. The overall findings and interpretations afford new insight into the origin of poor crystallinity in transition Al2O3, and also provide new perspectives on structural complexity that can emerge from intergrowth of closely related structural polymorphs.« less

Development of Specific Inhibitors for Breast Cancer-Associated Variants of ErbB2

DTIC Science & Technology

2015-10-01

Produce ErbB2 structures for drug-lead identification Months 1-12 Milestone #2: Production of computationally-derived pdb files of the structures of...crystallographic structures of the kinase domain of ErbB2 and its close relative EGFR (ErbB1). The kinase domains of ErbB2 and EGFR are highly...homologous as indicated by a sequence identity of ~ 78%. There are two currently available crystallographic structures of the ErbB2 kinase domain. One is

Experimental study on the flame behaviors of premixed methane/air mixture in horizontal rectangular ducts

NASA Astrophysics Data System (ADS)

Chen, Dongliang; Sun, Jinhua; Chen, Sining; Liu, Yi; Chu, Guanquan

2007-01-01

In order to explore the flame propagation characteristics and tulip flame formation mechanism of premixed methane/air mixture in horizontal rectangular ducts, the techniques of Schlieren and high-speed video camera are used to study the flame behaviors of the premixed gases in a closed duct and opened one respectively, and the propagation characteristics in both cases and the formation mechanism of the tulip flame are analyzed. The results show that, the propagation flame in a closed duct is prior to form a tulip flame structure than that in an opened duct, and the tulip flame structure formation in a closed duct is related to the flame propagation velocity decrease. The sharp decrease of the flame propagation velocity is one of the reasons to the tulip flame formation, and the decrease of the flame propagation velocity is due to the decrease of the burned product flow velocity mainly.

A new structure related to the layered cuprates: The {open_quotes}1201{angstrom} shear-like phase Tl{sub 5}Ba{sub 3}Sr{sub 5}Cu{sub 3}O{sub 19}, third member of the series (TlA{sub 2}CuO{sub 5}){sub m}{center_dot}Tl{sub 2}A{sub 2}O{sub 4}

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

Letouze, F.; Martin, C.; Hervieu, M.

1997-01-01

A thallium cuprate, Tl{sub 5}Ba{sub 3}Sr{sub 5}Cu{sub 3}O{sub 19}, whose structure can be derived by systematically shearing the {open_quotes}1201{close_quotes} structure has been synthesized for the first time. It crystallizes in an orthorhombic cell with a=3.7536(2) {angstrom}, b=30.631(2) {angstrom}, c=9.219(1) {angstrom}, and A-type symmetry. This new structure consists of {open_quotes}1201{close_quotes} ribbons parallel to (010) which are three CuO{sub 6} octahedra wide and are interconnected through {open_quotes}Tl{sub 2}A{sub 2}O{sub 4}{close_quotes} ribbons whose cationic configuration is that of the rock salt structure. This phase can be considered to be the m = 3 member of a new series with the generic formulation (TlA{submore » 2}CuO{sub 5}){sub m} {center_dot} Tl{sub 2}A{sub 2}O{sub 4} with A = Ba, Sr.« less

Insight into the transition between the open and closed conformations of Thermus thermophilus carboxypeptidase

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

Okai, Masahiko; Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477; Yamamura, Akihiro

Carboxypeptidase cleaves the C-terminal amino acid residue from proteins and peptides. Here, we report the functional and structural characterizations of carboxypeptidase belonging to the M32 family from the thermophilic bacterium Thermus thermophilus HB8 (TthCP). TthCP exhibits a relatively broad specificity for both hydrophilic (neutral and basic) and hydrophobic (aliphatic and aromatic) residues at the C-terminus and shows optimal activity in the temperature range of 75–80 °C and in the pH range of 6.8–7.2. Enzyme activity was significantly enhanced by cobalt or cadmium and was moderately inhibited by Tris at 25 °C. We also determined the crystal structure of TthCP at 2.6 Å resolution.more » Two dimer types of TthCP are present in the crystal. One type consists of two subunits in different states, open and closed, with a C{sup α} RMSD value of 2.2 Å; the other type consists of two subunits in the same open state. This structure enables us to compare the open and closed states of an M32 carboxypeptidase. The TthCP subunit can be divided into two domains, L and S, which are separated by a substrate-binding groove. The L and S domains in the open state are almost identical to those in the closed state, with C{sup α} RMSD values of 0.84 and 0.53 Å, respectively, suggesting that the transition between the open and closed states proceeds with a large hinge-bending motion. The superimposition between the closed states of TthCP and BsuCP, another M32 family member, revealed that most putative substrate-binding residues in the grooves are oriented in the same direction. - Highlights: • The enzyme activity of TthCP was inhibited moderately by Tris molecule. • We solved the crystal structure of TthCP at 2.6 Å resolution. • The crystal structure of TthCP revealed both the open and closed conformations.« less

Universals and Specifics of Math Self-Concept, Math Self-Efficacy, and Math Anxiety across 41 PISA 2003 Participating Countries

ERIC Educational Resources Information Center

Lee, Jihyun

2009-01-01

The overarching goal of the present study is to investigate the factorial structure of three closely related constructs: math self-concept, math self-efficacy, and math anxiety. The factorial structure consisting of three factors, each representing math self-concept, math self-efficacy, and math anxiety, is supported in all 41 countries employed…

A topological approach for protein classification

DOE PAGES

Cang, Zixuan; Mu, Lin; Wu, Kedi; ...

2015-11-04

Here, protein function and dynamics are closely related to its sequence and structure. However, prediction of protein function and dynamics from its sequence and structure is still a fundamental challenge in molecular biology. Protein classification, which is typically done through measuring the similarity between proteins based on protein sequence or physical information, serves as a crucial step toward the understanding of protein function and dynamics.

A Receptor on Acid.

PubMed

Chen, Qiuyan; Tesmer, John J G

2017-01-26

Wacker et al. report the crystal structure of LSD in complex with one of its major targets in the brain, the 5-HT 2B receptor, the first such structure for any psychedelic drug. The results shed light on the molecular mechanisms underlying its ability to induce hallucinations with greater duration and potency than closely related compounds. Copyright © 2017 Elsevier Inc. All rights reserved.

Chaperonin polymers in archaea: The cytoskeleton of prokaryotes?

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

Trent, J.D.; Kagawa, H.K.; Zaluzec, N.J.

Chaperonins are protein complexes that play a critical role in folding nascent polypeptides under normal conditions and refolding damaged proteins under stress conditions. In all organisms these complexes are composed of evolutionarily conserved 60-kDa proteins arranged in double-ring structures with between 7 and 9 protein subunits per ring. These double ring structures are assumed to be the functional units in vivo, although they have never been observed inside cells. Here the authors show that the purified chaperonin from the hyperthermophilic archaeon Sulfolobus shibatae, which is closely related to chaperonins in eukaryotes, has a double ring structure at low concentrations (0.1more » mg/ml), but at more physiological concentrations, the rings stack end to end to form polymers. The polymers are stable at physiological temperatures (75 C) and closely resemble structures observed inside unfixed S. shibatae cells. The authors suggest that in vivo chaperonin activity may be regulated by polymerization and that chaperonin polymers may act as a cytoskeleton-like structure in archaea and bacteria.« less

Chaperonin Polymers in Archaea: The Cytoskeleton of Prokaryotes?

DOE R&D Accomplishments Database

Trent, J. D.; Kagawa, H. K.; Zaluzec, N. J.

1997-07-01

Chaperonins are protein complexes that play a critical role in folding nascent polypeptides under normal conditions and refolding damaged proteins under stress conditions. In all organisms these complexes are composed of evolutionarily conserved 60-kDa proteins arranged in double-ring structures with between 7 and 9 protein subunits per ring. These double ring structures are assumed to be the functional units in vivo, although they have never been observed inside cells. Here the authors show that the purified chaperonin from the hyperthermophilic archaeon Sulfolobus shibatae, which is closely related to chaperonins in eukaryotes, has a double ring structure at low concentrations (0.1 mg/ml), but at more physiological concentrations, the rings stack end to end to form polymers. The polymers are stable at physiological temperatures (75 C) and closely resemble structures observed inside unfixed S. shibatae cells. The authors suggest that in vivo chaperonin activity may be regulated by polymerization and that chaperonin polymers may act as a cytoskeleton-like structure in archaea and bacteria.

Closing the research to practice gap in children's mental health: structures, solutions, and strategies.

PubMed

Jensen, Peter S; Foster, Michael

2010-03-01

Failure to apply research on effective interventions spans all areas of medicine, including children's mental health services. This article examines the policy, structural, and economic problems in which this gap originates. We identify four steps to close this gap. First, the field should develop scientific measures of the research-practice gap. Second, payors should link incentives to outcomes-based performance measures. Third, providers and others should develop improved understanding and application of effective dissemination and business models. Fourth, efforts to link EBP to clinical practice should span patient/consumers, providers, practices, plans, and purchasers. The paper discusses each of these in turn and relates them to fundamental problems of service delivery.

Structure of Boron Nitride Nanotubes: Tube Closing Vs. Chirality

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Menon, Madhu

1998-01-01

The structure of boron nitride nanotubes is investigated using a generalized tight-binding molecular dynamics method. It is shown that dynamic relaxation results in a wavelike or "rippled" surface in which the B atoms rotate inward and the N atoms move outward, reminiscent of the surface relaxation of the III-V semiconductors. More importantly, the three different morphologies of the tube closing with flat, conical and amorphous ends, as observed in experiments, are shown to be directly related to the tube chiralities. The abundance of flat end tubes observed in experiments is, thus, shown to be an indication of the greater stability of "zig-zag" BN tubes over the "arm-chair" tubes under experimental conditions.

Phylogenetic Structure of Tree Species across Different Life Stages from Seedlings to Canopy Trees in a Subtropical Evergreen Broad-Leaved Forest.

PubMed

Jin, Yi; Qian, Hong; Yu, Mingjian

2015-01-01

Investigating patterns of phylogenetic structure across different life stages of tree species in forests is crucial to understanding forest community assembly, and investigating forest gap influence on the phylogenetic structure of forest regeneration is necessary for understanding forest community assembly. Here, we examine the phylogenetic structure of tree species across life stages from seedlings to canopy trees, as well as forest gap influence on the phylogenetic structure of forest regeneration in a forest of the subtropical region in China. We investigate changes in phylogenetic relatedness (measured as NRI) of tree species from seedlings, saplings, treelets to canopy trees; we compare the phylogenetic turnover (measured as βNRI) between canopy trees and seedlings in forest understory with that between canopy trees and seedlings in forest gaps. We found that phylogenetic relatedness generally increases from seedlings through saplings and treelets up to canopy trees, and that phylogenetic relatedness does not differ between seedlings in forest understory and those in forest gaps, but phylogenetic turnover between canopy trees and seedlings in forest understory is lower than that between canopy trees and seedlings in forest gaps. We conclude that tree species tend to be more closely related from seedling to canopy layers, and that forest gaps alter the seedling phylogenetic turnover of the studied forest. It is likely that the increasing trend of phylogenetic clustering as tree stem size increases observed in this subtropical forest is primarily driven by abiotic filtering processes, which select a set of closely related evergreen broad-leaved tree species whose regeneration has adapted to the closed canopy environments of the subtropical forest developed under the regional monsoon climate.

Phylogenetic Structure of Tree Species across Different Life Stages from Seedlings to Canopy Trees in a Subtropical Evergreen Broad-Leaved Forest

PubMed Central

Jin, Yi; Qian, Hong; Yu, Mingjian

2015-01-01

Investigating patterns of phylogenetic structure across different life stages of tree species in forests is crucial to understanding forest community assembly, and investigating forest gap influence on the phylogenetic structure of forest regeneration is necessary for understanding forest community assembly. Here, we examine the phylogenetic structure of tree species across life stages from seedlings to canopy trees, as well as forest gap influence on the phylogenetic structure of forest regeneration in a forest of the subtropical region in China. We investigate changes in phylogenetic relatedness (measured as NRI) of tree species from seedlings, saplings, treelets to canopy trees; we compare the phylogenetic turnover (measured as βNRI) between canopy trees and seedlings in forest understory with that between canopy trees and seedlings in forest gaps. We found that phylogenetic relatedness generally increases from seedlings through saplings and treelets up to canopy trees, and that phylogenetic relatedness does not differ between seedlings in forest understory and those in forest gaps, but phylogenetic turnover between canopy trees and seedlings in forest understory is lower than that between canopy trees and seedlings in forest gaps. We conclude that tree species tend to be more closely related from seedling to canopy layers, and that forest gaps alter the seedling phylogenetic turnover of the studied forest. It is likely that the increasing trend of phylogenetic clustering as tree stem size increases observed in this subtropical forest is primarily driven by abiotic filtering processes, which select a set of closely related evergreen broad-leaved tree species whose regeneration has adapted to the closed canopy environments of the subtropical forest developed under the regional monsoon climate. PMID:26098916

The Dyad as a Centerless Structure: a Philosophical, Sociological and Psychoanalytic Study.

PubMed

Cohen, Tsiky

2018-06-04

This paper attempts to elucidate the phenomenological experience produced in the dyad from a structural perspective. It proposes to regard the dyadic configuration as a "centerless structure", containing the highest potential for actualization as "free play", both in a negative sense and a positive one. In the first part of the paper, the author uses Wittgenstein's "family- resemblances" method, to illustrate how the descriptions given to diverse dyadic relations in different domains and disciplines, share similarities and closeness with two main types of dyadic relations: a "synonymy relation" based on a common sense of similarity and likeness and an "antonymy relation" characterized by dominant and complementary relations. Although the two types of relations reflect through additional social forms, the author proposes that what is unique to the dyad structure is the repetitive movement that takes place, back and forth, between them. It indicates a lack of structural function that can organize, regulate and balance the intersubjective space. In the second part of the paper, inspired by Derrida and Simmel (Derrida, 1966; Simmel, 1950), the author suggests that the dyadic configuration struggles to produce a structured, stable center of meaning, and therefore it encourages the structure's free play potential.

Evolution in Action: N and C Termini of Subunits in Related T=4 Viruses Exchange Roles as Molecular Switches

PubMed Central

Speir, Jeffrey A.; Taylor, Derek J.; Natarajan, Padmaja; Pringle, Fiona M.; Ball, L. Andrew; Johnson, John E.

2010-01-01

Summary The T=4 tetravirus and T=3 nodavirus capsid proteins undergo closely similar autoproteolysis to produce the N-terminal ß and C-terminal, lipophilic γ polypeptides. The γ peptides and N-termini of ß also act as molecular switches that determine their quasi-equivalent capsid structures. The crystal structure of Providence virus (PrV), only the second of a tetravirus (the first was NωV), reveals conserved folds and cleavage sites, but the protein termini have completely different structures and the opposite functions of those in N⌉V. N-termini of ß form the molecular switch in PrV, while γ peptides have this role in N⌉V. PrV γ peptides instead interact with packaged RNA at the particle 2-folds using a repeating sequence pattern found in only four other RNA or membrane binding proteins. The disposition of peptide termini in PrV is closely related to those in nodaviruses suggesting that PrV may be closer to the primordial T=4 particle than NωV. PMID:20541507

A de novo redesign of the WW domain

PubMed Central

Kraemer-Pecore, Christina M.; Lecomte, Juliette T.J.; Desjarlais, John R.

2003-01-01

We have used a sequence prediction algorithm and a novel sampling method to design protein sequences for the WW domain, a small β-sheet motif. The procedure, referred to as SPANS, designs sequences to be compatible with an ensemble of closely related polypeptide backbones, mimicking the inherent flexibility of proteins. Two designed sequences (termed SPANS-WW1 and SPANS-WW2), using only naturally occurring l-amino acids, were selected for study and the corresponding polypeptides were prepared in Escherichia coli. Circular dichroism data suggested that both purified polypeptides adopted secondary structure features related to those of the target without the aid of disulfide bridges or bound cofactors. The structure exhibited by SPANS-WW2 melted cooperatively by raising the temperature of the solution. Further analysis of this polypeptide by proton nuclear magnetic resonance spectroscopy demonstrated that at 5°C, it folds into a structure closely resembling a natural WW domain. This achievement constitutes one of a small number of successful de novo protein designs through fully automated computational methods and highlights the feasibility of including backbone flexibility in the design strategy. PMID:14500877

A de novo redesign of the WW domain.

PubMed

Kraemer-Pecore, Christina M; Lecomte, Juliette T J; Desjarlais, John R

2003-10-01

We have used a sequence prediction algorithm and a novel sampling method to design protein sequences for the WW domain, a small beta-sheet motif. The procedure, referred to as SPANS, designs sequences to be compatible with an ensemble of closely related polypeptide backbones, mimicking the inherent flexibility of proteins. Two designed sequences (termed SPANS-WW1 and SPANS-WW2), using only naturally occurring L-amino acids, were selected for study and the corresponding polypeptides were prepared in Escherichia coli. Circular dichroism data suggested that both purified polypeptides adopted secondary structure features related to those of the target without the aid of disulfide bridges or bound cofactors. The structure exhibited by SPANS-WW2 melted cooperatively by raising the temperature of the solution. Further analysis of this polypeptide by proton nuclear magnetic resonance spectroscopy demonstrated that at 5 degrees C, it folds into a structure closely resembling a natural WW domain. This achievement constitutes one of a small number of successful de novo protein designs through fully automated computational methods and highlights the feasibility of including backbone flexibility in the design strategy.

Voltage-dependent conformational changes in connexin channels.

PubMed

Bargiello, Thaddeus A; Tang, Qingxiu; Oh, Seunghoon; Kwon, Taekyung

2012-08-01

Channels formed by connexins display two distinct types of voltage-dependent gating, termed V(j)- or fast-gating and loop- or slow-gating. Recent studies, using metal bridge formation and chemical cross-linking have identified a region within the channel pore that contributes to the formation of the loop-gate permeability barrier. The conformational changes are remarkably large, reducing the channel pore diameter from 15 to 20Å to less than 4Å. Surprisingly, the largest conformational change occurs in the most stable region of the channel pore, the 3(10) or parahelix formed by amino acids in the 42-51 segment. The data provide a set of positional constraints that can be used to model the structure of the loop-gate closed state. Less is known about the conformation of the V(j)-gate closed state. There appear to be two different mechanisms; one in which conformational changes in channel structure are linked to a voltage sensor contained in the N-terminus of Cx26 and Cx32 and a second in which the C-terminus of Cx43 and Cx40 may act either as a gating particle to block the channel pore or alternatively to stabilize the closed state. The later mechanism utilizes the same domains as implicated in effecting pH gating of Cx43 channels. It is unclear if the two V(j)-gating mechanisms are related or if they represent different gating mechanisms that operate separately in different subsets of connexin channels. A model of the V(j)-closed state of Cx26 hemichannel that is based on the X-ray structure of Cx26 and electron crystallographic structures of a Cx26 mutation suggests that the permeability barrier for V(j)-gating is formed exclusively by the N-terminus, but recent information suggests that this conformation may not represent a voltage-closed state. Closed state models are considered from a thermodynamic perspective based on information from the 3.5Å Cx26 crystal structure and molecular dynamics (MD) simulations. The applications of computational and experimental methods to define the path of allosteric molecular transitions that link the open and closed states are discussed. This article is part of a Special Issue entitled: The Communicating junctions, composition, structure and characteristics. Copyright © 2011 Elsevier B.V. All rights reserved.

High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans.

PubMed

Lipovich, Leonard; Hou, Zhuo-Cheng; Jia, Hui; Sinkler, Christopher; McGowen, Michael; Sterner, Kirstin N; Weckle, Amy; Sugalski, Amara B; Pipes, Lenore; Gatti, Domenico L; Mason, Christopher E; Sherwood, Chet C; Hof, Patrick R; Kuzawa, Christopher W; Grossman, Lawrence I; Goodman, Morris; Wildman, Derek E

2016-02-01

The human brain and human cognitive abilities are strikingly different from those of other great apes despite relatively modest genome sequence divergence. However, little is presently known about the interspecies divergence in gene structure and transcription that might contribute to these phenotypic differences. To date, most comparative studies of gene structure in the brain have examined humans, chimpanzees, and macaque monkeys. To add to this body of knowledge, we analyze here the brain transcriptome of the western lowland gorilla (Gorilla gorilla gorilla), an African great ape species that is phylogenetically closely related to humans, but with a brain that is approximately one-third the size. Manual transcriptome curation from a sample of the planum temporale region of the neocortex revealed 12 protein-coding genes and one noncoding-RNA gene with exons in the gorilla unmatched by public transcriptome data from the orthologous human loci. These interspecies gene structure differences accounted for a total of 134 amino acids in proteins found in the gorilla that were absent from protein products of the orthologous human genes. Proteins varying in structure between human and gorilla were involved in immunity and energy metabolism, suggesting their relevance to phenotypic differences. This gorilla neocortical transcriptome comprises an empirical, not homology- or prediction-driven, resource for orthologous gene comparisons between human and gorilla. These findings provide a unique repository of the sequences and structures of thousands of genes transcribed in the gorilla brain, pointing to candidate genes that may contribute to the traits distinguishing humans from other closely related great apes. © 2015 Wiley Periodicals, Inc.

The K-turn motif in riboswitches and other RNA species☆

PubMed Central

Lilley, David M.J.

2014-01-01

The kink turn is a widespread structure motif that introduces a tight bend into the axis of duplex RNA. This generally functions to mediate tertiary interactions, and to serve as a specific protein binding site. K-turns or closely related structures are found in at least seven different riboswitch structures, where they function as key architectural elements that help generate the ligand binding pocket. This article is part of a Special Issue entitled: Riboswitches. PMID:24798078

Principal component analysis of phenolic acid spectra

USDA-ARS?s Scientific Manuscript database

Phenolic acids are common plant metabolites that exhibit bioactive properties and have applications in functional food and animal feed formulations. The ultraviolet (UV) and infrared (IR) spectra of four closely related phenolic acid structures were evaluated by principal component analysis (PCA) to...

A Comparison of Four Estimators of a Population Measure of Model Fit in Covariance Structure Analysis

ERIC Educational Resources Information Center

Zhang, Wei

2008-01-01

A major issue in the utilization of covariance structure analysis is model fit evaluation. Recent years have witnessed increasing interest in various test statistics and so-called fit indexes, most of which are actually based on or closely related to F[subscript 0], a measure of model fit in the population. This study aims to provide a systematic…

Rub tolerant shroud

NASA Technical Reports Server (NTRS)

Lenahan, Dean T. (Inventor); Gay, Jr., Charles H. (Inventor)

1985-01-01

A seal structure between first and second relatively moveable members for preventing gas flow in the space between the members and transverse to their general direction of motion is disclosed. The seal structure includes a plurality of substantially parallel strips within 30.degree. of normal to the radial plane generally containing these first and second relatively moveable members. The strips are thin and closely spaced and arranged so that one strip edge is attached to the first member and another edge is free to resiliently deflect when in rubbing contact with the second member.

Differential effects of genetically distinct mechanisms of elevating amylose on barley starch characteristics.

PubMed

Regina, Ahmed; Blazek, Jaroslav; Gilbert, Elliot; Flanagan, Bernadine M; Gidley, Michael J; Cavanagh, Colin; Ral, Jean-Philippe; Larroque, Oscar; Bird, Anthony R; Li, Zhongyi; Morell, Matthew K

2012-07-01

The relationships between starch structure and functionality are important in underpinning the industrial and nutritional utilisation of starches. In this work, the relationships between the biosynthesis, structure, molecular organisation and functionality have been examined using a series of defined genotypes in barley with low (<20%), standard (20-30%), elevated (30-50%) and high (>50%) amylose starches. A range of techniques have been employed to determine starch physical features, higher order structure and functionality. The two genetic mechanisms for generating high amylose contents (down-regulation of branching enzymes and starch synthases, respectively) yielded starches with very different amylopectin structures but similar gelatinisation and viscosity properties driven by reduced granular order and increased amylose content. Principal components analysis (PCA) was used to elucidate the relationships between genotypes and starch molecular structure and functionality. Parameters associated with granule order (PC1) accounted for a large percentage of the variance (57%) and were closely related to amylose content. Parameters associated with amylopectin fine structure accounted for 18% of the variance but were less closely aligned to functionality parameters. Copyright © 2012 Elsevier Ltd. All rights reserved.

Neosordarin and hydroxysordarin, two new antifungal agents from Sordaria araneosa.

PubMed

Davoli, Paolo; Engel, Günther; Werle, Andreas; Sterner, Olov; Anke, Timm

2002-04-01

Two novel antifungal agents belonging to the sordarin family have been isolated from fermentations of Sordaria araneosa by bioassay-guided purification and their structures elucidated by NMR techniques. Neosordarin (1) is closely related to the recently discovered hypoxysordarin (2), with only small differences on the aliphatic side chain acylating the hydroxyl in the 3'-position of the sordarose moiety. Hydroxysordarin (3) closely resembles sordarin (4), the only slight difference being the replacement of sordarose with altrose as the sugar unit.

Compensating effect of sap velocity for stand density leads to uniform hillslope-scale forest transpiration across a steep valley cross-section

NASA Astrophysics Data System (ADS)

Renner, Maik; Hassler, Sibylle; Blume, Theresa; Weiler, Markus; Hildebrandt, Anke; Guderle, Marcus; Schymanski, Stan; Kleidon, Axel

2016-04-01

Roberts (1983) found that forest transpiration is relatively uniform across different climatic conditions and suggested that forest transpiration is a conservative process compensating for environmental heterogeneity. Here we test this hypothesis at a steep valley cross-section composed of European Beech in the Attert basin in Luxemburg. We use sapflow, soil moisture, biometric and meteorological data from 6 sites along a transect to estimate site scale transpiration rates. Despite opposing hillslope orientation, different slope angles and forest stand structures, we estimated relatively similar transpiration responses to atmospheric demand and seasonal transpiration totals. This similarity is related to a negative correlation between sap velocity and site-average sapwood area. At the south facing sites with an old, even-aged stand structure and closed canopy layer, we observe significantly lower sap velocities but similar stand-average transpiration rates compared to the north-facing sites with open canopy structure, tall dominant trees and dense understorey. This suggests that plant hydraulic co-ordination allows for flexible responses to environmental conditions leading to similar transpiration rates close to the water and energy limits despite the apparent heterogeneity in exposition, stand density and soil moisture. References Roberts, J. (1983). Forest transpiration: A conservative hydrological process? Journal of Hydrology 66, 133-141.

The serpentine optical waveguide: engineering the dispersion relations and the stopped light points.

PubMed

Scheuer, Jacob; Weiss, Ori

2011-06-06

We present a study a new type of optical slow-light structure comprising a serpentine shaped waveguide were the loops are coupled. The dispersion relation, group velocity and GVD are studied analytically using a transfer matrix method and numerically using finite difference time domain simulations. The structure exhibits zero group velocity points at the ends of the Brillouin zone, but also within the zone. The position of mid-zone zero group velocity point can be tuned by modifying the coupling coefficient between adjacent loops. Closed-form analytic expressions for the dispersion relations, group velocity and the mid-zone zero v(g) points are found and presented.

The structure of mushroom polysaccharides and their beneficial role in health.

PubMed

Huang, Xiaojun; Nie, Shaoping

2015-10-01

Mushroom is a kind of fungus that has been popular for its special flavour and renowned biological values. The polysaccharide contained in mushroom is regarded as one of the primary bioactive constituents and is beneficial for health. The structural features and bioactivities of mushroom polysaccharides have been studied extensively. It is believed that the diverse biological bioactivities of polysaccharides are closely related to their structure or conformation properties. In this review, the structural characteristics, conformational features and bioactivities of several mushroom polysaccharides are summarized, and their beneficial mechanisms and the relationships between their structure and bioactivities are also discussed.

Flexural fatigue life prediction of closed hat-section using materially nonlinear axial fatigue characteristics

NASA Technical Reports Server (NTRS)

Razzaq, Zia

1989-01-01

Straight or curved hat-section members are often used as structural stiffeners in aircraft. For instance, they are employed as stiffeners for the dorsal skin as well as in the aerial refueling adjacent area structure in F-106 aircraft. The flanges of the hat-section are connected to the aircraft skin. Thus, the portion of the skin closing the hat-section interacts with the section itself when resisting the stresses due to service loads. The flexural fatigue life of such a closed section is estimated using materially nonlinear axial fatigue characteristics. It should be recognized that when a structural shape is subjected to bending, the fatigue life at the neutral axis is infinity since the normal stresses are zero at that location. Conversely, the fatigue life at the extreme fibers where the normal bending stresses are maximum can be expected to be finite. Thus, different fatigue life estimates can be visualized at various distances from the neural axis. The problem becomes compounded further when significant portions away from the neutral axis are stressed into plastic range. A theoretical analysis of the closed hat-section subjected to flexural cyclic loading is first conducted. The axial fatigue characteristics together with the related axial fatigue life formula and its inverted form given by Manson and Muralidharan are adopted for an aluminum alloy used in aircraft construction. A closed-form expression for predicting the flexural fatigue life is then derived for the closed hat-section including materially nonlinear action. A computer program is written to conduct a study of the variables such as the thicknesses of the hat-section and the skin, and the type of alloy used. The study has provided a fundamental understanding of the flexural fatigue life characteristics of a practical structural component used in aircraft when materially nonlinear action is present.

Parents, Siblings, and Peers: Close Social Relationships and Adolescent Deviance.

ERIC Educational Resources Information Center

Ardelt, Monika; Day, Laurie

2002-01-01

Examined relations between parents, older siblings, peers, adolescents' individual characteristics, and adolescents' deviant attitudes and behaviors among inner-city families. Structural equation models showed that older deviant siblings had the strongest effect on adolescent deviance. Positive family relationships, parental support, and…

Bulimic symptoms and the social withdrawal syndrome.

PubMed

Rotenberg, Ken J; Bharathi, Carla; Davies, Helen; Finch, Tom

2013-08-01

One hundred and thirty-seven undergraduates (81 females; mean age = 21 years-10 months) completed the Bulimic SEDS subscale and standardized measures of trust beliefs in close others (mother, father, and friend), disclosure to them, and loneliness. Structural Equation Modelling yielded: (1) a negative path between Bulimic Symptoms and trust beliefs, (2) a positive path between trust beliefs and disclosure, (3) a negative path between trust beliefs and loneliness, and (4) a negative path between disclosure and loneliness. As expected, trust beliefs statistically mediated the relations between Bulimic Symptoms and both disclosure and loneliness and disclosure statistically mediated the relation between trust beliefs and loneliness. The findings supported the conclusion that individuals with bulimia nervosa are prone to the social withdrawal syndrome comprising a coherent and integrated pattern of low trust beliefs in close others, low disclosure to close others, and high loneliness. Copyright © 2013 Elsevier Ltd. All rights reserved.

The stabilities and electron structures of Al-Mg clusters with 18 and 20 valence electrons

NASA Astrophysics Data System (ADS)

Yang, Huihui; Chen, Hongshan

2017-07-01

The spherical jellium model predicts that metal clusters having 18 and 20 valence electrons correspond to the magic numbers and will show specific stabilities. We explore in detail the geometric structures, stabilities and electronic structures of Al-Mg clusters containing 18 and 20 valence electrons by using genetic algorithm combined with density functional theories. The stabilities of the clusters are governed by the electronic configurations and Mg/Al ratios. The clusters with lower Mg/Al ratios are more stable. The molecular orbitals accord with the shell structures predicted by the jellium model but the 2S level interweaves with the 1D levels and the 2S and 1D orbitals form a subgroup. The clusters having 20 valence electrons form closed 1S21P61D102S2 shells and show enhanced stability. The Al-Mg clusters with a valence electron count of 18 do not form closed shells because one 1D orbital is unoccupied. The ionization potential and electron affinity are closely related to the electronic configurations; their values are determined by the subgroups the HOMO or LUMO belong to. Supplementary material in the form of one pdf file available from the Journal web page at http://https://doi.org/10.1140/epjd/e2017-80042-9

The Ambient and Perturbed Solar Wind: From the Sun to 1 AU

NASA Technical Reports Server (NTRS)

Steinolfson, R. S.

1997-01-01

The overall objective of the proposed research was to use numerical solutions of the magnetohydrodynamic (MHD) equations along with comparisons of the computed results with observations to study the following topics: (1) ambient solar wind solutions that extend from the solar surface to 1 astronomical unit (AU), contain closed magnetic structures near the Sun, and are consistent with observed values; (2) magnetic and plasma structures in coronal mass ejections (CMES) as they propagate to the interplanetary medium; (3) relation of MHD shocks to CMEs in the interplanetary medium; (4) interaction of MHD shocks with structures (such as other shocks, corotating interaction regions, current sheets) in the interplanetary plasma; and (5) simulations of observed interplanetary structures. A planned close collaboration with data analysts served to make the model more relevant to the data. The outcome of this research program is an improved understanding of the physical processes occurring in solar-generated disturbances in the interplanetary medium between the Sun and 1 AU.

Energetics of subdomain movements and fluorescence probe solvation environment change in ATP-bound myosin.

PubMed

Harris, Michael J; Woo, Hyung-June

2008-11-01

Energetics of conformational changes experienced by an ATP-bound myosin head detached from actin was studied by all-atom explicit water umbrella sampling simulations. The statistics of coupling between large scale domain movements and smaller scale structural features were examined, including the closing of the ATP binding pocket, and a number of key hydrogen bond formations shown to play roles in structural and biochemical studies. The statistics for the ATP binding pocket open/close transition show an evolution of the relative stability from the open state in the early stages of the recovery stroke to the stable closed state after the stroke. The change in solvation environment of the fluorescence probe Trp507 (scallop numbering; 501 in Dictyostelium discoideum) indicates that the probe faithfully reflects the closing of the binding pocket as previously shown in experimental studies, while being directly coupled to roughly the early half of the overall large scale conformational change of the converter domain rotation. The free energy change of this solvation environment change, in particular, is -1.3 kcal/mol, in close agreement with experimental estimates. In addition, our results provide direct molecular level data allowing for interpretations of the fluorescence experiments of myosin conformational change in terms of the de-solvation of Trp side chain.

Calcium signaling in closely related protozoan groups (Alveolata): non-parasitic ciliates (Paramecium, Tetrahymena) vs. parasitic Apicomplexa (Plasmodium, Toxoplasma).

PubMed

Plattner, H; Sehring, I M; Mohamed, I K; Miranda, K; De Souza, W; Billington, R; Genazzani, A; Ladenburger, E-M

2012-05-01

The importance of Ca2+-signaling for many subcellular processes is well established in higher eukaryotes, whereas information about protozoa is restricted. Recent genome analyses have stimulated such work also with Alveolates, such as ciliates (Paramecium, Tetrahymena) and their pathogenic close relatives, the Apicomplexa (Plasmodium, Toxoplasma). Here we compare Ca2+ signaling in the two closely related groups. Acidic Ca2+ stores have been characterized in detail in Apicomplexa, but hardly in ciliates. Two-pore channels engaged in Ca2+-release from acidic stores in higher eukaryotes have not been stingently characterized in either group. Both groups are endowed with plasma membrane- and endoplasmic reticulum-type Ca2+-ATPases (PMCA, SERCA), respectively. Only recently was it possible to identify in Paramecium a number of homologs of ryanodine and inositol 1,3,4-trisphosphate receptors (RyR, IP3R) and to localize them to widely different organelles participating in vesicle trafficking. For Apicomplexa, physiological experiments suggest the presence of related channels although their identity remains elusive. In Paramecium, IP3Rs are constitutively active in the contractile vacuole complex; RyR-related channels in alveolar sacs are activated during exocytosis stimulation, whereas in the parasites the homologous structure (inner membrane complex) may no longer function as a Ca2+ store. Scrutinized comparison of the two closely related protozoan phyla may stimulate further work and elucidate adaptation to parasitic life. See also "Conclusions" section. Copyright © 2012 Elsevier Ltd. All rights reserved.

Sub-Planck structures and Quantum Metrology

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

Panigrahi, Prasanta K.; Kumar, Abhijeet; Roy, Utpal

The significance of sub-Planck structures in relation to quantum metrology is explored, in close contact with experimental setups. It is shown that an entangled cat state can enhance the accuracy of parameter estimations. The possibility of generating this state, in dissipative systems has also been demonstrated. Thereafter, the quantum Cramer-Rao bound for phase estimation through a pair coherent state is calculated, which achieves the maximum possible resolution in an interferometer.

The enigmatic genus Stenichnoteras scott from the seychelles (Coleoptera: Staphylinidae: Scydmaeninae).

PubMed

Jałoszyński, Paweł

2014-06-03

The genus Stenichnoteras, known from the Seychelles and represented by a single known species, St. montanum, is redescribed and redefined. The morphological structures of St. montanum are described and illustrated in detail. Similarities and possible affinities with other genera of Cyrtoscydmini are discussed, and it is concluded that Stenichnoteras may be closely related to Euconnus, despite an apparent difference in the shape of prothorax and some mesoventral structures.

The roles of host evolutionary relationships (genus: Nasonia) and development in structuring microbial communities.

PubMed

Brucker, Robert M; Bordenstein, Seth R

2012-02-01

The comparative structure of bacterial communities among closely related host species remains relatively unexplored. For instance, as speciation events progress from incipient to complete stages, does divergence in the composition of the species' microbial communities parallel the divergence of host nuclear genes? To address this question, we used the recently diverged species of the parasitoid wasp genus Nasonia to test whether the evolutionary relationships of their bacterial microbiotas recapitulate the Nasonia phylogenetic history. We also assessed microbial diversity in Nasonia at different stages of development to determine the role that host age plays in microbiota structure. The results indicate that all three species of Nasonia share simple larval microbiotas dominated by the γ-proteobacteria class; however, bacterial species diversity increases as Nasonia develop into pupae and adults. Finally, under identical environmental conditions, the relationships of the microbial communities reflect the phylogeny of the Nasonia host species at multiple developmental stages, which suggests that the structure of an animal's microbial community is closely allied with divergence of host genes. These findings highlight the importance of host evolutionary relationships on microbiota composition and have broad implications for future studies of microbial symbiosis and animal speciation. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Effects of TT8 and HB12 Silencing on the Relations between the Molecular Structures of Alfalfa ( Medicago sativa) Plants and Their Nutritional Profiles and In Vitro Gas Production.

PubMed

Lei, Yaogeng; Hannoufa, Abdelali; Prates, Luciana Louzada; Shi, Haitao; Wang, Yuxi; Biligetu, Bill; Christensen, David; Yu, Peiqiang

2018-06-06

The objective of this study was to investigate the effects of silencing the TT8 and HB12 genes on the nutritive profiles and in vitro gas production of alfalfa in relation to the spectral molecular structures of alfalfa. TT8-silenced (TT8i, n = 5) and HB12-silenced (HB12i, n = 11) alfalfa were generated by RNA interference (RNAi) and grown with nontransgenic wild type controls (WT, n = 4) in a greenhouse. Alfalfa plants were harvested at early-to-mid vegetative stage. Samples were analyzed for their chemical compositions, CNCPS fractions, and in vitro gas production. Correlations and regressions of the nutritional profiles and in vitro gas production with the molecular spectral structures were also determined. The results showed that the transformed alfalfa had higher digestible fiber and lower crude protein with higher proportions of indigestible protein than WT. HB12 RNAi had lower gas production compared with those of the others. Some chemical, CNCPS, and gas-production profiles were closely correlated with spectral structures and could be well predicted from spectral parameters. In conclusion, the RNAi silencing of TT8 and HB12 in alfalfa altered the chemical, CNCPS and gas-production profiles of alfalfa, and such alterations were closely correlated with the inherent spectral structures of alfalfa.

Structure of the USP15 N-terminal domains: a β-hairpin mediates close association between the DUSP and UBL domains.

PubMed

Harper, Stephen; Besong, Tabot M D; Emsley, Jonas; Scott, David J; Dreveny, Ingrid

2011-09-20

Ubiquitin specific protease 15 (USP15) functions in COP9 signalosome mediated regulation of protein degradation and cellular signaling through catalyzing the ubiquitin deconjugation reaction of a discrete number of substrates. It influences the stability of adenomatous polyposis coli, IκBα, caspase-3, and the human papillomavirus type 16 E6. USP15 forms a subfamily with USP4 and USP11 related through a shared presence of N-terminal "domain present in ubiquitin specific proteases" (DUSP) and "ubiquitin-like" (UBL) domains (DU subfamily). Here we report the 1.5 Å resolution crystal structure of the human USP15 N-terminal domains revealing a 80 Å elongated arrangement with the DU domains aligned in tandem. This architecture is generated through formation of a defined interface that is dominated by an intervening β-hairpin structure (DU finger) that engages in an intricate hydrogen-bonding network between the domains. The UBL domain is closely related to ubiquitin among β-grasp folds but is characterized by the presence of longer loop regions and different surface characteristics, indicating that this domain is unlikely to act as ubiquitin mimic. Comparison with the related murine USP4 DUSP-UBL crystal structure reveals that the main DU interdomain contacts are conserved. Analytical ultracentrifugation, small-angle X-ray scattering, and gel filtration experiments revealed that USP15 DU is monomeric in solution. Our data provide a framework to advance study of the structure and function of the DU subfamily. © 2011 American Chemical Society

Do common eiders nest in kin groups? Microgeographic genetic structure in a philopatric sea duck

USGS Publications Warehouse

Sonsthagen, S.A.; Talbot, S.L.; Lanctot, Richard B.; McCracken, K.G.

2010-01-01

We investigated local genetic associations among female Pacific common eiders (Somateria mollissima v-nigrum) nesting in a stochastic Arctic environment within two groups of barrier islands (Simpson Lagoon and Mikkelsen Bay) in the Beaufort Sea, Alaska. Nonrandom genetic associations were observed among nesting females using regional spatial autocorrelation analyses for distance classes up to 1000 m in Simpson Lagoon. Nearest-neighbour analyses identified clusters of genetically related females with positive lr values observed for 0-13% and 0-7% of the comparisons in Simpson Lagoon and Mikkelsen Bay, respectively, across years. These results indicate that a proportion of females are nesting in close proximity to more genetically related individuals, albeit at low frequency. Such kin groupings may form through active association between relatives or through natal philopatry and breeding site fidelity. Eiders nest in close association with driftwood, which is redistributed annually by seasonal storms. Yet, genetic associations were still observed. Microgeographic structure may thus be more attributable to kin association than natal philopatry and site fidelity. However, habitat availability may also influence the level of structure observed. Regional structure was present only within Simpson Lagoon and this island group includes at least three islands with sufficient driftwood for colonies, whereas only one island at Mikkelsen Bay has these features. A long-term demographic study is needed to understand more fully the mechanisms that lead to fine-scale genetic structure observed in common eiders breeding in the Beaufort Sea. ?? Published 2010. This article is a US Government work and is in the public domain in the USA.

Forest structure affects trophic linkages: How silvicultural disturbance impacts bats and their insect prey

USGS Publications Warehouse

Dodd, L.E.; Lacki, M.J.; Britzke, E.R.; Buehler, D.A.; Keyser, P.D.; Larkin, J.L.; Rodewald, A.D.; Wigley, T.B.; Wood, P.B.; Rieske, L.K.

2012-01-01

Vertebrate insectivores such as bats are a pervasive top-down force on prey populations in forest ecosystems. Conservation focusing on forest-dwelling bats requires understanding of community-level interactions between these predators and their insect prey. Our study assessed bat activity and insect occurrence (abundance and diversity) across a gradient of forest disturbance and structure (silvicultural treatments) in the Central Appalachian region of North America. We conducted acoustic surveys of bat echolocation concurrent with insect surveys using blacklight and malaise traps over 2 years. Predator activity, prey occurrence and prey biomass varied seasonally and across the region. The number of bat echolocation pulses was positively related with forest disturbance, whereas prey demonstrated varied trends. Lepidopteran abundance was negatively related with disturbance, while dipteran abundance and diversity was positively related with disturbance. Coleoptera were unaffected. Neither bat nor insect response variables differed between plot interiors and edges. Correlations between bat activity and vegetative structure reflected differences in foraging behavior among ensembles. Activity of myotine bats was correlated with variables describing sub-canopy vegetation, whereas activity of lasiurine bats was more closely correlated with canopy-level vegetation. Lepidopteran abundance was correlated with variables describing canopy and sub-canopy vegetation, whereas coleopteran and dipteran occurrence were more closely correlated with canopy-level vegetative structure. Our study demonstrates regional variation in bat activity and prey occurrence across a forested disturbance gradient. Land management and conservation efforts should consider the importance of vegetation structure and plant species richness to sustain forest-dwelling bats and their insect prey.

The Strategic Systems Therapies: Measuring the Models.

ERIC Educational Resources Information Center

Rohrbaugh, Michael

As family therapy becomes a serious intellectual disipline, the relationships among its leading variations require closer examination. To examine similarities and differences among four closely related approaches (brief, problem-focused therapy; structural family therapy; strategic family therapy; and systemic family therapy) and to determine if…

The solar probe and coronal dynamics

NASA Technical Reports Server (NTRS)

Belcher, J.; Heinemann, M.; Goodrich, C.

1978-01-01

The discovery of coronal holes led to basic changes in ideas about the structure of the low corona and its expansion into the solar wind. The nature of the energy flux is not understood. Current ideas include enhanced thermal conductivities, extended MHD wave heating, and wave momentum transfer, all in rapidly diverging geometries. There is little feel for the relative importance of these processes. The Solar Probe, with its penetration deep into the solar corona, could lead to observational constraints on their relative importance, and thus to an understanding of the origin of the solar wind. Observations from the Solar Probe will also bear on such questions as to whether small scale "intrastream" structure is common close to the Sun in open field-line regions, whether the properties of the wind are pronouncedly different over closed and open field-line regions at five solar radii, and many others. The resolution of these questions requires measurements of the magnetic field and of the proton and electron distribution functions.

Precise structural analysis of α-helical polypeptide by quantum-chemical calculation related to reciprocal side-chain combination of two L-phenylalanine residues

NASA Astrophysics Data System (ADS)

Niimura, Subaru; Kurosu, Hiromichi; Shoji, Akira

2010-04-01

To clarify the positive role of side-chain conformation in the stability of protein secondary structure (main-chain conformation), we successfully calculated the optimization structure of a series of well-defined α-helical octadecapeptides composed of two L-phenylalanine (Phe) and 16 L-alanine (Ala) residues, based on the molecular orbital calculation with density functional theory (DFT/B3LYP/6-31G(d)). From the total energy calculation and the precise secondary structural analysis, we found that the conformational stability of the α-helix is closely related to the reciprocal side-chain combinations (such as positional relation and side-chain conformation) of two Phe residues in this system. Furthermore, we demonstrated that the 1H, 13C, 15N and 17O isotropic chemical shifts of each Phe residue depend on the respective side-chain conformations of the Phe residue.

Application of Lidar remote sensing to the estimation of forest canopy and stand structure

NASA Astrophysics Data System (ADS)

Lefsky, Michael Andrew

A new remote sensing instrument, SLICER (Scanning Lidar Imager of Canopies by Echo Recovery), has been applied to the problem of remote sensing the canopy and stand structure of two groups of deciduous forests, Tulip Poplar-Oak stands in the vicinity of Annapolis, MD. and bottomland hardwood stands near Williamston, NC. The ability of the SLICER instrument to remotely sense the vertical distribution of canopy structure (Canopy Height Profile), bulk canopy transmittance, and several indices of canopy height has been successfully validated using twelve stands with coincident field and SLICER estimates of canopy structure. Principal components analysis has been applied to canopy height profiles from both field sites, and three significant factors were identified, each closely related to the amount of foliage in a recognizable layer of the forest, either understory, midstory, or overstory. The distribution of canopy structure to these layers is significantly correlated with the size and number of stems supporting them. The same layered structure was shown to apply to both field and SLICER remotely sensed canopy height profiles, and to apply to SLICER remotely sensed canopy profiles from both the bottomland hardwood stands in the coastal plain of North Carolina, and to mesic Tulip-Poplars stands in the upland coastal plain of Maryland. Linear regressions have demonstrated that canopy and stand structure are correlated to both a statistically significant and useful degree. Stand age and stem density is more highly correlated to stand height, while stand basal area and aboveground biomass are more closely related to a new measure of canopy structure, the quadratic mean canopy height. A geometric model of canopy structure has been shown to explain the differing relationships between canopy structure and stand basal area for stands of Eastern Deciduous Forest and Douglas Fir Forest.

Transformation of BCC and B2 High Temperature Phases to HCP and Orthorhombic Structures in the Ti-Al-Nb System. Part II: Experimental TEM Study of Microstructures

PubMed Central

Bendersky, L. A.; Boettinger, W. J.

1993-01-01

Possible transformation paths that involve no long range diffusion and their corresponding microstructural details were predicted by Bendersky, Roytburd, and Boettinger [J. Res. Natl. Inst. Stand. Technol. 98, 561 (1993)] for Ti-Al-Nb alloys cooled from the high temperature BCC/B2 phase field into close-packed orthorhombic or hexagonal phase fields. These predictions were based on structural and symmetry relations between the known phases. In the present paper experimental TEM results show that two of the predicted transformation paths are indeed followed for different alloy compositions. For Ti-25Al-12.5Nb (at%), the path includes the formation of intermediate hexagonal phases, A3 and DO19, and subsequent formation of a metastable domain structure of the low-temperature O phase. For alloys close to Ti-25Al-25Nb (at%), the path involves an intermediate B19 structure and subsequent formation of a translational domain structure of the O phase. The path selection depends on whether B2 order forms in the high temperature cubic phase prior to transformation to the close-packed structure. The paper also analyzes the formation of a two-phase modulated microstructure during long term annealing at 700 °C. The structure forms by congruent ordering of the DO19 phase to the O phase, and then reprecipitation of the DO19 phase, possibly by a spinodal mechanism. The thermodynamics underlying the path selection and the two-phase formation are also discussed. PMID:28053488

Changes in bacterioplankton community structure during early lake ontogeny resulting from the retreat of the Greenland Ice Sheet

PubMed Central

Peter, Hannes; Jeppesen, Erik; De Meester, Luc; Sommaruga, Ruben

2018-01-01

Retreating glaciers and ice sheets are among the clearest signs of global climate change. One consequence of glacier retreat is the formation of new meltwater-lakes in previously ice-covered terrain. These lakes provide unique opportunities to understand patterns in community organization during early lake ontogeny. Here, we analyzed the bacterial community structure and diversity in six lakes recently formed by the retreat of the Greenland Ice Sheet (GrIS). The lakes represented a turbidity gradient depending on their past and present connectivity to the GrIS meltwaters. Bulk (16S rRNA genes) and putatively active (16S rRNA) fractions of the bacterioplankton communities were structured by changes in environmental conditions associated to the turbidity gradient. Differences in community structure among lakes were attributed to both, rare and abundant community members. Further, positive co-occurrence relationships among phylogenetically closely related community members dominate in these lakes. Our results show that environmental conditions along the turbidity gradient structure bacterial community composition, which shifts during lake ontogeny. Rare taxa contribute to these shifts, suggesting that the rare biosphere has an important ecological role during early lakes ontogeny. Members of the rare biosphere may be adapted to the transient niches in these nutrient poor lakes. The directionality and phylogenetic structure of co-occurrence relationships indicate that competitive interactions among closely related taxa may be important in the most turbid lakes. PMID:29087379

Changes in bacterioplankton community structure during early lake ontogeny resulting from the retreat of the Greenland Ice Sheet.

PubMed

Peter, Hannes; Jeppesen, Erik; De Meester, Luc; Sommaruga, Ruben

2017-10-31

Retreating glaciers and ice sheets are among the clearest signs of global climate change. One consequence of glacier retreat is the formation of new meltwater-lakes in previously ice-covered terrain. These lakes provide unique opportunities to understand patterns in community organization during early lake ontogeny. Here, we analyzed the bacterial community structure and diversity in six lakes recently formed by the retreat of the Greenland Ice Sheet (GrIS). The lakes represented a turbidity gradient depending on their past and present connectivity to the GrIS meltwaters. Bulk (16S rRNA genes) and putatively active (16S rRNA) fractions of the bacterioplankton communities were structured by changes in environmental conditions associated to the turbidity gradient. Differences in community structure among lakes were attributed to both, rare and abundant community members. Further, positive co-occurrence relationships among phylogenetically closely related community members dominate in these lakes. Our results show that environmental conditions along the turbidity gradient structure bacterial community composition, which shifts during lake ontogeny. Rare taxa contribute to these shifts, suggesting that the rare biosphere has an important ecological role during early lakes ontogeny. Members of the rare biosphere may be adapted to the transient niches in these nutrient poor lakes. The directionality and phylogenetic structure of co-occurrence relationships indicate that competitive interactions among closely related taxa may be important in the most turbid lakes.The ISME Journal advance online publication, 31 October 2017; doi:10.1038/ismej.2017.191.

Bayesian Multiscale Modeling of Closed Curves in Point Clouds

PubMed Central

Gu, Kelvin; Pati, Debdeep; Dunson, David B.

2014-01-01

Modeling object boundaries based on image or point cloud data is frequently necessary in medical and scientific applications ranging from detecting tumor contours for targeted radiation therapy, to the classification of organisms based on their structural information. In low-contrast images or sparse and noisy point clouds, there is often insufficient data to recover local segments of the boundary in isolation. Thus, it becomes critical to model the entire boundary in the form of a closed curve. To achieve this, we develop a Bayesian hierarchical model that expresses highly diverse 2D objects in the form of closed curves. The model is based on a novel multiscale deformation process. By relating multiple objects through a hierarchical formulation, we can successfully recover missing boundaries by borrowing structural information from similar objects at the appropriate scale. Furthermore, the model’s latent parameters help interpret the population, indicating dimensions of significant structural variability and also specifying a ‘central curve’ that summarizes the collection. Theoretical properties of our prior are studied in specific cases and efficient Markov chain Monte Carlo methods are developed, evaluated through simulation examples and applied to panorex teeth images for modeling teeth contours and also to a brain tumor contour detection problem. PMID:25544786

Hierarchical Safety Cases

NASA Technical Reports Server (NTRS)

Denney, Ewen W.; Whiteside, Iain J.

2012-01-01

We introduce hierarchical safety cases (or hicases) as a technique to overcome some of the difficulties that arise creating and maintaining industrial-size safety cases. Our approach extends the existing Goal Structuring Notation with abstraction structures, which allow the safety case to be viewed at different levels of detail. We motivate hicases and give a mathematical account of them as well as an intuition, relating them to other related concepts. We give a second definition which corresponds closely to our implementation of hicases in the AdvoCATE Assurance Case Editor and prove the correspondence between the two. Finally, we suggest areas of future enhancement, both theoretically and practically.

A comparative study of the inner ear structures of artiodactyls and early cetaceans

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

Klingshirn, M.A.; Luo, Z.

1994-12-31

It has been suggested that the order Cetacea (whales and porpoises) are closely related to artiodactyls, even-hoofed ungulate mammals such as the pig and cow. Paleontological and molecular data strongly supports this concept of phylogenetic relationships. In a study of DNA sequences of two mitochondrial ribosomal gene segments of cetaceans, the artiodactyls were found to be closest related to Cetaceans. These well accepted studies on the phylogenetic affinities of artiodactyls and cetaceans cause us to conduct a comparative study of the bony structure of the inner ear of these two taxa.

Relational-interdependent self-construal as a predictor of relationship quality: the mediating roles of one's own behaviors and perceptions of the fulfillment of friendship functions.

PubMed

Morry, Marian M; Kito, Mie

2009-06-01

Relational-interdependent self-construal (RISC) is the tendency to think of oneself in terms of relationships with close others, and it influences relationship cognitions (e.g., closeness, commitment, perceived similarity). The authors expected individuals high in RISC to report more relationship supportive behaviors (RSB; e.g., higher levels of trust, more intimate disclosures), experience greater fulfillment of friendship functions (FrFu; e.g., help, emotional security, stimulating companionship), and report higher relationship quality than individuals low in RISC. The authors also hypothesized that RSB would mediate the RISC-friendship function and the RISC-relationship quality relations and that FrFu would mediate the relation between RSB and relationship quality. Structural equation modeling supported the authors' hypotheses. These effects did not differ across friendship type (same or cross sex). The authors discuss the importance of self-construal for relationship research.

The Sla2p/HIP1/HIP1R family: similar structure, similar function in endocytosis?

PubMed

Gottfried, Irit; Ehrlich, Marcelo; Ashery, Uri

2010-02-01

HIP1 (huntingtin interacting protein 1) has two close relatives: HIP1R (HIP1-related) and yeast Sla2p. All three members of the family have a conserved domain structure, suggesting a common function. Over the past decade, a number of studies have characterized these proteins using a combination of biochemical, imaging, structural and genetic techniques. These studies provide valuable information on binding partners, structure and dynamics of HIP1/HIP1R/Sla2p. In general, all suggest a role in CME (clathrin-mediated endocytosis) for the three proteins, though some differences have emerged. In this mini-review we summarize the current views on the roles of these proteins, while emphasizing the unique attributes of each family member.

Multimedia Information Networks in Social Media

NASA Astrophysics Data System (ADS)

Cao, Liangliang; Qi, Guojun; Tsai, Shen-Fu; Tsai, Min-Hsuan; Pozo, Andrey Del; Huang, Thomas S.; Zhang, Xuemei; Lim, Suk Hwan

The popularity of personal digital cameras and online photo/video sharing community has lead to an explosion of multimedia information. Unlike traditional multimedia data, many new multimedia datasets are organized in a structural way, incorporating rich information such as semantic ontology, social interaction, community media, geographical maps, in addition to the multimedia contents by themselves. Studies of such structured multimedia data have resulted in a new research area, which is referred to as Multimedia Information Networks. Multimedia information networks are closely related to social networks, but especially focus on understanding the topics and semantics of the multimedia files in the context of network structure. This chapter reviews different categories of recent systems related to multimedia information networks, summarizes the popular inference methods used in recent works, and discusses the applications related to multimedia information networks. We also discuss a wide range of topics including public datasets, related industrial systems, and potential future research directions in this field.

Trends of Educational Policy in Socialist Countries.

ERIC Educational Resources Information Center

Kluczynski, J.

Education in Eastern Europe's socialist countries is closely related to national development, emphasizes this report on the structure and goals of education in seven nations and two Soviet federated states. The author discusses the relationship of educational development to technical and organizational progress, changes in socioeconomic and…

[Phylogenetic analysis of human/swine/avian gene reassortant H1N2 influenza A virus isolated from a pig in China].

PubMed

Chen, Yixiang; Meng, Xueqiong; Liu, Qi; Huang, Xia; Huang, Shengbin; Liu, Cuiquan; Shi, Kaichuang; Guo, Jiangang; Chen, Fangfang; Hu, Liping

2008-04-01

Our aim in this study was to determine the genetic characterization and probable origin of the H1N2 swine influenza virus (A/Swine/Guangxi/13/2006) (Sw/GX/13/06) from lung tissue of a pig in Guangxi province, China. Eight genes of Sw/GX/13/06 were cloned and genetically analyzed. The hemagglutinin (HA), nucleoprotein (NP), matrix (M) and non-structural (NS) genes of Sw/GX/13/06 were most closely related to genes from the classical swine H1N1 influenza virus lineage. The neuraminidase (NA) and PB1 genes were most closely related to the corresponding genes from the human influenza H3N2 virus lineage. The remaining two genes PA and PB2 polymerase genes were most closely related to the genes from avian influenza virus lineage. Phylogenetic analyses revealed that Sw/GX/13/06 was a human/swine/avian H1N2 virus, and closely related to H1N2 viruses isolated from pigs in United States (1999-2001) and Korea (2002). To our knowledge, Sw/GX/13/06 was the first triple-reassortant H1N2 influenza A virus isolated from a pig in China. Whether the Sw/GX/13/06 has a potential threat to breeding farm and human health remains to be further investigated.

Light Use Efficiency and Photochemical Reflectance Index: do we have a common basis defining them? Implications for productivity estimation (Invited)

NASA Astrophysics Data System (ADS)

Gitelson, A. A.; Gamon, J. A.

2013-12-01

There are at least three commonly used definitions of photosynthetic Light Use Efficiency (LUE) based on: (a) incident radiation (LUEinc); (b) total absorbed light (LUEtotal); and (c) radiation absorbed by photosynthetically active vegetation (LUEps). Consequently, LUE values reported do not have a common basis, bringing confusion and limiting the utility of reported LUE values for comparative analyses. Not surprisingly, the value of LUE reported in literature varies by a factor of three. Similarly, the Photochemical Reflectance Index (PRI) has different operational definitions, resulting in a wide range of reported values for comparable conditions. The objectives of this paper are to investigate (a) temporal behavior of each definition of LUE; and (b) factors affecting PRI, often used as a surrogate of LUE at leaf and canopy levels. We focused on annual and winter-deciduous vegetation where total chlorophyll content is closely tied to the seasonal dynamics of GPP. In these conditions, LUEinc is closely related to total plant chlorophyll (Chl) content. LUEtotal oscillates around a constant value during the vegetative stage, depending mainly on plant physiological status, PAR composition and magnitude, while in reproductive and senescence stages it relates closely to Chl content. LUEps may vary 2- to 3-fold during the growing season with no clear seasonal pattern, and does not seem to be related to any biophysical characteristic studied; rather, it depends on the physiological status of vegetation, PAR composition and magnitude as well as air temperature and soil moisture. At the leaf level, PRI depends greatly on pigment content and composition and relates closely to the ratio of Chl to carotenoid content. At the canopy and stand levels, both total plant Chl content and green LAI are responsible for more than 95% of PRI variation, demonstrating that PRI is confounded by pigment pool sizes and canopy structure in these conditions. Importantly, the close relationship between PRI, Chl, and green LAI varies with canopy growth stage. PRI relates to LUEinc over the whole growing season and to LUEtotal in reproductive and senescence stages. For estimating seasonal vegetation productivity, we recommend the establishment of standard LUE definitions and PRI applications that explicitly consider canopy structure and pigmentation. In cases where total chlorophyll content is closely tied to the seasonal dynamics of GPP, before using PRI as a proxy of LUEps one needs to accurately subtract the effect of Chl and LAI.

Closely related, yet unique: Distinct homo- and heterodimerization patterns of G protein coupled chemokine receptors and their fine-tuning by cholesterol

PubMed Central

Gahbauer, Stefan; Pluhackova, Kristyna

2018-01-01

Chemokine receptors, a subclass of G protein coupled receptors (GPCRs), play essential roles in the human immune system, they are involved in cancer metastasis as well as in HIV-infection. A plethora of studies show that homo- and heterodimers or even higher order oligomers of the chemokine receptors CXCR4, CCR5, and CCR2 modulate receptor function. In addition, membrane cholesterol affects chemokine receptor activity. However, structural information about homo- and heterodimers formed by chemokine receptors and their interplay with cholesterol is limited. Here, we report homo- and heterodimer configurations of the chemokine receptors CXCR4, CCR5, and CCR2 at atomistic detail, as obtained from thousands of molecular dynamics simulations. The observed homodimerization patterns were similar for the closely related CC chemokine receptors, yet they differed significantly between the CC receptors and CXCR4. Despite their high sequence identity, cholesterol modulated the CC homodimer interfaces in a subtype-specific manner. Chemokine receptor heterodimers display distinct dimerization patterns for CXCR4/CCR5 and CXCR4/CCR2. Furthermore, associations between CXCR4 and CCR5 reveal an increased cholesterol-sensitivity as compared to CXCR4/CCR2 heterodimerization patterns. This work provides a first comprehensive structural overview over the complex interaction network between chemokine receptors and indicates how heterodimerization and the interaction with the membrane environment diversifies the function of closely related GPCRs. PMID:29529028

Staging in polyacetylene-iodine conductors

NASA Astrophysics Data System (ADS)

Baughman, R. H.; Murthy, N. S.; Miller, G. G.; Shacklette, L. W.

1983-07-01

Evidence is presented for the existence of highly conducting polyacetylene complexes with structures related to high-stage graphite, as well as structures related to first-stage graphite. X-ray diffraction measurements on polyacetylene-iodine complexes indicate equatorial lines at 7.7-8.0 and 13.8-14.3 Å. The shorter spacing arises in part from a structure in which iodine-rich planes alternate with planes of polyacetylene chains. The longer spacing, which disappears upon atmospheric exposure, is consistent with a structure analogous to third-stage graphite in which dopant-rich planes are separated by three close-packed planes of polyacetylene chains. The third-stage complex can be viewed as a perturbation of the structure of undoped polyacetylene, with the region between dopant layers consisting essentially of a one unit cell thickness of the parent polymer structure. Packing calculations for this model, in which a linear column of anions (I3- and/or I5-) displaces either every chain or every other chain in the dopant-rich layer, provide an interlayer spacing which is equal to that observed. Evidence consistent with third-stage structures (with both fractional occupation and complete occupation of the dopant plane) is also found by reexamination of published sorption data, which provides slope changes at close to the calculated limiting compositions for these structures [(CHI0.056)x and (CHI0.13)x]. However, a first-stage structure with alternating dopant arrays and polymer chains in the dopant plane [for which (CHI0.13)x is calculated] provides a better explanation for the second slope change, as well as for the composition obtained under dynamic vacuum, (CHI0.14)x. These results for iodine complexes are compared with those derived for the group VA halide complexes of polyacetylene.

Inverse spin Hall effect in a closed loop circuit

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

Omori, Y.; Auvray, F.; Wakamura, T.

We present measurements of inverse spin Hall effects (ISHEs), in which the conversion of a spin current into a charge current via the ISHE is detected not as a voltage in a standard open circuit but directly as the charge current generated in a closed loop. The method is applied to the ISHEs of Bi-doped Cu and Pt. The derived expression of ISHE for the loop structure can relate the charge current flowing into the loop to the spin Hall angle of the SHE material and the resistance of the loop.

Crustal subsidence, seismicity, and structure near Medicine Lake Volcano, California

USGS Publications Warehouse

Dzurisin, D.; Donnelly-Nolan, J. M.; Evans, J.R.; Walter, S.R.

1991-01-01

The pattern of historical ground deformation, seismicity, and crustal structure near Medicine Lake volcano illustrates a close relation between magmatism and tectonism near the margin of the Cascade volcanic chain and the Basin and Range tectonic province. Subsidence occurs mainly by aseismic creep within 25km of the summit, where the crust has been heated and weakened by intrusions, and by normal faulting during episodic earthquake swarms in surrounding, cooler terrain. -from Authors

A 45-ns molecular dynamics simulation of hemoglobin in water by vectorizing and parallelizing COSMOS90 on the earth simulator: dynamics of tertiary and quaternary structures.

PubMed

Saito, Minoru; Okazaki, Isao

2007-04-30

Molecular dynamics (MD) simulations of human adult hemoglobin (HbA) were carried out for 45 ns in water with all degrees of freedom including bond stretching and without any artificial constraints. To perform such large-scale simulations, one of the authors (M.S.) accelerated his own software COSMOS90 on the Earth Simulator by vectorization and parallelization. The dynamical features of HbA were investigated by evaluating root-mean-square deviations from the initial X-ray structure (an oxy T-state hemoglobin with PDB code: 1GZX) and root-mean-square fluctuations around the average structure from the simulation trajectories. The four subunits (alpha(1), alpha(2), beta(1), and beta(2)) of HbA maintained structures close to their respective X-ray structures during the simulations even though no constraints were applied to HbA in the simulations. Dimers alpha(1)beta(1) and alpha(2)beta(2) also maintained structures close to their respective X-ray structures while they moved relative to each other like two stacks of dumbbells. The distance between the two dimers (alpha(1)beta(1) and alpha(2)beta(2)) increased by 2 A (7.4%) in the initial 15 ns and stably fluctuated at the distance with the standard deviation 0.2 A. The relative orientation of the two dimers fluctuated between the initial X-ray angle -100 degrees and about -105 degrees with intervals of a few tens of nanoseconds.

FAST TRACK COMMUNICATION: \\ {P}\\ {T}-symmetry, Cartan decompositions, Lie triple systems and Krein space-related Clifford algebras

NASA Astrophysics Data System (ADS)

Günther, Uwe; Kuzhel, Sergii

2010-10-01

Gauged \\ {P}\\ {T} quantum mechanics (PTQM) and corresponding Krein space setups are studied. For models with constant non-Abelian gauge potentials and extended parity inversions compact and noncompact Lie group components are analyzed via Cartan decompositions. A Lie-triple structure is found and an interpretation as \\ {P}\\ {T}-symmetrically generalized Jaynes-Cummings model is possible with close relation to recently studied cavity QED setups with transmon states in multilevel artificial atoms. For models with Abelian gauge potentials a hidden Clifford algebra structure is found and used to obtain the fundamental symmetry of Krein space-related J-self-adjoint extensions for PTQM setups with ultra-localized potentials.

An unusually strong Einstein ring in the radio source PKS1830 - 211

NASA Technical Reports Server (NTRS)

Jauncey, D. L.; Reynolds, J. E.; Tzioumis, A. K.; Murphy, D. W.; Preston, R. A.; Jones, D. L.; Meier, D. L.; Hoard, D. W.; Lobdell, E. T.; Skjerve, L.

1991-01-01

High-resolution radio images of PKS1830 - 211 are obtained to study the possibility that the double structure is a gravitationally lensed object. The VLBI observations, taken from interferometric radiotelescope networks, reveal an elliptical ring that connects two bright spots of similar composition. Because the lens and the lensed object are closely aligned, and because of the structure of the two spots, the source is concluded to be a radio Einstein ring. The source is found to be close to the galactic plane, and the lens and the lensed object are extragalactic. The source is also found to be unusually bright, suggesting that it is aligned with a bright background source or amplified by some mechanism related to a source that is not so bright.

Structures of Staphylococcus aureus D-tagatose-6-phosphate kinase implicate domain motions in specificity and mechanism.

PubMed

Miallau, Linda; Hunter, William N; McSweeney, Sean M; Leonard, Gordon A

2007-07-06

High resolution structures of Staphylococcus aureus d-tagatose-6-phosphate kinase (LacC) in two crystal forms are herein reported. The structures define LacC in apoform, in binary complexes with ADP or the co-factor analogue AMP-PNP, and in a ternary complex with AMP-PNP and D-tagatose-6-phosphate. The tertiary structure of the LacC monomer, which is closely related to other members of the pfkB subfamily of carbohydrate kinases, is composed of a large alpha/beta core domain and a smaller, largely beta "lid." Four extended polypeptide segments connect these two domains. Dimerization of LacC occurs via interactions between lid domains, which come together to form a beta-clasp structure. Residues from both subunits contribute to substrate binding. LacC adopts a closed structure required for phosphoryl transfer only when both substrate and co-factor are bound. A reaction mechanism similar to that used by other phosphoryl transferases is proposed, although unusually, when both substrate and co-factor are bound to the enzyme two Mg(2+) ions are observed in the active site. A new motif of amino acid sequence conservation common to the pfkB subfamily of carbohydrate kinases is identified.

Maturation of the Concept of Death in Elementary School Children.

ERIC Educational Resources Information Center

Townley, Kim; Thornburg, Kathy R.

1980-01-01

A structured interview was used to ascertain the level of understanding of the concept of death in 52 elementary school children. Data analysis showed sex, religious affilation, and the death of a close relative had little or no relationship to the level of understanding of death. (Author/RL)

An orthologous transcriptional signature differentiates responses towards closely related chemicals in Arabidopsis thaliana and brassica napus

EPA Science Inventory

Herbicides are structurally diverse chemicals that inhibit plant-specific targets, however their off-target and potentially differentiating side-effects are less well defined. In this study, genome-wide expression profiling based on Affymetrix AtH1 arrays was used to identify dis...

Ground State Structure of a Coupled 2-Fermion System in Supersymmetric Quantum Mechanics

NASA Astrophysics Data System (ADS)

Finster, Felix

1997-05-01

We prove the uniqueness of the ground state for a supersymmetric quantum mechanical system of two fermions and two bosons, which is closely related to theN=1 WZ-model. The proof is constructive and gives detailed information on what the ground state looks like

Imperfect/I'm Perfect: Bodies/Embodiment in Post-Secondary and Elementary Settings

ERIC Educational Resources Information Center

Winters, Kari-Lynn; Code, Mary

2017-01-01

Using researched perspectives of bodies and embodiment, alongside dramatic structures, where bodies are foregrounded, this article looks closely at bodies and embodiment inside of school settings. Specifically, it investigates a community in Southern Ontario and the perceived, affective, relational, and critical ways that study participants story…

Fair Assessment of Team Assignments in Business Communication and Architecture

ERIC Educational Resources Information Center

Fermelis, Jan; Tucker, Richard; Palmer, Stuart

2008-01-01

Cross-faculty and cross-disciplinary collaborations within higher education are rare, no doubt largely due to the location of academics within discipline- and faculty-based structures. When collaborations do occur, they are frequently problematic, even when the collaborators stem from closely related disciplines. However, collaborations are…

Stresses in adhesively bonded joints - A closed-form solution

NASA Technical Reports Server (NTRS)

Delale, F.; Erdogan, F.; Aydinoglu, M. N.

1981-01-01

The general plane strain problem of adhesively bonded structures consisting of two different, orthotropic adherends is considered, under the assumption that adherend thicknesses are constant and small in relation to the lateral dimensions of the bonded region, so that they may be treated as plates. The problem is reduced to a system of differential equations for the adhesive stresses which is solved in closed form, with a single lap joint and a stiffened plate under various loading conditions being considered as examples. It is found that the plate theory used in the analysis not only predicts the correct trend for adhesive stresses but gives surprisingly accurate results, the solution being obtained by assuming linear stress-strain relations for the adhesive.

Anomalous partitioning of water in coexisting liquid phases of lipid multilayers near 100% relative humidity

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

Ma, Yicong; Ghosh, Sajal K.; Bera, Sambhunath

2015-11-30

X-ray diffraction is used to determine the hydration dependence of a ternary mixture lipid multilayer structure which has phase separated into liquid-ordered (Lo) and liquid-disordered (Ld) phases. An anomaly is observed in the swelling behavior of the Ld phase at a relative humidity (RH) close to 100%, which is different from the anomalous swelling happens close to the main lipid gel-fluid transition. The lamellar repeat distance of the Ld phase swells by an extra 4 Å, well beyond the equilibrium spacing predicted by the inter-bilayer forces. This anomalous swelling is caused by the hydrophobic mismatch energy at the domain boundaries,more » which produces surprisingly long range effect.« less

Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin

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

Ecale Zhou, C L; Zemla, A T; Roe, D

2005-01-29

Specific and sensitive ligand-based protein detection assays that employ antibodies or small molecules such as peptides, aptamers, or other small molecules require that the corresponding surface region of the protein be accessible and that there be minimal cross-reactivity with non-target proteins. To reduce the time and cost of laboratory screening efforts for diagnostic reagents, we developed new methods for evaluating and selecting protein surface regions for ligand targeting. We devised combined structure- and sequence-based methods for identifying 3D epitopes and binding pockets on the surface of the A chain of ricin that are conserved with respect to a set ofmore » ricin A chains and unique with respect to other proteins. We (1) used structure alignment software to detect structural deviations and extracted from this analysis the residue-residue correspondence, (2) devised a method to compare corresponding residues across sets of ricin structures and structures of closely related proteins, (3) devised a sequence-based approach to determine residue infrequency in local sequence context, and (4) modified a pocket-finding algorithm to identify surface crevices in close proximity to residues determined to be conserved/unique based on our structure- and sequence-based methods. In applying this combined informatics approach to ricin A we identified a conserved/unique pocket in close proximity (but not overlapping) the active site that is suitable for bi-dentate ligand development. These methods are generally applicable to identification of surface epitopes and binding pockets for development of diagnostic reagents, therapeutics, and vaccines.« less

Veering and nonlinear interactions of a clamped beam in bending and torsion

NASA Astrophysics Data System (ADS)

Ehrhardt, David A.; Hill, Thomas L.; Neild, Simon A.; Cooper, Jonathan E.

2018-03-01

Understanding the linear and nonlinear dynamic behaviour of beams is critical for the design of many engineering structures such as spacecraft antennae, aircraft wings, and turbine blades. When the eigenvalues of such structures are closely-spaced, nonlinearity may lead to interactions between the underlying linear normal modes (LNMs). This work considers a clamped-clamped beam which exhibits nonlinear behaviour due to axial tension from large amplitudes of deformation. An additional cross-beam, mounted transversely and with a movable mass at each tip, allows tuning of the primary torsion LNM such that it is close to the primary bending LNM. Perturbing the location of one mass relative to that of the other leads to veering between the eigenvalues of the bending and torsion LNMs. For a number of selected geometries in the region of veering, a nonlinear reduced order model (NLROM) is created and the nonlinear normal modes (NNMs) are used to describe the underlying nonlinear behaviour of the structure. The relationship between the 'closeness' of the eigenvalues and the nonlinear dynamic behaviour is demonstrated in the NNM backbone curves, and veering-like behaviour is observed. Finally, the forced and damped dynamics of the structure are predicted using several analytical and numerical tools and are compared to experimental measurements. As well as showing a good agreement between the predicted and measured responses, phenomena such as a 1:1 internal resonance and quasi-periodic behaviour are identified.

Phylogenetic trait-based analyses of ecological networks

PubMed Central

Rafferty, Nicole E.; Ives, Anthony R.

2013-01-01

Ecological networks of two interacting guilds of species, such as flowering plants and pollinators, are common in nature, and studying their structure can yield insights into their resilience to environmental disturbances. Here we develop analytical methods for exploring the strengths of interactions within bipartite networks consisting of two guilds of phylogenetically related species. We then apply these methods to investigate the resilience of a plant–pollinator community to anticipated climate change. The methods allow the statistical assessment of, for example, whether closely related pollinators are more likely to visit plants with similar relative frequencies, and whether closely related pollinators tend to visit closely related plants. The methods can also incorporate trait information, allowing us to identify which plant traits are likely responsible for attracting different pollinators. These questions are important for our study of 14 prairie plants and their 22 insect pollinators. Over the last 70 years, six of the plants have advanced their flowering, while eight have not. When we experimentally forced earlier flowering times, five of the six advanced-flowering species experienced higher pollinator visitation rates, whereas only one of the eight other species had more visits; this network thus appears resilient to climate change, because those species with advanced flowering have ample pollinators earlier in the season. Using the methods developed here, we show that advanced-flowering plants did not have a distinct pollinator community from the other eight species. Furthermore, pollinator phylogeny did not explain pollinator community composition; closely related pollinators were not more likely to visit the same plant species. However, differences among pollinator communities visiting different plants were explained by plant height, floral color, and symmetry. As a result, closely related plants attracted similar numbers of pollinators. By parsing out characteristics that explain why plants share pollinators, we can identify plant species that likely share a common fate in a changing climate. PMID:24358717

Phylogenetic trait-based analyses of ecological networks.

PubMed

Rafferty, Nicole E; Ives, Anthony R

2013-10-01

Ecological networks of two interacting guilds of species, such as flowering plants and pollinators, are common in nature, and studying their structure can yield insights into their resilience to environmental disturbances. Here we develop analytical methods for exploring the strengths of interactions within bipartite networks consisting of two guilds of phylogenetically related species. We then apply these methods to investigate the resilience of a plant-pollinator community to anticipated climate change. The methods allow the statistical assessment of, for example, whether closely related pollinators are more likely to visit plants with similar relative frequencies, and whether closely related pollinators tend to visit closely related plants. The methods can also incorporate trait information, allowing us to identify which plant traits are likely responsible for attracting different pollinators. These questions are important for our study of 14 prairie plants and their 22 insect pollinators. Over the last 70 years, six of the plants have advanced their flowering, while eight have not. When we experimentally forced earlier flowering times, five of the six advanced-flowering species experienced higher pollinator visitation rates, whereas only one of the eight other species had more visits; this network thus appears resilient to climate change, because those species with advanced flowering have ample pollinators earlier in the season. Using the methods developed here, we show that advanced-flowering plants did not have a distinct pollinator community from the other eight species. Furthermore, pollinator phylogeny did not explain pollinator community composition; closely related pollinators were not more likely to visit the same plant species. However, differences among pollinator communities visiting different plants were explained by plant height, floral color, and symmetry. As a result, closely related plants attracted similar numbers of pollinators. By parsing out characteristics that explain why plants share pollinators, we can identify plant species that likely share a common fate in a changing climate.

Oh sister, where art thou? Spatial population structure and the evolution of an altruistic defence trait.

PubMed

Pamminger, T; Foitzik, S; Metzler, D; Pennings, P S

2014-11-01

The evolution of parasite virulence and host defences is affected by population structure. This effect has been confirmed in studies focusing on large spatial scales, whereas the importance of local structure is not well understood. Slavemaking ants are social parasites that exploit workers of another species to rear their offspring. Enslaved workers of the host species Temnothorax longispinosus have been found to exhibit an effective post-enslavement defence behaviour: enslaved workers were observed killing a large proportion of the parasites' offspring. As enslaved workers do not reproduce, they gain no direct fitness benefit from this 'rebellion' behaviour. However, there may be an indirect benefit: neighbouring host nests that are related to 'rebel' nests can benefit from a reduced raiding pressure, as a result of the reduction in parasite nest size due to the enslaved workers' killing behaviour. We use a simple mathematical model to examine whether the small-scale population structure of the host species could explain the evolution of this potentially altruistic defence trait against slavemaking ants. We find that this is the case if enslaved host workers are related to nearby host nests. In a population genetic study, we confirm that enslaved workers are, indeed, more closely related to host nests within the raiding range of their resident slavemaker nest, than to host nests outside the raiding range. This small-scale population structure seems to be a result of polydomy (e.g. the occupation of several nests in close proximity by a single colony) and could have enabled the evolution of 'rebellion' by kin selection. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Gating of Connexin Channels by transjunctional-voltage: Conformations and models of open and closed states.

PubMed

Bargiello, Thaddeus A; Oh, Seunghoon; Tang, Qingxiu; Bargiello, Nicholas K; Dowd, Terry L; Kwon, Taekyung

2018-01-01

Voltage is an important physiologic regulator of channels formed by the connexin gene family. Connexins are unique among ion channels in that both plasma membrane inserted hemichannels (undocked hemichannels) and intercellular channels (aggregates of which form gap junctions) have important physiological roles. The hemichannel is the fundamental unit of gap junction voltage-gating. Each hemichannel displays two distinct voltage-gating mechanisms that are primarily sensitive to a voltage gradient formed along the length of the channel pore (the transjunctional voltage) rather than sensitivity to the absolute membrane potential (V m or V i-o ). These transjunctional voltage dependent processes have been termed V j - or fast-gating and loop- or slow-gating. Understanding the mechanism of voltage-gating, defined as the sequence of voltage-driven transitions that connect open and closed states, first and foremost requires atomic resolution models of the end states. Although ion channels formed by connexins were among the first to be characterized structurally by electron microscopy and x-ray diffraction in the early 1980's, subsequent progress has been slow. Much of the current understanding of the structure-function relations of connexin channels is based on two crystal structures of Cx26 gap junction channels. Refinement of crystal structure by all-atom molecular dynamics and incorporation of charge changing protein modifications has resulted in an atomic model of the open state that arguably corresponds to the physiologic open state. Obtaining validated atomic models of voltage-dependent closed states is more challenging, as there are currently no methods to solve protein structure while a stable voltage gradient is applied across the length of an oriented channel. It is widely believed that the best approach to solve the atomic structure of a voltage-gated closed ion channel is to apply different but complementary experimental and computational methods and to use the resulting information to derive a consensus atomic structure that is then subjected to rigorous validation. In this paper, we summarize our efforts to obtain and validate atomic models of the open and voltage-driven closed states of undocked connexin hemichannels. This article is part of a Special Issue entitled: Gap Junction Proteins edited by Jean Claude Herve. Copyright © 2017 Elsevier B.V. All rights reserved.

Landscaping the structures of GAVI country vaccine supply chains and testing the effects of radical redesign.

PubMed

Lee, Bruce Y; Connor, Diana L; Wateska, Angela R; Norman, Bryan A; Rajgopal, Jayant; Cakouros, Brigid E; Chen, Sheng-I; Claypool, Erin G; Haidari, Leila A; Karir, Veena; Leonard, Jim; Mueller, Leslie E; Paul, Proma; Schmitz, Michelle M; Welling, Joel S; Weng, Yu-Ting; Brown, Shawn T

2015-08-26

Many of the world's vaccine supply chains do not adequately provide vaccines, prompting several questions: how are vaccine supply chains currently structured, are these structures closely tailored to individual countries, and should these supply chains be radically redesigned? We segmented the 57 GAVI-eligible countries' vaccine supply chains based on their structure/morphology, analyzed whether these segments correlated with differences in country characteristics, and then utilized HERMES to develop a detailed simulation model of three sample countries' supply chains and explore the cost and impact of various alternative structures. The majority of supply chains (34 of 57) consist of four levels, despite serving a wide diversity of geographical areas and population sizes. These four-level supply chains loosely fall into three clusters [(1) 18 countries relatively more bottom-heavy, i.e., many more storage locations lower in the supply chain, (2) seven with relatively more storage locations in both top and lower levels, and (3) nine comparatively more top-heavy] which do not correlate closely with any of the country characteristics considered. For all three cluster types, our HERMES modeling found that simplified systems (a central location shipping directly to immunization locations with a limited number of Hubs in between) resulted in lower operating costs. A standard four-tier design template may have been followed for most countries and raises the possibility that simpler and more tailored designs may be warranted. Copyright © 2015 Elsevier Ltd. All rights reserved.

Scaling of mode shapes from operational modal analysis using harmonic forces

NASA Astrophysics Data System (ADS)

Brandt, A.; Berardengo, M.; Manzoni, S.; Cigada, A.

2017-10-01

This paper presents a new method for scaling mode shapes obtained by means of operational modal analysis. The method is capable of scaling mode shapes on any structure, also structures with closely coupled modes, and the method can be used in the presence of ambient vibration from traffic or wind loads, etc. Harmonic excitation can be relatively easily accomplished by using general-purpose actuators, also for force levels necessary for driving large structures such as bridges and highrise buildings. The signal processing necessary for mode shape scaling by the proposed method is simple and the method can easily be implemented in most measurement systems capable of generating a sine wave output. The tests necessary to scale the modes are short compared to typical operational modal analysis test time. The proposed method is thus easy to apply and inexpensive relative to some other methods for scaling mode shapes that are available in literature. Although it is not necessary per se, we propose to excite the structure at, or close to, the eigenfrequencies of the modes to be scaled, since this provides better signal-to-noise ratio in the response sensors, thus permitting the use of smaller actuators. An extensive experimental activity on a real structure was carried out and the results reported demonstrate the feasibility and accuracy of the proposed method. Since the method utilizes harmonic excitation for the mode shape scaling, we propose to call the method OMAH.

A plasma membrane sucrose-binding protein that mediates sucrose uptake shares structural and sequence similarity with seed storage proteins but remains functionally distinct.

PubMed

Overvoorde, P J; Chao, W S; Grimes, H D

1997-06-20

Photoaffinity labeling of a soybean cotyledon membrane fraction identified a sucrose-binding protein (SBP). Subsequent studies have shown that the SBP is a unique plasma membrane protein that mediates the linear uptake of sucrose in the presence of up to 30 mM external sucrose when ectopically expressed in yeast. Analysis of the SBP-deduced amino acid sequence indicates it lacks sequence similarity with other known transport proteins. Data presented here, however, indicate that the SBP shares significant sequence and structural homology with the vicilin-like seed storage proteins that organize into homotrimers. These similarities include a repeated sequence that forms the basis of the reiterated domain structure characteristic of the vicilin-like protein family. In addition, analytical ultracentrifugation and nonreducing SDS-polyacrylamide gel electrophoresis demonstrate that the SBP appears to be organized into oligomeric complexes with a Mr indicative of the existence of SBP homotrimers and homodimers. The structural similarity shared by the SBP and vicilin-like proteins provides a novel framework to explore the mechanistic basis of SBP-mediated sucrose uptake. Expression of the maize Glb protein (a vicilin-like protein closely related to the SBP) in yeast demonstrates that a closely related vicilin-like protein is unable to mediate sucrose uptake. Thus, despite sequence and structural similarities shared by the SBP and the vicilin-like protein family, the SBP is functionally divergent from other members of this group.

Model of cohesive properties and structural phase transitions in non-metallic solids

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

Majewski, J.A.; Vogl, P.

1986-01-01

We have developed a simple, yet microscopic and universal model for cohesive properties of solids. This model explains the physical mechanisms determining the chemical and predicts semiquantitatively static and dynamic cohesive properties. It predicts a substantial softening of the long-wavelength transverse optical phonons across the pressure induced phase transition from the zincblenda to rocksalt structure in II-VI compounds. The origin of this softening is shown to be closely related to ferroelectricity.

Microhabitat use, trophic patterns, and the evolution of brain structure in African cichlids.

PubMed

Huber, R; van Staaden, M J; Kaufman, L S; Liem, K F

1997-01-01

The species assemblages of cichlids in the three largest African Great Lakes are among the richest concentrations of vertebrate species on earth. The faunas are broadly similar in terms of trophic diversity, species richness, rates of endemism, and taxonomic composition, yet they are historically independent of each other. Hence, they offer a true and unique evolutionary experiment to test hypotheses concerning the mutual dependencies of ecology and brain morphology. We examined the brains of 189 species of cichlids from the three large lakes: Victoria, Tanganyika, and Malawi. A first paper demonstrated that patterns of evolutionary change in cichlid brain morphology are similar across taxonomic boundaries as well as across the three lakes [van Staaden et al., 1995 ZACS 98: 165-178]. Here we report a close relationship between the relative sizes of various brain structures and variables related to the utilization of habitat and prey. Causality is difficult to assign in this context, nonetheless, prey size and agility, turbidity levels, depth, and substrate complexity are all highly predictive of variation in brain structure. Areas associated with primary sensory functions such as vision and taste relate significantly to differences in feeding habits. Turbidity and depth are closely associated with differences in eye size, and large eyes are associated with species that pick plankton from the water column. Piscivorous taxa and others that utilize motile prey are characterized by a well developed optic tectum and a large cerebellum compared to species that prey on molluscs or plants. Structures relating to taste are well developed in species feeding on benthos over muddy or sandy substrates. The data militated against the existence of compensatory changes in brain structure. Thus enhanced development of a particular function is generally not accompanied by a parallel reduction of structures related to other modalities. Although genetic and environmental influences during ontogeny of the brain cannot be isolated, this study provides a rich source of hypotheses concerning the way the nervous system functions under various environmental conditions and how it has responded to natural selection.

The Baby Care Questionnaire: A measure of parenting principles and practices during infancy☆

PubMed Central

Winstanley, Alice; Gattis, Merideth

2013-01-01

The current report provides a new framework to explore the role of parenting practices and principles during infancy. We identify structure and attunement as key parenting principles during infancy. Structure represents reliance on regularity and routines in daily life. Attunement represents reliance on infant cues and close physical contact. We suggest parents’ relative endorsement of these parenting principles is related to their choices about practices such as feeding, holding and night-time sleeping. We designed the Baby Care Questionnaire to measure parents’ endorsement of structure and attunement, as well as their daily parenting practices. We report data demonstrating the factor structure, reliability and validity of the BCQ. The BCQ, to our knowledge, is the first comprehensive measure of parenting practices and principles during infancy. We conclude with a discussion of future directions for the measure. PMID:24050932

Using Social Networking to Understand Social Networks: Analysis of a Mobile Phone Closed User Group Used by a Ghanaian Health Team

PubMed Central

Akosah, Eric; Ohemeng-Dapaah, Seth; Sakyi Baah, Joseph; Kanter, Andrew S

2013-01-01

Background The network structure of an organization influences how well or poorly an organization communicates and manages its resources. In the Millennium Villages Project site in Bonsaaso, Ghana, a mobile phone closed user group has been introduced for use by the Bonsaaso Millennium Villages Project Health Team and other key individuals. No assessment on the benefits or barriers of the use of the closed user group had been carried out. Objective The purpose of this research was to make the case for the use of social network analysis methods to be applied in health systems research—specifically related to mobile health. Methods This study used mobile phone voice records of, conducted interviews with, and reviewed call journals kept by a mobile phone closed user group consisting of the Bonsaaso Millennium Villages Project Health Team. Social network analysis methodology complemented by a qualitative component was used. Monthly voice data of the closed user group from Airtel Bharti Ghana were analyzed using UCINET and visual depictions of the network were created using NetDraw. Interviews and call journals kept by informants were analyzed using NVivo. Results The methodology was successful in helping identify effective organizational structure. Members of the Health Management Team were the more central players in the network, rather than the Community Health Nurses (who might have been expected to be central). Conclusions Social network analysis methodology can be used to determine the most productive structure for an organization or team, identify gaps in communication, identify key actors with greatest influence, and more. In conclusion, this methodology can be a useful analytical tool, especially in the context of mobile health, health services, and operational and managerial research. PMID:23552721

Using social networking to understand social networks: analysis of a mobile phone closed user group used by a Ghanaian health team.

PubMed

Kaonga, Nadi Nina; Labrique, Alain; Mechael, Patricia; Akosah, Eric; Ohemeng-Dapaah, Seth; Sakyi Baah, Joseph; Kodie, Richmond; Kanter, Andrew S; Levine, Orin

2013-04-03

The network structure of an organization influences how well or poorly an organization communicates and manages its resources. In the Millennium Villages Project site in Bonsaaso, Ghana, a mobile phone closed user group has been introduced for use by the Bonsaaso Millennium Villages Project Health Team and other key individuals. No assessment on the benefits or barriers of the use of the closed user group had been carried out. The purpose of this research was to make the case for the use of social network analysis methods to be applied in health systems research--specifically related to mobile health. This study used mobile phone voice records of, conducted interviews with, and reviewed call journals kept by a mobile phone closed user group consisting of the Bonsaaso Millennium Villages Project Health Team. Social network analysis methodology complemented by a qualitative component was used. Monthly voice data of the closed user group from Airtel Bharti Ghana were analyzed using UCINET and visual depictions of the network were created using NetDraw. Interviews and call journals kept by informants were analyzed using NVivo. The methodology was successful in helping identify effective organizational structure. Members of the Health Management Team were the more central players in the network, rather than the Community Health Nurses (who might have been expected to be central). Social network analysis methodology can be used to determine the most productive structure for an organization or team, identify gaps in communication, identify key actors with greatest influence, and more. In conclusion, this methodology can be a useful analytical tool, especially in the context of mobile health, health services, and operational and managerial research.

Comparative analyses of quaternary arrangements in homo-oligomeric proteins in superfamilies: Functional implications.

PubMed

Sudha, Govindarajan; Srinivasan, Narayanaswamy

2016-09-01

A comprehensive analysis of the quaternary features of distantly related homo-oligomeric proteins is the focus of the current study. This study has been performed at the levels of quaternary state, symmetry, and quaternary structure. Quaternary state and quaternary structure refers to the number of subunits and spatial arrangements of subunits, respectively. Using a large dataset of available 3D structures of biologically relevant assemblies, we show that only 53% of the distantly related homo-oligomeric proteins have the same quaternary state. Considering these homologous homo-oligomers with the same quaternary state, conservation of quaternary structures is observed only in 38% of the pairs. In 36% of the pairs of distantly related homo-oligomers with different quaternary states the larger assembly in a pair shows high structural similarity with the entire quaternary structure of the related protein with lower quaternary state and it is referred as "Russian doll effect." The differences in quaternary state and structure have been suggested to contribute to the functional diversity. Detailed investigations show that even though the gross functions of many distantly related homo-oligomers are the same, finer level differences in molecular functions are manifested by differences in quaternary states and structures. Comparison of structures of biological assemblies in distantly and closely related homo-oligomeric proteins throughout the study differentiates the effects of sequence divergence on the quaternary structures and function. Knowledge inferred from this study can provide insights for improved protein structure classification and function prediction of homo-oligomers. Proteins 2016; 84:1190-1202. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure

PubMed Central

Koczyk, Grzegorz; Berezovsky, Igor N.

2008-01-01

Domain hierarchy and closed loops (DHcL) (http://sitron.bccs.uib.no/dhcl/) is a web server that delineates energy hierarchy of protein domain structure and detects domains at different levels of this hierarchy. The server also identifies closed loops and van der Waals locks, which constitute a structural basis for the protein domain hierarchy. The DHcL can be a useful tool for an express analysis of protein structures and their alternative domain decompositions. The user submits a PDB identifier(s) or uploads a 3D protein structure in a PDB format. The results of the analysis are the location of domains at different levels of hierarchy, closed loops, van der Waals locks and their interactive visualization. The server maintains a regularly updated database of domains, closed loop and van der Waals locks for all X-ray structures in PDB. DHcL server is available at: http://sitron.bccs.uib.no/dhcl. PMID:18502776

Relation between alternating open/closed-conduit conditions and deformation patterns: An example from the Somma-Vesuvius volcano (southern Italy)

NASA Astrophysics Data System (ADS)

Tramparulo, F. D. A.; Vitale, S.; Isaia, R.; Tadini, A.; Bisson, M.; Prinzi, E. P.

2018-07-01

We present the results of a meso-scale systematic structural analysis of fractures, faults and dykes exposed at the Somma-Vesuvius volcano (southern Italy). Observed fractures include: (i) radial and tangential (with respect the caldera axis), sub-metric to metric joints associated with the edifice load and volcano-tectonic activity (i.e. inflation, deflation and caldera collapse stages) and (ii) decameter-scale fractures related to volcano flank instabilities. For the Somma-Vesuvius volcano, preexisting radial joints were commonly reactivated as transfer faults during the caldera formation, allowing different blocks to move toward the center of the collapsing area. Dykes occur with different geometries, including en-echelon structures bounding structural depressions. The orientation analysis of all structures indicates that they are preferentially oriented. Furthermore, we provide a morphological lineament analysis using high-resolution Digital Terrain Models of Somma-Vesuvius. Azimuth and spatial distribution of dykes and morphological lineaments were analyzed for comparison with the old Somma Crater and Gran Cono axes, respectively. Results highlight the overprinting of radial and clustered strain patterns recorded in different volcano-tectonic evolution stages. We suggest a possible deformation evolution model in which structures develop along either radial or preferential trends, highlighting different volcanic conditions: (i) where radial patterns occur, the structures developed during volcanic inflation cycles with a closed magmatic conduit condition whereas (ii) clustered patterns are probably associated with a regional strain field that overcomes the local deformation field, a situation typical in the case of open-conduit activity.

Single substitutions to closely related amino acids contribute to the functional diversification of an insect-inducible, positively selected plant cystatin.

PubMed

Rasoolizadeh, Asieh; Goulet, Marie-Claire; Sainsbury, Frank; Cloutier, Conrad; Michaud, Dominique

2016-04-01

A causal link has been reported between positively selected amino acids in plant cystatins and the inhibitory range of these proteins against insect digestive cysteine (Cys) proteases. Here we assessed the impact of single substitutions to closely related amino acids on the contribution of positive selection to cystatin diversification. Cystatin sequence alignments, while confirming hypervariability, indicated a preference for related amino acids at positively selected sites. For example, the non-polar residues leucine (Leu), isoleucine (Ile) and valine (Val) were shown to predominate at positively selected site 2 in the N-terminal region, unlike selected sites 6 and 10, where polar residues are preferred. The model cystatin SlCYS8 and single variants with Leu, Ile or Val at position 2 were compared with regard to their ability to bind digestive proteases of the coleopteran pest Leptinotarsa decemlineata and to induce compensatory responses in this insect. A functional proteomics procedure to capture target Cys proteases in midgut extracts allowed confirmation of distinct binding profiles for the cystatin variants. A shotgun proteomics procedure to monitor whole Cys protease complements revealed protease family specific compensatory responses in the insect, dependent on the variant ingested. Our data confirm the contribution of closely related amino acids to the functional diversity of positively selected plant cystatins in a broader structure/function context imposing physicochemical constraints to primary structure alterations. They also underline the complexity of protease/inhibitor interactions in plant-insect systems, and the challenges still to be met in order to harness the full potential of ectopically expressed protease inhibitors in crop protection. © 2016 Federation of European Biochemical Societies.

Female chacma baboons form strong, equitable, and enduring social bonds

PubMed Central

Beehner, Jacinta C.; Bergman, Thore J.; Crockford, Catherine; Engh, Anne L.; Moscovice, Liza R.; Wittig, Roman M.; Seyfarth, Robert M.; Cheney, Dorothy L.

2010-01-01

Analyses of the pattern of associations, social interactions, coalitions, and aggression among chacma baboons (Papio hamadryas ursinus) in the Okavango Delta of Botswana over a 16-year period indicate that adult females form close, equitable, supportive, and enduring social relationships. They show strong and stable preferences for close kin, particularly their own mothers and daughters. Females also form strong attachments to unrelated females who are close to their own age and who are likely to be paternal half-sisters. Although absolute rates of aggression among kin are as high as rates of aggression among nonkin, females are more tolerant of close relatives than they are of others with whom they have comparable amounts of contact. These findings complement previous work which indicates that the strength of social bonds enhances the fitness of females in this population and support findings about the structure and function of social bonds in other primate groups. PMID:20976293

Estimation of combined sewer overflow discharge: a software sensor approach based on local water level measurements.

PubMed

Ahm, Malte; Thorndahl, Søren; Nielsen, Jesper E; Rasmussen, Michael R

2016-12-01

Combined sewer overflow (CSO) structures are constructed to effectively discharge excess water during heavy rainfall, to protect the urban drainage system from hydraulic overload. Consequently, most CSO structures are not constructed according to basic hydraulic principles for ideal measurement weirs. It can, therefore, be a challenge to quantify the discharges from CSOs. Quantification of CSO discharges are important in relation to the increased environmental awareness of the receiving water bodies. Furthermore, CSO discharge quantification is essential for closing the rainfall-runoff mass-balance in combined sewer catchments. A closed mass-balance is an advantage for calibration of all urban drainage models based on mass-balance principles. This study presents three different software sensor concepts based on local water level sensors, which can be used to estimate CSO discharge volumes from hydraulic complex CSO structures. The three concepts were tested and verified under real practical conditions. All three concepts were accurate when compared to electromagnetic flow measurements.

A Close Look At The Relationship Between WMAP (ILC) Small-Scale Features And Galactic HI Structure

NASA Astrophysics Data System (ADS)

Verschuur, Gerrit L.

2012-05-01

Galactic HI emission profiles surrounding two pairs of features located where large-scale filaments at very different velocities overlap were decomposed into Gaussian components. Families of components defined by similarity of center velocities and line widths were identified and found to be spatially related. Each of the two pairs of HI peaks straddle a high-frequency continuum source revealed in the WMAP survey data. It is suggested that where filamentary HI features are directly interacting high-frequency continuum radiation is being produced. The previously hypothesized mechanism for producing high-frequency continuum radiation involving free-free emission from electrons in the interstellar medium, in this case created where HI filaments interact to produce fractional ionizations of order 5 to 15%, fit the data very closely. The results confirm that WMAP data on small-scale structures believed to be cosmological in origin are in fact compromised by the presence of intervening galactic sources of interstellar electrons clumped on scales typical of interstellar HI structure.

The Crystal Structures of Potentially Tautomeric Compounds

NASA Astrophysics Data System (ADS)

Furmanova, Nina G.

1981-08-01

Data on the structures of potentially proto-, metallo-, and carbono-tropic compounds, obtained mainly by X-ray diffraction, are surveyed. The results of neutron and electron diffraction studies have also been partly used. It is shown that a characteristic feature of all the systems considered is the formation of hydrogen or secondary bonds ensuring the contribution of both possible tautomeric forms to the structure. Systematic consideration of the experimental data leads to the conclusion that there is a close relation between the crystal structure and the dynamic behaviour of the molecules in solution and that secondary and hydrogen bonds play a significant role in the tautomeric transition. The bibliography includes 152 references.

A damage mechanics based approach to structural deterioration and reliability

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

Bhattcharya, B.; Ellingwood, B.

1998-02-01

Structural deterioration often occurs without perceptible manifestation. Continuum damage mechanics defines structural damage in terms of the material microstructure, and relates the damage variable to the macroscopic strength or stiffness of the structure. This enables one to predict the state of damage prior to the initiation of a macroscopic flaw, and allows one to estimate residual strength/service life of an existing structure. The accumulation of damage is a dissipative process that is governed by the laws of thermodynamics. Partial differential equations for damage growth in terms of the Helmholtz free energy are derived from fundamental thermodynamical conditions. Closed-form solutions tomore » the equations are obtained under uniaxial loading for ductile deformation damage as a function of plastic strain, for creep damage as a function of time, and for fatigue damage as function of number of cycles. The proposed damage growth model is extended into the stochastic domain by considering fluctuations in the free energy, and closed-form solutions of the resulting stochastic differential equation are obtained in each of the three cases mentioned above. A reliability analysis of a ring-stiffened cylindrical steel shell subjected to corrosion, accidental pressure, and temperature is performed.« less

Gravitationally confined relativistic neutrinos

NASA Astrophysics Data System (ADS)

Vayenas, C. G.; Fokas, A. S.; Grigoriou, D.

2017-09-01

Combining special relativity, the equivalence principle, and Newton’s universal gravitational law with gravitational rather than rest masses, one finds that gravitational interactions between relativistic neutrinos with kinetic energies above 50 MeV are very strong and can lead to the formation of gravitationally confined composite structures with the mass and other properties of hadrons. One may model such structures by considering three neutrinos moving symmetrically on a circular orbit under the influence of their gravitational attraction, and by assuming quantization of their angular momentum, as in the Bohr model of the H atom. The model contains no adjustable parameters and its solution, using a neutrino rest mass of 0.05 eV/c2, leads to composite state radii close to 1 fm and composite state masses close to 1 GeV/c2. Similar models of relativistic rotating electron - neutrino pairs give a mass of 81 GeV/c2, close to that of W bosons. This novel mechanism of generating mass suggests that the Higgs mass generation mechanism can be modeled as a latent gravitational field which gets activated by relativistic neutrinos.

Experimental investigations of aeration efficiency in high-head gated circular conduits.

PubMed

Cihat Tuna, M; Ozkan, Fahri; Baylar, Ahmet

2014-01-01

The primary purpose of water aeration is to increase the oxygen saturation of the water. This can be achieved by using hydraulic structures because of substantial air bubble entrainment at these structures. Closed conduit aeration is a particular instance of this. While there has been a great deal of research on air-demand ratio within closed conduit, very little research has specifically addressed aeration efficiency of closed conduit. In the present work an experimental study was conducted to investigate the aeration efficiency of high-head gated circular conduits. Results showed that high-head gated circular conduits were effective for oxygen transfer. The effects of Froude number and ratio of the water cross-sectional flow area to the conduit cross-sectional area on aeration efficiency were particularly significant, whereas the effect of conduit length was only moderate. Further, a design formula for the aeration efficiency was presented relating the aeration efficiency to ratio of water cross-sectional flow area to conduit cross-sectional area and Froude number. The obtained results will be useful in future modeling processes and aid the practicing engineer in predicting aeration efficiency for design purposes.

Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates

PubMed Central

Tuszynski, Jack A.; Gallo, Diego; Morbiducci, Umberto; Danani, Andrea

2016-01-01

The Josephin Domain (JD), i.e. the N-terminal domain of Ataxin 3 (At3) protein, is an interesting example of competition between physiological function and aggregation risk. In fact, the fibrillogenesis of Ataxin 3, responsible for the spinocerebbellar ataxia 3, is strictly related to the JD thermodynamic stability. Whereas recent NMR studies have demonstrated that different JD conformations exist, the likelihood of JD achievable conformational states in solution is still an open issue. Marked differences in the available NMR models are located in the hairpin region, supporting the idea that JD has a flexible hairpin in dynamic equilibrium between open and closed states. In this work we have carried out an investigation on the JD conformational arrangement by means of both classical molecular dynamics (MD) and Metadynamics employing essential coordinates as collective variables. We provide a representation of the free energy landscape characterizing the transition pathway from a JD open-like structure to a closed-like conformation. Findings of our in silico study strongly point to the closed-like conformation as the most likely for a Josephin Domain in water. PMID:26745628

Dynamics of the Transition Corona

NASA Technical Reports Server (NTRS)

Masson, Sophie; McCauley, Patrick; Golub, Leon; Reeves, Katharine K.; DeLuca, Edward E.

2014-01-01

Magnetic reconnection between the open and closed magnetic fields in the corona is believed to play a crucial role in the corona/heliosphere coupling. At large scale, the exchange of open/closed connectivity is expected to occur in pseudo-streamer (PS) structures. However, there is neither clear observational evidence of how such coupling occurs in PSs, nor evidence for how the magnetic reconnection evolves. Using a newly developed technique, we enhance the off-limb magnetic fine structures observed with the Atmospheric Imaging Assembly and identify a PS-like feature located close to the northern coronal hole. We first identify that the magnetic topology associated with the observation is a PS, null-point (NP) related topology bounded by the open field. By comparing the magnetic field configuration with the extreme ultraviolet (EUV) emission regions, we determined that most of the magnetic flux associated with plasma emission are small loops below the PS basic NP and open field bounding the PS topology. In order to interpret the evolution of the PS, we referred to a three-dimensional MHD interchange reconnection modeling the exchange of connectivity between small closed loops and the open field. The observed PS fine structures follow the dynamics of the magnetic field before and after reconnecting at the NP obtained by the interchange model. Moreover, the pattern of the EUV plasma emission is the same as the shape of the expected plasma emission location derived from the simulation. These morphological and dynamical similarities between the PS observations and the results from the simulation strongly suggest that the evolution of the PS, and in particular the opening/closing of the field, occurs via interchange/slipping reconnection at the basic NP of the PS. Besides identifying the mechanism at work in the large-scale coupling between the open and closed fields, our results highlight that interchange reconnection in PSs is a gradual physical process that differs from the impulsive reconnection of the solar-jet model.

Structures of Human CCL18, CCL3, and CCL4 Reveal Molecular Determinants for Quaternary Structures and Sensitivity to Insulin-Degrading Enzyme

DOE PAGES

Liang, Wenguang G.; Ren, Min; Zhao, Fan; ...

2015-01-27

CC chemokine ligands (CCL) are 8-14 kDa signaling proteins involved in diverse immune functions. While CCLs share similar tertiary structures, oligomerization produces highly diverse quaternary structures that protect chemokines from proteolytic degradation and modulate their functions. CCL18 is closely related to CCL3 and CCL4 with respect to both protein sequence and genomic location, yet CCL18 has distinct biochemical and biophysical properties. Here in this paper, we report a crystal structure of human CCL18 and its oligomerization states in solution based on crystallographic and small angle X-ray scattering (SAXS) analyses. Our data shows that CCL18 adopts an α-helical conformation at itsmore » N-terminus that weakens its dimerization, explaining CCL18’s preference for the monomeric state. Multiple contacts between monomers allow CCL18 to reversibly form a unique open-ended oligomer different from those of CCL3, CCL4, and CCL5. Furthermore, these differences hinge on proline 8, which is conserved in CCL3 and CCL4, but is replaced by lysine in human CCL18. Our structural analyses suggest that a proline 8 to alanine mutation stabilizes a type I β-turn at the N-terminus of CCL4 to prevent dimerization but prevents dimers from making key contacts with each other in CCL3. Thus, the P8A mutation induces depolymerization of CCL3 and CCL4 by distinct mechanisms. Finally, we used structural, biochemical, and functional analyses to unravel why insulin-degrading enzyme (IDE) degrades CCL3 and CCL4 but not CCL18. Lastly, our results elucidate the molecular basis for the oligomerization of three closely related CC chemokines and suggest how oligomerization shapes CCL chemokine function.« less

Structures of human CCL18, CCL3, and CCL4 reveal molecular determinants for quaternary structures and sensitivity to insulin-degrading enzyme.

PubMed

Liang, Wenguang G; Ren, Min; Zhao, Fan; Tang, Wei-Jen

2015-03-27

CC chemokine ligands (CCLs) are 8- to 14-kDa signaling proteins involved in diverse immune functions. While CCLs share similar tertiary structures, oligomerization produces highly diverse quaternary structures that protect chemokines from proteolytic degradation and modulate their functions. CCL18 is closely related to CCL3 and CCL4 with respect to both protein sequence and genomic location, yet CCL18 has distinct biochemical and biophysical properties. Here, we report a crystal structure of human CCL18 and its oligomerization states in solution based on crystallographic and small-angle X-ray scattering analyses. Our data show that CCL18 adopts an α-helical conformation at its N-terminus that weakens its dimerization, explaining CCL18's preference for the monomeric state. Multiple contacts between monomers allow CCL18 to reversibly form a unique open-ended oligomer different from those of CCL3, CCL4, and CCL5. Furthermore, these differences hinge on proline 8, which is conserved in CCL3 and CCL4 but is replaced by lysine in human CCL18. Our structural analyses suggest that a mutation of proline 8 to alanine stabilizes a type 1 β-turn at the N-terminus of CCL4 to prevent dimerization but prevents dimers from making key contacts with each other in CCL3. Thus, the P8A mutation induces depolymerization of CCL3 and CCL4 by distinct mechanisms. Finally, we used structural, biochemical, and functional analyses to unravel why insulin-degrading enzyme degrades CCL3 and CCL4 but not CCL18. Our results elucidate the molecular basis for the oligomerization of three closely related CC chemokines and suggest how oligomerization shapes CCL chemokine function. Copyright © 2015 Elsevier Ltd. All rights reserved.

Nonproductive events in ring-closing metathesis using ruthenium catalysts.

PubMed

Stewart, Ian C; Keitz, Benjamin K; Kuhn, Kevin M; Thomas, Renee M; Grubbs, Robert H

2010-06-30

The relative TONs of productive and nonproductive metathesis reactions of diethyl diallylmalonate are compared for eight different ruthenium-based catalysts. Nonproductive cross metathesis is proposed to involve a chain-carrying ruthenium methylidene. A second more-challenging substrate (dimethyl allylmethylallylmalonate) that forms a trisubstituted olefin product is used to further delineate the effect of catalyst structure on the relative efficiencies of these processes. A steric model is proposed to explain the observed trends.

Structuring Mentoring Relationships for Competence, Character, and Purpose

ERIC Educational Resources Information Center

Rhodes, Jean E.; Spencer, Renee

2010-01-01

We close this volume with a final commentary from two leaders in the mentoring field. Rhodes and Spencer articulate how the contributions to this volume offer a richer, more complex rendering of relational styles and processes than has been laid out previously in the mentoring literature. They suggest that these efforts should provoke discussion…

Dimensions of Eighteenth-Century Educational Thinking in Germany: Rhetoric and Gender Anthropology

ERIC Educational Resources Information Center

Lohmann, Ingrid; Mayer, Christine

2008-01-01

The development of pedagogical science in eighteenth-century Germany unfolded in close connection with the emergence of the modern bourgeoisie and its emancipation from a still absolutist society. While social and political structures in Britain and France were changed by revolutions, the relative weakness of the German bourgeoisie led to the…

Aesthetic Creativity: Insights from Classical Literary Theory on Creative Learning

ERIC Educational Resources Information Center

Hellstrom, Tomas Georg

2011-01-01

This paper addresses the subject of textual creativity by drawing on work done in classical literary theory and criticism, specifically new criticism, structuralism and early poststructuralism. The question of how readers and writers engage creatively with the text is closely related to educational concerns, though they are often thought of as…

Epipona media cooper (Hymenoptera: Vespidae), a social wasp new to the Brazilian Atlantic Forest.

PubMed

Menezes, Rodolpho S T; Carvalho Filho, Antonio F; Raw, Anthony; Costa, Marco A

2010-01-01

An occupied nest of Epipona media Cooper was discovered and collected in a cabruca (cocoa plantation with native tree cover). This is the first record of E. media from Bahia State. We described the nest structure and compared the adults with the closely related species Epipona tatua Cuvier.

How Will Welfare Reform Affect Childbearing and Family Structure Decisions? Discussion Paper.

ERIC Educational Resources Information Center

Peters, H. Elizabeth; Plotnick, Robert D.; Jeong, Se-Ook

This paper summarizes changes in key elements of welfare policy and in closely related policies on child support enforcement and sex education and family planning programs. Drawing on a conceptual framework that highlights how incentives created by public policy can affect demographic behaviors, the paper concludes that, as Congress intended,…

The role of habitat shift in the evolution of lizard morphology: evidence from tropical Tropidurus

PubMed Central

Vitt, Laurie J.; Caldwell, Janalee P.; Zani, Peter A.; Titus, Tom A.

1997-01-01

We compared morphology of two geographically close populations of the tropical lizard Tropidurus hispidus to test the hypothesis that habitat structure influences the evolution of morphology and ecology at the population level. T. hispidus isolated on a rock outcrop surrounded by tropical forest use rock crevices for refuge and appear dorsoventrally compressed compared with those in open savanna. A principal components analysis revealed that the populations were differentially distributed along an axis representing primarily three components of shape: body width, body height, and hind-leg length. Morphological divergence was supported by a principal components analysis of size-free morphological variables. Mitochondrial DNA sequences of ATPase 6 indicate that these populations are closely related relative to other T. hispidus, the rock outcrop morphology and ecology are derived within T. hispidus, and morphological and ecological divergence has occurred more rapidly than genetic divergence. This suggests that natural selection can rapidly adjust morphology and ecology in response to a recent history of exposure to habitats differing in structure, a result heretofore implied from comparative studies among lizard species. PMID:9108063

The role of habitat shift in the evolution of lizard morphology: evidence from tropical Tropidurus.

PubMed

Vitt, L J; Caldwell, J P; Zani, P A; Titus, T A

1997-04-15

We compared morphology of two geographically close populations of the tropical lizard Tropidurus hispidus to test the hypothesis that habitat structure influences the evolution of morphology and ecology at the population level. T. hispidus isolated on a rock outcrop surrounded by tropical forest use rock crevices for refuge and appear dorsoventrally compressed compared with those in open savanna. A principal components analysis revealed that the populations were differentially distributed along an axis representing primarily three components of shape: body width, body height, and hind-leg length. Morphological divergence was supported by a principal components analysis of size-free morphological variables. Mitochondrial DNA sequences of ATPase 6 indicate that these populations are closely related relative to other T. hispidus, the rock outcrop morphology and ecology are derived within T. hispidus, and morphological and ecological divergence has occurred more rapidly than genetic divergence. This suggests that natural selection can rapidly adjust morphology and ecology in response to a recent history of exposure to habitats differing in structure, a result heretofore implied from comparative studies among lizard species.

Estimation of ground motion parameters

USGS Publications Warehouse

Boore, David M.; Joyner, W.B.; Oliver, A.A.; Page, R.A.

1978-01-01

Strong motion data from western North America for earthquakes of magnitude greater than 5 are examined to provide the basis for estimating peak acceleration, velocity, displacement, and duration as a function of distance for three magnitude classes. A subset of the data (from the San Fernando earthquake) is used to assess the effects of structural size and of geologic site conditions on peak motions recorded at the base of structures. Small but statistically significant differences are observed in peak values of horizontal acceleration, velocity and displacement recorded on soil at the base of small structures compared with values recorded at the base of large structures. The peak acceleration tends to b3e less and the peak velocity and displacement tend to be greater on the average at the base of large structures than at the base of small structures. In the distance range used in the regression analysis (15-100 km) the values of peak horizontal acceleration recorded at soil sites in the San Fernando earthquake are not significantly different from the values recorded at rock sites, but values of peak horizontal velocity and displacement are significantly greater at soil sites than at rock sites. Some consideration is given to the prediction of ground motions at close distances where there are insufficient recorded data points. As might be expected from the lack of data, published relations for predicting peak horizontal acceleration give widely divergent estimates at close distances (three well known relations predict accelerations between 0.33 g to slightly over 1 g at a distance of 5 km from a magnitude 6.5 earthquake). After considering the physics of the faulting process, the few available data close to faults, and the modifying effects of surface topography, at the present time it would be difficult to accept estimates less than about 0.8 g, 110 cm/s, and 40 cm, respectively, for the mean values of peak acceleration, velocity, and displacement at rock sites within 5 km of fault rupture in a magnitude 6.5 earthquake. These estimates can be expected to change as more data become available.

Use of Pom Pons to Illustrate Cubic Crystal Structures.

ERIC Educational Resources Information Center

Cady, Susan G.

1997-01-01

Describes a method that uses olefin pom pons to illustrate cubic crystal structure. Facilitates hands-on examination of different packing arrangements such as hexagonal close-packed and cubic close-packed structures. (JRH)

Evidence for nonallopatric speciation among closely related sympatric Heliotropium species in the Atacama Desert

PubMed Central

Luebert, Federico; Jacobs, Pit; Hilger, Hartmut H; Muller, Ludo A H

2014-01-01

The genetic structure of populations of closely related, sympatric species may hold the signature of the geographical mode of the speciation process. In fully allopatric speciation, it is expected that genetic differentiation between species is homogeneously distributed across the genome. In nonallopatric speciation, the genomes may remain undifferentiated to a large extent. In this article, we analyzed the genetic structure of five sympatric species from the plant genus Heliotropium in the Atacama Desert. We used amplified fragment length polymorphisms (AFLPs) to characterize the genetic structure of these species and evaluate their genetic differentiation as well as the number of loci subject to positive selection using divergence outlier analysis (DOA). The five species form distinguishable groups in the genetic space, with zones of overlap, indicating that they are possibly not completely isolated. Among-species differentiation accounts for 35% of the total genetic differentiation (FST = 0.35), and FST between species pairs is positively correlated with phylogenetic distance. DOA suggests that few loci are subject to positive selection, which is in line with a scenario of nonallopatric speciation. These results support the idea that sympatric species of Heliotropium sect. Cochranea are under an ongoing speciation process, characterized by a fluctuation of population ranges in response to pulses of arid and humid periods during Quaternary times. PMID:24558582

Evidence for nonallopatric speciation among closely related sympatric Heliotropium species in the Atacama Desert.

PubMed

Luebert, Federico; Jacobs, Pit; Hilger, Hartmut H; Muller, Ludo A H

2014-02-01

The genetic structure of populations of closely related, sympatric species may hold the signature of the geographical mode of the speciation process. In fully allopatric speciation, it is expected that genetic differentiation between species is homogeneously distributed across the genome. In nonallopatric speciation, the genomes may remain undifferentiated to a large extent. In this article, we analyzed the genetic structure of five sympatric species from the plant genus Heliotropium in the Atacama Desert. We used amplified fragment length polymorphisms (AFLPs) to characterize the genetic structure of these species and evaluate their genetic differentiation as well as the number of loci subject to positive selection using divergence outlier analysis (DOA). The five species form distinguishable groups in the genetic space, with zones of overlap, indicating that they are possibly not completely isolated. Among-species differentiation accounts for 35% of the total genetic differentiation (F ST = 0.35), and F ST between species pairs is positively correlated with phylogenetic distance. DOA suggests that few loci are subject to positive selection, which is in line with a scenario of nonallopatric speciation. These results support the idea that sympatric species of Heliotropium sect. Cochranea are under an ongoing speciation process, characterized by a fluctuation of population ranges in response to pulses of arid and humid periods during Quaternary times.

Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system.

PubMed

Psonis, Nikolaos; Antoniou, Aglaia; Karameta, Emmanouela; Leaché, Adam D; Kotsakiozi, Panayiota; Darriba, Diego; Kozlov, Alexey; Stamatakis, Alexandros; Poursanidis, Dimitris; Kukushkin, Oleg; Jablonski, Daniel; Crnobrnja-Isailović, Jelka; Gherghel, Iulian; Lymberakis, Petros; Poulakakis, Nikos

2018-08-01

The Balkan Peninsula constitutes a biodiversity hotspot with high levels of species richness and endemism. The complex geological history of the Balkans in conjunction with the climate evolution are hypothesized as the main drivers generating this biodiversity. We investigated the phylogeography, historical demography, and population structure of closely related wall-lizard species from the Balkan Peninsula and southeastern Europe to better understand diversification processes of species with limited dispersal ability, from Late Miocene to the Holocene. We used several analytical methods integrating genome-wide SNPs (ddRADseq), microsatellites, mitochondrial and nuclear DNA data, as well as species distribution modelling. Phylogenomic analysis resulted in a completely resolved species level phylogeny, population level analyses confirmed the existence of at least two cryptic evolutionary lineages and extensive within species genetic structuring. Divergence time estimations indicated that the Messinian Salinity Crisis played a key role in shaping patterns of species divergence, whereas intraspecific genetic structuring was mainly driven by Pliocene tectonic events and Quaternary climatic oscillations. The present work highlights the effectiveness of utilizing multiple methods and data types coupled with extensive geographic sampling to uncover the evolutionary processes that shaped the species over space and time. Copyright © 2018 Elsevier Inc. All rights reserved.

Mechanical design of an intracranial stent for treating cerebral aneurysms.

PubMed

Shobayashi, Yasuhiro; Tanoue, Tetsuya; Tateshima, Satoshi; Tanishita, Kazuo

2010-11-01

Endovascular treatment of cerebral aneurysms using stents has advanced markedly in recent years. Mechanically, a cerebrovascular stent must be very flexible longitudinally and have low radial stiffness. However, no study has examined the stress distribution and deformation of cerebrovascular stents using the finite element method (FEM) and experiments. Stents can have open- and closed-cell structures, and open-cell stents are used clinically in the cerebrovasculature because of their high flexibility. However, the open-cell structure confers a risk of in-stent stenosis due to protrusion of stent struts into the normal parent artery. Therefore, a flexible stent with a closed-cell structure is required. To design a clinically useful, highly flexible, closed-cell stent, one must examine the mechanical properties of the closed-cell structure. In this study, we investigated the relationship between mesh patterns and the mechanical properties of closed-cell stents. Several mesh patterns were designed and their characteristics were studied using numerical simulation. The results showed that the bending stiffness of a closed-cell stent depends on the geometric configuration of the stent cell. It decreases when the stent cell is stretched in the circumferential direction. Mechanical flexibility equal to an open-cell structure was obtained in a closed-cell structure by varying the geometric configuration of the stent cell. Copyright © 2010 IPEM. Published by Elsevier Ltd. All rights reserved.

Actinoranone, A Cytotoxic Meroterpenoid of Unprecedented Structure from a Marine Adapted Streptomyces sp

PubMed Central

Nam, Sang-Jip; Kauffman, Christopher A.; Paul, Lauren A.; Jensen, Paul R.

2014-01-01

The isolation and structure elucidation of a new meroterpenoid, actinoranone (1), produced by a marine bacterium closely related to the genus Streptomyces is reported. Actinoranone is composed of an unprecedented dihydronaphthalenone polyketide linked to a bicyclic diterpenoid. The stereochemistry of 1 was defined by application of the advanced Mosher's method and by interpretation of spectroscopic data. Actinoranone (1) is significantly cytotoxic to HCT-116 human colon cancer cells with an LD50 = 2.0 μg/mL. PMID:24152065

Isolation and biological evaluation of jatrophane diterpenoids from Euphorbia dendroides.

PubMed

Aljancić, Ivana S; Pesić, Milica; Milosavljević, Slobodan M; Todorović, Nina M; Jadranin, Milka; Milosavljević, Goran; Povrenović, Dragan; Banković, Jasna; Tanić, Nikola; Marković, Ivanka D; Ruzdijić, Sabera; Vajs, Vlatka E; Tesević, Vele V

2011-07-22

From the Montenegrin spurge Euphorbia dendroides, seven new diterpenoids [jatrophanes (1-6) and a tigliane (7)] were isolated and their structures elucidated by spectroscopic techniques. The biological activity of the new compounds was studied against four human cancer cell lines. The most effective jatrophane-type compound (2) and its structurally closely related derivative (1) were evaluated for their interactions with paclitaxel and doxorubicin using a multi-drug-resistant cancer cell line. Both compounds exerted a strong reversal potential resulting from inhibition of P-glycoprotein transport.

Structural changes in the nano-oxide layer with annealing in specular spin valves

NASA Astrophysics Data System (ADS)

Jang, S. H.; Kim, Y. W.; Kang, T.; Kim, H. J.; Kim, K. Y.

2003-05-01

We investigated microstructural changes in a nano-oxide layer (NOL) with annealing in specular spin valves (SVs) by cross-sectional transmission electron microscopy and x-ray photoelectron spectroscopy analysis. In the SV annealed at high temperature of 400 °C, an increase in thickness and a local breakdown of the NOL were observed. This local coarsening of the NOL is closely related to the formation of Mn oxides in the oxide-rich part of the NOL through Mn diffusion. Thus, the chemical structure of the NOL changes to the structure with Mn oxide-rich content after annealing.

The effect of liquid hot water pretreatment on the chemical–structural alteration and the reduced recalcitrance in poplar

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

Li, Mi; Cao, Shilin; Meng, Xianzhi

Hydrothermal pretreatment using liquid hot water (LHW) is capable of substantially reducing the cell wall recalcitrance of lignocellulosic biomass. It enhances the saccharification of polysaccharides, particularly cellulose, into glucose with relatively low capital required. Due to the close association with biomass recalcitrance, the structural change of the components of lignocellulosic materials during the pretreatment is crucial to understand pretreatment chemistry and advance the bio-economy. Although the LHW pretreatment has been extensively applied and studied, the molecular structural alteration during pretreatment and its significance to reduced recalcitrance have not been well understood.

The effect of liquid hot water pretreatment on the chemical–structural alteration and the reduced recalcitrance in poplar

DOE PAGES

Li, Mi; Cao, Shilin; Meng, Xianzhi; ...

2017-11-30

Hydrothermal pretreatment using liquid hot water (LHW) is capable of substantially reducing the cell wall recalcitrance of lignocellulosic biomass. It enhances the saccharification of polysaccharides, particularly cellulose, into glucose with relatively low capital required. Due to the close association with biomass recalcitrance, the structural change of the components of lignocellulosic materials during the pretreatment is crucial to understand pretreatment chemistry and advance the bio-economy. Although the LHW pretreatment has been extensively applied and studied, the molecular structural alteration during pretreatment and its significance to reduced recalcitrance have not been well understood.

Endohedral beryllium atoms in germanium clusters with eight and fewer vertices: how small can a cluster be and still encapsulate a central atom?

PubMed

Uţă, M M; King, R B

2012-05-31

Structures of the beryllium-centered germanium clusters Be@Ge(n)(z) (n = 8, 7, 6; z = -4, -2, 0, +2) have been investigated by density functional theory to provide some insight regarding the smallest metal cluster that can encapsulate an interstitial atom. The lowest energy structures of the eight-vertex Be@Ge(8)(z) clusters (z = -4, -2, 0, +2) all have the Be atom at the center of a closed polyhedron, namely, a D(4d) square antiprism for Be@Ge(8)(4-), a D(2d) bisdisphenoid for Be@Ge(8)(2-), an ideal O(h) cube for Be@Ge(8), and a C(2v) distorted cube for Be@Ge(8)(2+). The Be-centered cubic structures predicted for Be@Ge(8) and Be@Ge(8)(2+) differ from the previously predicted lowest energy structures for the isoelectronic Ge(8)(2-) and Ge(8). This appears to be related to the larger internal volume of the cube relative to other closed eight-vertex polyhedra. The lowest energy structures for the smaller seven- and six-vertex clusters Be@Ge(n)(z) (n = 7, 6; z = -4, -2, 0, +2) no longer have the Be atom at the center of a closed Ge(n) polyhedron. Instead, either the Ge(n) polyhedron has opened up to provide a larger volume for the Be atom or the Be atom has migrated to the surface of the polyhedron. However, higher energy structures are found in which the Be atom is located at the center of a Ge(n) (n = 7, 6) polyhedron. Examples of such structures are a centered C(2v) capped trigonal prismatic structure for Be@Ge(7)(2-), a centered D(5h) pentagonal bipyramidal structure for Be@Ge(7), a centered D(3h) trigonal prismatic structure for Be@Ge(6)(4-), and a centered octahedral structure for Be@Ge(6). Cluster buildup reactions of the type Be@Ge(n)(z) + Ge(2) → Be@Ge(n+2)(z) (n = 6, 8; z = -4, -2, 0, +2) are all predicted to be highly exothermic. This suggests that interstitial clusters having an endohedral atom inside a bare post transition element polyhedron with eight or fewer vertices are less than the optimum size. This is consistent with the experimental observation of several types of 10-vertex polyhedral bare post transition element clusters with interstitial atoms but the failure to observe such clusters with external polyhedra having eight or fewer vertices.

The impact of selection on population genetic structure in the clam Meretrix petechialis revealed by microsatellite markers.

PubMed

Lu, Xia; Wang, Hongxia; Li, Yan; Liu, Baozhong

2016-02-01

The aim of our work is to evaluate the impact of mass selection on genetic structure in artificially closed populations of the clam Meretrix petechialis. In the present study, we performed mass selection over four generations (from 2004 to 2010) on two clam populations [shell features of purple lines (SP) and black dots (SB)] and analyzed their temporal genetic variation and structure using microsatellite makers. The two closed populations originated from the natural Shandong population (SD); thus, a natural SD population (10SD) was used to detect the current genetic structure after 6 years of natural selection. The results showed that the genetic diversity of the four generations of SB and SP was gradually reduced but remained at relatively high levels (SB, A = 18.9.4-16.8, Ho = 0.7389-0.6971, and He = 0.8897-0.8591; SP, A = 20.0-17.8, Ho = 0.7512-0.7043, and He = 0.8938-0.8625), which has not been reduced compared with that of the 10SD population (A = 17.8, Ho = 0.6803, and He = 0.8302). The Ne estimates for the two populations were almost at the same levels as the actual numbers of parental individuals. In addition, a low inbreeding coefficient was detected in the two populations (SB, 0.00201-0.00639; SP, 0.00176-0.00541). Based on the results, the present mass selection has not made a large impact on the population genetic structure of the closed populations. The present investigation provides important information for the development of management strategies for genetic breeding of the clam.

Bursting and critical layer frequencies in minimal turbulent dynamics and connections to exact coherent states

NASA Astrophysics Data System (ADS)

Park, Jae Sung; Shekar, Ashwin; Graham, Michael D.

2018-01-01

The dynamics of the turbulent near-wall region is known to be dominated by coherent structures. These near-wall coherent structures are observed to burst in a very intermittent fashion, exporting turbulent kinetic energy to the rest of the flow. In addition, they are closely related to invariant solutions known as exact coherent states (ECS), some of which display nonlinear critical layer dynamics (motions that are highly localized around the surface on which the streamwise velocity matches the wave speed of ECS). The present work aims to investigate temporal coherence in minimal channel flow relevant to turbulent bursting and critical layer dynamics and its connection to the instability of ECS. It is seen that the minimal channel turbulence displays frequencies very close to those displayed by an ECS family recently identified in the channel flow geometry. The frequencies of these ECS are determined by critical layer structures and thus might be described as "critical layer frequencies." While the bursting frequency is predominant near the wall, the ECS frequencies (critical layer frequencies) become predominant over the bursting frequency at larger distances from the wall, and increasingly so as Reynolds number increases. Turbulent bursts are classified into strong and relatively weak classes with respect to an intermittent approach to a lower branch ECS. This temporally intermittent approach is closely related to an intermittent low drag event, called hibernating turbulence, found in minimal and large domains. The relationship between the strong burst and the instability of the lower branch ECS is further discussed in state space. The state-space dynamics of strong bursts is very similar to that of the unstable manifolds of the lower branch ECS. In particular, strong bursting processes are always preceded by hibernation events. This precursor dynamics to strong turbulence may aid in development of more effective control schemes by a way of anticipating dynamics such as intermittent hibernating dynamics.

Nature and biosynthesis of galacto-oligosaccharides related to oligosaccharides in human breast milk

PubMed Central

Intanon, Montira; Arreola, Sheryl Lozel; Pham, Ngoc Hung; Kneifel, Wolfgang; Haltrich, Dietmar; Nguyen, Thu-Ha

2014-01-01

Human milk oligosaccharides (HMO) are prominent among the functional components of human breast milk. While HMO have potential applications in both infants and adults, this potential is limited by the difficulties in manufacturing these complex structures. Consequently, functional alternatives such as galacto-oligosaccharides are under investigation, and nowadays, infant formulae are supplemented with galacto-oligosaccharides to mimic the biological effects of HMO. Recently, approaches toward the production of defined human milk oligosaccharide structures using microbial, fermentative methods employing single, appropriately engineered microorganisms were introduced. Furthermore, galactose-containing hetero-oligosaccharides have attracted an increasing amount of attention because they are structurally more closely related to HMO. The synthesis of these novel oligosaccharides, which resemble the core of HMO, is of great interest for applications in the food industry. PMID:24571717

Active alignment/contact verification system

DOEpatents

Greenbaum, William M.

2000-01-01

A system involving an active (i.e. electrical) technique for the verification of: 1) close tolerance mechanical alignment between two component, and 2) electrical contact between mating through an elastomeric interface. For example, the two components may be an alumina carrier and a printed circuit board, two mating parts that are extremely small, high density parts and require alignment within a fraction of a mil, as well as a specified interface point of engagement between the parts. The system comprises pairs of conductive structures defined in the surfaces layers of the alumina carrier and the printed circuit board, for example. The first pair of conductive structures relate to item (1) above and permit alignment verification between mating parts. The second pair of conductive structures relate to item (2) above and permit verification of electrical contact between mating parts.

A Review of Structure Construction of Silk Fibroin Biomaterials from Single Structures to Multi-Level Structures.

PubMed

Qi, Yu; Wang, Hui; Wei, Kai; Yang, Ya; Zheng, Ru-Yue; Kim, Ick Soo; Zhang, Ke-Qin

2017-03-03

The biological performance of artificial biomaterials is closely related to their structure characteristics. Cell adhesion, migration, proliferation, and differentiation are all strongly affected by the different scale structures of biomaterials. Silk fibroin (SF), extracted mainly from silkworms, has become a popular biomaterial due to its excellent biocompatibility, exceptional mechanical properties, tunable degradation, ease of processing, and sufficient supply. As a material with excellent processability, SF can be processed into various forms with different structures, including particulate, fiber, film, and three-dimensional (3D) porous scaffolds. This review discusses and summarizes the various constructions of SF-based materials, from single structures to multi-level structures, and their applications. In combination with single structures, new techniques for creating special multi-level structures of SF-based materials, such as micropatterning and 3D-printing, are also briefly addressed.

The role of nonconserved residues of Archaeoglobus fulgidus ferritin on its unique structure and biophysical properties.

PubMed

Sana, Barindra; Johnson, Eric; Le Magueres, Pierre; Criswell, Angela; Cascio, Duilio; Lim, Sierin

2013-11-08

Archaeoglobus fulgidus ferritin (AfFtn) is the only tetracosameric ferritin known to form a tetrahedral cage, a structure that remains unique in structural biology. As a result of the tetrahedral (2-3) symmetry, four openings (∼45 Å in diameter) are formed in the cage. This open tetrahedral assembly contradicts the paradigm of a typical ferritin cage: a closed assembly having octahedral (4-3-2) symmetry. To investigate the molecular mechanism affecting this atypical assembly, amino acid residues Lys-150 and Arg-151 were replaced by alanine. The data presented here shed light on the role that these residues play in shaping the unique structural features and biophysical properties of the AfFtn. The x-ray crystal structure of the K150A/R151A mutant, solved at 2.1 Å resolution, indicates that replacement of these key residues flips a "symmetry switch." The engineered molecule no longer assembles with tetrahedral symmetry but forms a typical closed octahedral ferritin cage. Small angle x-ray scattering reveals that the overall shape and size of AfFtn and AfFtn-AA in solution are consistent with those observed in their respective crystal structures. Iron binding and release kinetics of the AfFtn and AfFtn-AA were investigated to assess the contribution of cage openings to the kinetics of iron oxidation, mineralization, or reductive iron release. Identical iron binding kinetics for AfFtn and AfFtn-AA suggest that Fe(2+) ions do not utilize the triangular pores for access to the catalytic site. In contrast, relatively slow reductive iron release was observed for the closed AfFtn-AA, demonstrating involvement of the large pores in the pathway for iron release.

Closed-form nonlinear frequency of flexoelectric nanobeams with surface and nonlocal effects under closed circuit electric field

NASA Astrophysics Data System (ADS)

Barati, Mohammad Reza

2018-02-01

Nonlocal and surface effects on nonlinear vibration characteristics of a flexoelectric nanobeams under magnetic field are examined. Eringen’s nonlocal elasticity as well as surface elasticity theories are employed to describe the size-dependency of the flexoelectric nanobeam. Also, flexoelectricity is an important size-dependent phenomena for piezoelectric structures at nanoscale, related to the strain gradient-electric polarization coupling. After the derivation of governing equation via Hamilton’s principle, Galerkin method is employed to satisfy boundary conditions. Also, analytical procedures are implemented to obtain the closed-form nonlinear frequency of flexoelectric nanobeam. It is showed that magnetic field intensity, flexoelectric parameter, nonlocal parameter, elastic foundation and applied voltage on the top surface of the nanobeam have great influences on nonlinear vibration frequency.

Roles of Communication Problems and Communication Strategies on Resident-Related Role Demand and Role Satisfaction.

PubMed

Savundranayagam, Marie Y; Lee, Christopher

2017-03-01

This study investigated the impact of dementia-related communication difficulties and communication strategies used by staff on resident-related indicators of role demand and role satisfaction. Formal/paid long-term care staff caregivers (N = 109) of residents with dementia completed questionnaires on dementia-related communication difficulties, communication strategies, role demand (ie, residents make unreasonable demands), and role satisfaction (measured by relationship closeness and influence over residents). Three types of communication strategies were included: (a) effective repair strategies, (b) completing actions by oneself, and (c) tuning out or ignoring the resident. Analyses using structural equation modeling revealed that communication problems were positively linked with role demand. Repair strategies were positively linked with relationship closeness and influence over residents. Completing actions by oneself was positively linked to role demand and influence over residents, whereas tuning out was negatively linked with influence over residents. The findings underscore that effective caregiver communication skills are essential in enhancing staff-resident relationships.

A close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria.

PubMed Central

Diffley, J F; Stillman, B

1991-01-01

ABF2 (ARS-binding factor 2), a small, basic DNA-binding protein that binds specifically to the autonomously replicating sequence ARS1, is located primarily in the mitochondria of the yeast Saccharomyces cerevisiae. The abundance of ABF2 and the phenotype of abf2- null mutants argue that this protein plays a key role in the structure, maintenance, and expression of the yeast mitochondrial genome. The predicted amino acid sequence of ABF2 is closely related to the high-mobility group proteins HMG1 and HMG2 from vertebrate cell nuclei and to several other DNA-binding proteins. Additionally, ABF2 and the other HMG-related proteins are related to a globular domain from the heat shock protein hsp70 family. ABF2 interacts with DNA both nonspecifically and in a specific manner within regulatory regions, suggesting a mechanism whereby it may aid in compacting the mitochondrial genome without interfering with expression. Images PMID:1881919

Conservative whole-organ scaling contrasts with highly labile suborgan scaling differences among compound eyes of closely related Formica ants.

PubMed

Perl, Craig D; Rossoni, Sergio; Niven, Jeremy E

2017-03-01

Static allometries determine how organ size scales in relation to body mass. The extent to which these allometric relationships are free to evolve, and how they differ among closely related species, has been debated extensively and remains unclear; changes in intercept appear common, but changes in slope are far rarer. Here, we compare the scaling relationships that govern the structure of compound eyes of four closely related ant species from the genus Formica . Comparison among these species revealed changes in intercept but not slope in the allometric scaling relationships governing eye area, facet number, and mean facet diameter. Moreover, the scaling between facet diameter and number was conserved across all four species. In contrast, facet diameters from distinct regions of the compound eye differed in both intercept and slope within a single species and when comparing homologous regions among species. Thus, even when species are conservative in the scaling of whole organs, they can differ substantially in regional scaling within organs. This, at least partly, explains how species can produce organs that adhere to genus wide scaling relationships while still being able to invest differentially in particular regions of organs to produce specific features that match their ecology.

Static high pressure studies on Nd and Sc

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

Akella, J.; Xu, J.; Smith, G.S.

1985-06-24

We have investigated the crystal structural transformations in neodymium and scandium up to 4.0 GPa pressure and at room temperature, in a diamond-anvil high pressure apparatus. Nd has a double hexagonal-close packed (dhcp) structure at ambient pressure and temperature. Then it transforms to a face-centered cubic (fcc) structure at 3.8 GPa, which further transforms to a triple hexagonal-close packed structure (thcp) at about 18.0 GPa. In scandium we observed only one transformation from the hexagonal-close packed (hcp) structure at room temperature to a tetragonal structure. This transformation occurs between 19.0 and 23.2 GPa pressure.

Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species

PubMed Central

Kastman, Erik K.; Kamelamela, Noelani; Norville, Josh W.; Cosetta, Casey M.; Dutton, Rachel J.

2016-01-01

ABSTRACT Many metagenomic sequencing studies have observed the presence of closely related bacterial species or genotypes in the same microbiome. Previous attempts to explain these patterns of microdiversity have focused on the abiotic environment, but few have considered how biotic interactions could drive patterns of microbiome diversity. We dissected the patterns, processes, and mechanisms shaping the ecological distributions of three closely related Staphylococcus species in cheese rind biofilms. Paradoxically, the most abundant species (S. equorum) is the slowest colonizer and weakest competitor based on growth and competition assays in the laboratory. Through in vitro community reconstructions, we determined that biotic interactions with neighboring fungi help resolve this paradox. Species-specific stimulation of the poor competitor by fungi of the genus Scopulariopsis allows S. equorum to dominate communities in vitro as it does in situ. Results of comparative genomic and transcriptomic experiments indicate that iron utilization pathways, including a homolog of the S. aureus staphyloferrin B siderophore operon pathway, are potential molecular mechanisms underlying Staphylococcus-Scopulariopsis interactions. Our integrated approach demonstrates that fungi can structure the ecological distributions of closely related bacterial species, and the data highlight the importance of bacterium-fungus interactions in attempts to design and manipulate microbiomes. PMID:27795388

A novel fluorescent aptasensor based on hairpin structure of complementary strand of aptamer and nanoparticles as a signal amplification approach for ultrasensitive detection of cocaine.

PubMed

Emrani, Ahmad Sarreshtehdar; Danesh, Noor Mohammad; Ramezani, Mohammad; Taghdisi, Seyed Mohammad; Abnous, Khalil

2016-05-15

Cocaine is one of the most commonly misused stimulant which could influence the central nervous system. In this study, a fluorescent aptamer-based sensor (aptasensor) was designed for sensitive and selective detection of cocaine, based on hairpin structure of complementary strand of aptamer (CS), target-induced release of aptamer (Apt) from CS and two kinds of nanoparticles, including silica nanoparticles (SNPs) coated with streptavidin and gold nanoparticles (AuNPs). The designed aptasensor acquires characteristics of AuNPs such as unique optical properties and large surface area, SNPs as amplifiers of fluorescence intensity, higher affinity of Apt toward its target relative to its CS, and finally the hairpin structure of CS that brings the fluorophore (FAM) to close proximity to the surface of SNPs. In the absence of cocaine, FAM is in close proximity to the surface of AuNPs, resulting in a weak fluorescence emission. In the presence of target, FAM comes to close proximity to the surface of SNPs because of the formation of hairpin structure of CS, leading to a very strong fluorescence emission. The fabricated fluorescent aptasensor exhibited a good selectivity toward cocaine with a limit of detection (LOD) as low as 209 pM. Moreover, the designed aptasensor was successfully utilized to detect cocaine in serum with a LOD as low as 293 pM. Copyright © 2015 Elsevier B.V. All rights reserved.

Shipping device for heater unit assembly

DOEpatents

Blaushild, Ronald M.; Abbott, Stephan L.; Miller, Phillip E.; Shaffer, Robert

1991-01-01

A shipping device for a heater unit assembly (23), the heater unit assembly (23) including a cylindrical wall (25) and a top plate (31) secured to the cylindrical wall (25) and having a flange portion which projects radially beyond the outer surface of the cylindrical wall (25), and the shipping device including: a cylindrical container (3) having a closed bottom (13); a support member (47) secured to the container (3) and having an inwardly directed flange for supporting the flange portion of the top plate (31); a supplemental supporting system (1) for positioning the heater unit assembly (23) in the container (3) at a spaced relation from the inner surface and bottom wall (13) of the container (3); a cover (15) for closing the top of the container (3); and a container supporting structure (5,7,8) supporting the container (3) in a manner to permit the container (3) to be moved, relative to the supporting structure (5,7,8 ), between a vertical position for loading and unloading the assembly (23) and a horizontal position for transport of the assembly (23). A seal (57) is interposed between the container (3) and the cover (15) for sealing the interior of the container (3) from the environment. An abutment member (41) is mounted on the container supporting structure (5,7,8) for supporting the container bottom (13), when the container (3) is in the vertical position, to prevent the container (3) from moving past the vertical position in the direction away from the horizontal position, and a retainer member (55) is secured within the cover (15) for retaining the assembly top plate (31) in contact with the support member (47) when the cover (15) closes the top of the container (3).

Design and implementation of a database for Brucella melitensis genome annotation.

PubMed

De Hertogh, Benoît; Lahlimi, Leïla; Lambert, Christophe; Letesson, Jean-Jacques; Depiereux, Eric

2008-03-18

The genome sequences of three Brucella biovars and of some species close to Brucella sp. have become available, leading to new relationship analysis. Moreover, the automatic genome annotation of the pathogenic bacteria Brucella melitensis has been manually corrected by a consortium of experts, leading to 899 modifications of start sites predictions among the 3198 open reading frames (ORFs) examined. This new annotation, coupled with the results of automatic annotation tools of the complete genome sequences of the B. melitensis genome (including BLASTs to 9 genomes close to Brucella), provides numerous data sets related to predicted functions, biochemical properties and phylogenic comparisons. To made these results available, alphaPAGe, a functional auto-updatable database of the corrected sequence genome of B. melitensis, has been built, using the entity-relationship (ER) approach and a multi-purpose database structure. A friendly graphical user interface has been designed, and users can carry out different kinds of information by three levels of queries: (1) the basic search use the classical keywords or sequence identifiers; (2) the original advanced search engine allows to combine (by using logical operators) numerous criteria: (a) keywords (textual comparison) related to the pCDS's function, family domains and cellular localization; (b) physico-chemical characteristics (numerical comparison) such as isoelectric point or molecular weight and structural criteria such as the nucleic length or the number of transmembrane helix (TMH); (c) similarity scores with Escherichia coli and 10 species phylogenetically close to B. melitensis; (3) complex queries can be performed by using a SQL field, which allows all queries respecting the database's structure. The database is publicly available through a Web server at the following url: http://www.fundp.ac.be/urbm/bioinfo/aPAGe.

Children's strategies to solving additive inverse problems: a preliminary analysis

NASA Astrophysics Data System (ADS)

Ding, Meixia; Auxter, Abbey E.

2017-03-01

Prior studies show that elementary school children generally "lack" formal understanding of inverse relations. This study goes beyond lack to explore what children might "have" in their existing conception. A total of 281 students, kindergarten to third grade, were recruited to respond to a questionnaire that involved both contextual and non-contextual tasks on inverse relations, requiring both computational and explanatory skills. Results showed that children demonstrated better performance in computation than explanation. However, many students' explanations indicated that they did not necessarily utilize inverse relations for computation. Rather, they appeared to possess partial understanding, as evidenced by their use of part-whole structure, which is a key to understanding inverse relations. A close inspection of children's solution strategies further revealed that the sophistication of children's conception of part-whole structure varied in representation use and unknown quantity recognition, which suggests rich opportunities to develop students' understanding of inverse relations in lower elementary classrooms.

Acetylcholinesterase of Rhipicephalus (Boophilus) microplus and Phlebotomus papatasi: Gene Identification, Expression, and Biochemical Properties of Recombinant Proteins

DTIC Science & Technology

2013-01-01

predicted amino acid sequences of the three encoded BmAChEs were no more closely related to one another than AChEs from different organisms and their...solely on nucleotide and amino acid sequence similarity; however, the cholinesterase gene family contains a number of related enzymes and structural...acetylcholinesterase of P. papatasi was cloned, sequenced , and expressed in the baculo- virus system to generate a recombinant enzyme for biochemical

Macroinformational analysis of conditions for controllability of space-vehicle orbit

NASA Astrophysics Data System (ADS)

Glazov, B. I.

2011-12-01

The general axiomatics of information measures for the macro analysis of relations of an information-cybernetic system in the control is introduced. The general structure of a semantically marked graph of open and closed relations of an information-cybernetic system between the participants in the environment, as well as thenecessary axiomatic and technological information-cybernetic system conditions of controllability and observability of objects, for the case of a space vehicle in orbit, are justified.

Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species.

PubMed

Kastman, Erik K; Kamelamela, Noelani; Norville, Josh W; Cosetta, Casey M; Dutton, Rachel J; Wolfe, Benjamin E

2016-10-18

Many metagenomic sequencing studies have observed the presence of closely related bacterial species or genotypes in the same microbiome. Previous attempts to explain these patterns of microdiversity have focused on the abiotic environment, but few have considered how biotic interactions could drive patterns of microbiome diversity. We dissected the patterns, processes, and mechanisms shaping the ecological distributions of three closely related Staphylococcus species in cheese rind biofilms. Paradoxically, the most abundant species (S. equorum) is the slowest colonizer and weakest competitor based on growth and competition assays in the laboratory. Through in vitro community reconstructions, we determined that biotic interactions with neighboring fungi help resolve this paradox. Species-specific stimulation of the poor competitor by fungi of the genus Scopulariopsis allows S. equorum to dominate communities in vitro as it does in situ Results of comparative genomic and transcriptomic experiments indicate that iron utilization pathways, including a homolog of the S. aureus staphyloferrin B siderophore operon pathway, are potential molecular mechanisms underlying Staphylococcus-Scopulariopsis interactions. Our integrated approach demonstrates that fungi can structure the ecological distributions of closely related bacterial species, and the data highlight the importance of bacterium-fungus interactions in attempts to design and manipulate microbiomes. Decades of culture-based studies and more recent metagenomic studies have demonstrated that bacterial species in agriculture, medicine, industry, and nature are unevenly distributed across time and space. The ecological processes and molecular mechanisms that shape these distributions are not well understood because it is challenging to connect in situ patterns of diversity with mechanistic in vitro studies in the laboratory. Using tractable cheese rind biofilms and a focus on coagulase-negative staphylococcus (CNS) species, we demonstrate that fungi can mediate the ecological distributions of closely related bacterial species. One of the Staphylococcus species studied, S. saprophyticus, is a common cause of urinary tract infections. By identifying processes that control the abundance of undesirable CNS species, cheese producers will have more precise control on the safety and quality of their products. More generally, Staphylococcus species frequently co-occur with fungi in mammalian microbiomes, and similar bacterium-fungus interactions may structure bacterial diversity in these systems. Copyright © 2016 Kastman et al.

Temporal and geographic patterns of kinship structure in common dolphins (Delphinus delphis) suggest site fidelity and female-biased long-distance dispersal.

PubMed

Ball, Laura; Shreves, Kypher; Pilot, Małgorzata; Moura, André E

2017-01-01

Social structure plays a crucial role in determining a species' dispersal patterns and genetic structure. Cetaceans show a diversity of social and mating systems, but their effects on dispersal and genetic structure are not well known, in part because of technical difficulties in obtaining robust observational data. Here, we combine genetic profiling and GIS analysis to identify patterns of kin distribution over time and space, to infer mating structure and dispersal patterns in short-beaked common dolphins ( Delphinus delphis ). This species is highly social, and exhibits weak spatial genetic structure in the Northeast Atlantic and Mediterranean Sea, thought to result from fluid social structure and low levels of site fidelity. We found that although sampled groups were not composed of closely related individuals, close kin were frequently found in the same geographic location over several years. Our results suggest that common dolphin exhibits some level of site fidelity, which could be explained by foraging for temporally varying prey resource in areas familiar to individuals. Dispersal from natal area likely involves long-distance movements of females, as males are found more frequently than females in the same locations as their close kin. Long-distance dispersal may explain the near panmixia observed in this species. By analysing individuals sampled in the same geographic location over multiple years, we avoid caveats associated with divergence-based methods of inferring sex-biased dispersal. We thus provide a unique perspective on this species' social structure and dispersal behaviour, and how it relates to the observed low levels of population genetic structure in European waters. Movement patterns and social interactions are aspects of wild animal's behaviour important for understanding their ecology. However, tracking these behaviours directly can be very challenging in wide-ranging species such as whales and dolphins. In this study, we used genetic information to detect how patterns of kin associations change in space and time, to infer aspects of movement and social structure. We identified previously unknown site fidelity, and suggested that dispersal usually involves females, travelling long distances from the natal area. Our data analysis strategy overcomes known limitations of previously used genetic inference methods, and provides a new approach to identify differences in dispersal between the sexes, which contribute to better understanding of the species' behaviour and ecology. In this case, we suggest that females are more likely to disperse than males, a pattern unusual amongst mammals.

Structural determinants of hydration, mechanics and fluid flow in freeze-dried collagen scaffolds.

PubMed

Offeddu, G S; Ashworth, J C; Cameron, R E; Oyen, M L

2016-09-01

Freeze-dried scaffolds provide regeneration templates for a wide range of tissues, due to their flexibility in physical and biological properties. Control of structure is crucial for tuning such properties, and therefore scaffold functionality. However, the common approach of modeling these scaffolds as open-cell foams does not fully account for their structural complexity. Here, the validity of the open-cell model is examined across a range of physical characteristics, rigorously linking morphology to hydration and mechanical properties. Collagen scaffolds with systematic changes in relative density were characterized using Scanning Electron Microscopy, X-ray Micro-Computed Tomography and spherical indentation analyzed in a time-dependent poroelastic framework. Morphologically, all scaffolds were mid-way between the open- and closed-cell models, approaching the closed-cell model as relative density increased. Although pore size remained constant, transport pathway diameter decreased. Larger collagen fractions also produced greater volume swelling on hydration, although the change in pore diameter was constant, and relatively small at ∼6%. Mechanically, the dry and hydrated scaffold moduli varied quadratically with relative density, as expected of open-cell materials. However, the increasing pore wall closure was found to determine the time-dependent nature of the hydrated scaffold response, with a decrease in permeability producing increasingly elastic rather than viscoelastic behavior. These results demonstrate that characterizing the deviation from the open-cell model is vital to gain a full understanding of scaffold biophysical properties, and provide a template for structural studies of other freeze-dried biomaterials. Freeze-dried collagen sponges are three-dimensional microporous scaffolds that have been used for a number of exploratory tissue engineering applications. The characterization of the structure-properties relationships of these scaffolds is necessary to understand their biophysical behavior in vivo. In this work, the relationship between morphology and physical properties in the dry and hydrated states was investigated across a range of solid concentrations in the scaffolds. The quantitative results provided can aid the design of scaffolds with a target trade-off between mechanical properties and structural features important for their biological activity. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Microbiome analysis and confocal microscopy of used kitchen sponges reveal massive colonization by Acinetobacter, Moraxella and Chryseobacterium species.

PubMed

Cardinale, Massimiliano; Kaiser, Dominik; Lueders, Tillmann; Schnell, Sylvia; Egert, Markus

2017-07-19

The built environment (BE) and in particular kitchen environments harbor a remarkable microbial diversity, including pathogens. We analyzed the bacterial microbiome of used kitchen sponges by 454-pyrosequencing of 16S rRNA genes and fluorescence in situ hybridization coupled with confocal laser scanning microscopy (FISH-CLSM). Pyrosequencing showed a relative dominance of Gammaproteobacteria within the sponge microbiota. Five of the ten most abundant OTUs were closely related to risk group 2 (RG2) species, previously detected in the BE and kitchen microbiome. Regular cleaning of sponges, indicated by their users, significantly affected the microbiome structure. Two of the ten dominant OTUs, closely related to the RG2-species Chryseobacterium hominis and Moraxella osloensis, showed significantly greater proportions in regularly sanitized sponges, thereby questioning such sanitation methods in a long term perspective. FISH-CLSM showed an ubiquitous distribution of bacteria within the sponge tissue, concentrating in internal cavities and on sponge surfaces, where biofilm-like structures occurred. Image analysis showed local densities of up to 5.4 * 10 10 cells per cm 3 , and confirmed the dominance of Gammaproteobacteria. Our study stresses and visualizes the role of kitchen sponges as microbiological hot spots in the BE, with the capability to collect and spread bacteria with a probable pathogenic potential.

A comprehensive physiologically based pharmacokinetic ...

EPA Pesticide Factsheets

Published physiologically based pharmacokinetic (PBPK) models from peer-reviewed articles are often well-parameterized, thoroughly-vetted, and can be utilized as excellent resources for the construction of models pertaining to related chemicals. Specifically, chemical-specific parameters and in vivo pharmacokinetic data used to calibrate these published models can act as valuable starting points for model development of new chemicals with similar molecular structures. A knowledgebase for published PBPK-related articles was compiled to support PBPK model construction for new chemicals based on their close analogues within the knowledgebase, and a web-based interface was developed to allow users to query those close analogues. A list of 689 unique chemicals and their corresponding 1751 articles was created after analysis of 2,245 PBPK-related articles. For each model, the PMID, chemical name, major metabolites, species, gender, life stages and tissue compartments were extracted from the published articles. PaDEL-Descriptor, a Chemistry Development Kit based software, was used to calculate molecular fingerprints. Tanimoto index was implemented in the user interface as measurement of structural similarity. The utility of the PBPK knowledgebase and web-based user interface was demonstrated using two case studies with ethylbenzene and gefitinib. Our PBPK knowledgebase is a novel tool for ranking chemicals based on similarities to other chemicals associated with existi

Structural and electronic properties for atomic clusters

NASA Astrophysics Data System (ADS)

Sun, Yan

We have studied the structural and electronic properties for different groups of atomic clusters by doing a global search on the potential energy surface using the Taboo Search in Descriptors Space (TSDS) method and calculating the energies with Kohn-Sham Density Functional Theory (KS-DFT). Our goal was to find the structural and electronic principles for predicting the structure and stability of clusters. For Ben (n = 3--20), we have found that the evolution of geometric and electronic properties with size reflects a change in the nature of the bonding from van der Waals to metallic and then bulk-like. The cluster sizes with extra stability agree well with the predictions of the jellium model. In the 4d series of transition metal (TM) clusters, as the d-type bonding becomes more important, the preferred geometric structure changes from icosahedral (Y, Zr), to distorted compact structures (Nb, Mo), and FCC or simple cubic crystal fragments (Tc, Ru, Rh) due to the localized nature of the d-type orbital. Analysis of relative isomer energies and their electronic density of states suggest that these clusters tend to follow a maximum hardness principle (MHP). For A4B12 clusters (A is divalent, B is monovalent), we found unusually large (on average 1.95 eV) HOMO-LUMO gap values. This shows the extra stability at an electronic closed shell (20 electrons) predicted by the jellium model. The importance of symmetry, closed electronic and ionic shells in stability is shown by the relative stability of homotops of Mg4Ag12 which also provides support for the hypothesis that clusters that satisfy more than one stability criterion ("double magic") should be particularly stable.

THE EXCEPTIONAL CHILD IN THE FAMILY, HELPING PARENTS OF EXCEPTIONAL CHILDREN.

ERIC Educational Resources Information Center

ROSS, ALAN O.

THE BOOK IS CONCERNED WITH THE ADJUSTMENTS PARENTS MAKE WHEN AN EXCEPTIONAL CHILD IS INCLUDED IN THE FAMILY STRUCTURE. THE DYNAMICS OF FAMILY INTERACTION ARE DESCRIBED. THE FAMILY AS A SOCIAL SYSTEM IS DEFINED, AND ROLES OF FAMILY MEMBERS ARE DISCUSSED. PARENTAL ATTITUDES AND BEHAVIORS ARE PRESENTED AS CLOSELY RELATED TO ADJUSTMENT OF THE…

Open-Ended Cases in Agroecology: Farming and Food Systems in the Nordic Region and the US Midwest

ERIC Educational Resources Information Center

Francis, Charles; King, James; Lieblein, Geir; Breland, Tor Arvid; Salomonsson, Lennart; Sriskandarajah, Nadarajah; Porter, Paul; Wiedenhoeft, Mary

2009-01-01

Our aim is to describe open-ended case studies for learning real-life problem solving skills, and relate this approach to conventional, closed-ended decision case studies. Teaching methods are open-ended cases in agroecology, an alternative to traditional strategies that lead students through prepared materials and structured discussions to…

Patterns of forest phylogenetic community structure across the United States and their possible forest health implications

Treesearch

Kevin M. Potter; Frank H. Koch

2014-01-01

The analysis of phylogenetic relationships among co-occurring tree species offers insights into the ecological organization of forest communities from an evolutionary perspective and, when employed regionally across thousands of plots, can assist in forest health assessment. Phylogenetic clustering of species, when species are more closely related than expected by...

Where Are the Quantum Jumps in Quality Assurance? Developments of a Decade of Research on a Heavy Particle.

ERIC Educational Resources Information Center

Westerheijden, Don F.

2000-01-01

Reviews the literature on developments in quality assurance in European higher education over the last decade. Applies the metaphor of sub-atomic structure to order the literature, moving from publications closely related to the practice of quality assurance methods to more theoretical publications. Identifies some seminal publications as…

Foraging ecology of pileated woodpeckers in coastal forests of Washington.

Treesearch

C.M. Raley; K.B. Aubry

2006-01-01

Providing habitat for pileated woodpeckers in the Pacific Northwest has been a key component of forest management strategies for over 20 years. We investigated the diet of pileated woodpeckers, and selection by birds of both individual structure and site characteristics for foraging. Birds foraged amost exclusively in closed-canopy habitats and selected relatively tall...

Shattuckite and plancheite: A crystal chemical study

USGS Publications Warehouse

Evans, Howard T.; Mrose, Mary E.

1966-01-01

The orthorhombic crystal structures of shattuckite, Cu5( SiO3)4(OH)2 and planchétite, Cu8(Si4011)2(OH)4 H2O, have been solved. Shattuckite contains silicate chains similar to pyroxene in a complex association with copper atoms, while the closely related planchéite contains silicate chains similar to amphibole.

Enhanced Born Charge and Proximity to Ferroelectricity in Thallium Halides

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

Du, Mao-Hua; Singh, David J

2010-01-01

Electronic structure and lattice dynamics calculations on thallium halides show that the Born effective charges in these compounds are more than twice larger than the nominal ionic charges. This is a result of cross-band-gap hybridization between Tl-p and halogen-p states. The large Born charges cause giant splitting between longitudinal and transverse optic phonon modes, bringing the lattice close to ferroelectric instability. Our calculations indeed show spontaneous lattice polarization upon lattice expansion starting at 2%. It is remarkable that the apparently ionic thallium halides with a simple cubic CsCl structure and large differences in electronegativity between cations and anions can bemore » very close to ferroelectricity. This can lead to effective screening of defects and impurities that would otherwise be strong carrier traps and may therefore contribute to the relatively good carrier transport properties in TlBr radiation detectors.« less

Enhanced Born charge and proximity to ferroelectricity in thallium halides

NASA Astrophysics Data System (ADS)

Du, Mao-Hua; Singh, David J.

2010-04-01

Electronic-structure and lattice-dynamics calculations on thallium halides show that the Born effective charges in these compounds are more than twice larger than the nominal ionic charges. This is a result of cross-band-gap hybridization between Tlp and halogen- p states. The large Born charges cause giant splitting between longitudinal and transverse-optic phonon modes, bringing the lattice close to ferroelectric instability. Our calculations indeed show that cubic TlBr develops ferroelectric instabilities upon lattice expansion starting at 2%. It is remarkable that the apparently ionic thallium halides with a simple cubic CsCl structure and large differences in electronegativity between cations and anions can be very close to ferroelectricity. This can lead to effective screening of defects and impurities that would otherwise be strong carrier traps and may therefore contribute to the relatively good carrier transport properties in TlBr radiation detectors.

Nanoparticles of CdI 2 with closed cage structures obtained via electron-beam irradiation

NASA Astrophysics Data System (ADS)

Sallacan, N.; Popovitz-Biro, R.; Tenne, R.

2003-06-01

Nanoparticles of various layered compounds were shown to form closed cage or nanotubular structures, which were designated as inorganic fullerene-like ( IF) materials. In particular, closed cage structures and nanotubes were synthesized from NiCl 2 and CdCl 2 in the past. In the present work IF-CdI 2 nanoparticles were synthesized by electron-beam irradiation of the source powder leading to evaporation and subsequent recrystallization into closed nanoparticles with a non-hollow core. This process created polyhedral nanoparticles with hexagonal or elongated rectangular characters. Consistent with previous observations, this study shows that the seamless structure of the IF materials can stabilize phases, which are otherwise unstable under the electron-beam irradiation.

Structural studies of the polysaccharides from the lipopolysaccharides of Azospirillum brasilense Sp246 and SpBr14.

PubMed

Sigida, Elena N; Fedonenko, Yuliya P; Shashkov, Alexander S; Grinev, Vyacheslav S; Zdorovenko, Evelina L; Konnova, Svetlana A; Ignatov, Vladimir V; Knirel, Yuriy A

2014-10-29

Lipopolysaccharides from closely related Azospirillum brasilense strains, Sp246 and SpBr14, were obtained by phenol-water extraction. Mild acid hydrolysis of the lipopolysaccharides followed by GPC on Sephadex G-50 resulted in polysaccharide mixtures. On the basis of sugar and methylation analyses, Smith degradation and (1)H and (13)C NMR spectroscopy data, it was concluded that both bacteria possess the same two distinct polysaccharides having structures 1 and 2: [structure: see text]. Structure 1 has been reported earlier for a polysaccharide of A. brasilense 54 [Fedonenko et al., 2011] whereas to our knowledge structure 2 has not been hitherto found in bacterial polysaccharides. Copyright © 2014 Elsevier Ltd. All rights reserved.

User document for computer programs for ring-stiffened shells of revolution

NASA Technical Reports Server (NTRS)

Cohen, G. A.

1973-01-01

A user manual and related program documentation is presented for six compatible computer programs for structural analysis of axisymmetric shell structures. The programs apply to a common structural model but analyze different modes of structural response. In particular, they are: (1) Linear static response under asymmetric loads; (2) Buckling of linear states under asymmetric loads; (3) Nonlinear static response under axisymmetric loads; (4) Buckling nonlinear states under axisymmetric (5) Imperfection sensitivity of buckling modes under axisymmetric loads; and (6) Vibrations about nonlinear states under axisymmetric loads. These programs treat branched shells of revolution with an arbitrary arrangement of a large number of open branches but with at most one closed branch.

Magnetic structure of Ba (TiO ) Cu4(PO4)4 probed using spherical neutron polarimetry

NASA Astrophysics Data System (ADS)

Babkevich, P.; Testa, L.; Kimura, K.; Kimura, T.; Tucker, G. S.; Roessli, B.; Rønnow, H. M.

2017-12-01

The antiferromagnetic compound Ba (TiO ) Cu4(PO4)4 contains square cupola of corner-sharing CuO4 plaquettes, which were proposed to form effective quadrupolar order. To identify the magnetic structure, we have performed spherical neutron polarimetry measurements. Based on symmetry analysis and careful measurements, we conclude that the orientation of the Cu2 + spins form a noncollinear in-out structure with spins approximately perpendicular to the CuO4 motif. Strong Dzyaloshinskii-Moriya interaction naturally lends itself to explain this phenomenon. The identification of the ground-state magnetic structure should serve well for future theoretical and experimental studies into this and closely related compounds.

Architectural design influences the diversity and structure of the built environment microbiome

PubMed Central

Kembel, Steven W; Jones, Evan; Kline, Jeff; Northcutt, Dale; Stenson, Jason; Womack, Ann M; Bohannan, Brendan JM; Brown, G Z; Green, Jessica L

2012-01-01

Buildings are complex ecosystems that house trillions of microorganisms interacting with each other, with humans and with their environment. Understanding the ecological and evolutionary processes that determine the diversity and composition of the built environment microbiome—the community of microorganisms that live indoors—is important for understanding the relationship between building design, biodiversity and human health. In this study, we used high-throughput sequencing of the bacterial 16S rRNA gene to quantify relationships between building attributes and airborne bacterial communities at a health-care facility. We quantified airborne bacterial community structure and environmental conditions in patient rooms exposed to mechanical or window ventilation and in outdoor air. The phylogenetic diversity of airborne bacterial communities was lower indoors than outdoors, and mechanically ventilated rooms contained less diverse microbial communities than did window-ventilated rooms. Bacterial communities in indoor environments contained many taxa that are absent or rare outdoors, including taxa closely related to potential human pathogens. Building attributes, specifically the source of ventilation air, airflow rates, relative humidity and temperature, were correlated with the diversity and composition of indoor bacterial communities. The relative abundance of bacteria closely related to human pathogens was higher indoors than outdoors, and higher in rooms with lower airflow rates and lower relative humidity. The observed relationship between building design and airborne bacterial diversity suggests that we can manage indoor environments, altering through building design and operation the community of microbial species that potentially colonize the human microbiome during our time indoors. PMID:22278670

31 CFR 515.339 - Close relative.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false Close relative. 515.339 Section 515... § 515.339 Close relative. (a) For purposes of this part, the term close relative used with respect to.... Your mother's first cousin is your close relative for purposes of this part, because you are both no...

A Review of Structure Construction of Silk Fibroin Biomaterials from Single Structures to Multi-Level Structures

PubMed Central

Qi, Yu; Wang, Hui; Wei, Kai; Yang, Ya; Zheng, Ru-Yue; Kim, Ick Soo; Zhang, Ke-Qin

2017-01-01

The biological performance of artificial biomaterials is closely related to their structure characteristics. Cell adhesion, migration, proliferation, and differentiation are all strongly affected by the different scale structures of biomaterials. Silk fibroin (SF), extracted mainly from silkworms, has become a popular biomaterial due to its excellent biocompatibility, exceptional mechanical properties, tunable degradation, ease of processing, and sufficient supply. As a material with excellent processability, SF can be processed into various forms with different structures, including particulate, fiber, film, and three-dimensional (3D) porous scaffolds. This review discusses and summarizes the various constructions of SF-based materials, from single structures to multi-level structures, and their applications. In combination with single structures, new techniques for creating special multi-level structures of SF-based materials, such as micropatterning and 3D-printing, are also briefly addressed. PMID:28273799

Numerical model updating technique for structures using firefly algorithm

NASA Astrophysics Data System (ADS)

Sai Kubair, K.; Mohan, S. C.

2018-03-01

Numerical model updating is a technique used for updating the existing experimental models for any structures related to civil, mechanical, automobiles, marine, aerospace engineering, etc. The basic concept behind this technique is updating the numerical models to closely match with experimental data obtained from real or prototype test structures. The present work involves the development of numerical model using MATLAB as a computational tool and with mathematical equations that define the experimental model. Firefly algorithm is used as an optimization tool in this study. In this updating process a response parameter of the structure has to be chosen, which helps to correlate the numerical model developed with the experimental results obtained. The variables for the updating can be either material or geometrical properties of the model or both. In this study, to verify the proposed technique, a cantilever beam is analyzed for its tip deflection and a space frame has been analyzed for its natural frequencies. Both the models are updated with their respective response values obtained from experimental results. The numerical results after updating show that there is a close relationship that can be brought between the experimental and the numerical models.

Toward elucidating the heat activation mechanism of the TRPV1 channel gating by molecular dynamics simulation

PubMed Central

Wen, Han; Qin, Feng; Zheng, Wenjun

2016-01-01

As a key cellular sensor, the TRPV1 cation channel undergoes a gating transition from a closed state to an open state in response to various physical and chemical stimuli including noxious heat. Despite years of study, the heat activation mechanism of TRPV1 gating remains enigmatic at the molecular level. Toward elucidating the structural and energetic basis of TRPV1 gating, we have performed molecular dynamics (MD) simulations (with cumulative simulation time of 3 μs), starting from the high-resolution closed and open structures of TRPV1 solved by cryo-electron microscopy. In the closed-state simulations at 30°C, we observed a stably closed channel constricted at the lower gate (near residue I679), while the upper gate (near residues G643 and M644) is dynamic and undergoes flickery opening/closing. In the open-state simulations at 60°C, we found higher conformational variation consistent with a large entropy increase required for the heat activation, and both the lower and upper gates are dynamic with transient opening/closing. Through ensemble-based structural analyses of the closed state vs. the open state, we revealed pronounced closed-to-open conformational changes involving the membrane proximal domain (MPD) linker, the outer pore, and the TRP helix, which are accompanied by breaking/forming of a network of closed/open-state specific hydrogen bonds. By comparing the closed-state simulations at 30°C and 60°C, we observed heat-activated conformational changes in the MPD linker, the outer pore, and the TRP helix that resemble the closed-to-open conformational changes, along with partial formation of the open-state specific hydrogen bonds. Some of the residues involved in the above key hydrogen bonds were validated by previous mutational studies. Taken together, our MD simulations have offered rich structural and dynamic details beyond the static structures of TRPV1, and promising targets for future mutagenesis and functional studies of the TRPV1 channel. PMID:27699868

AAPI college students' willingness to seek counseling: the role of culture, stigma, and attitudes.

PubMed

Choi, Na-Yeun; Miller, Matthew J

2014-07-01

This study tested 4 theoretically and empirically derived structural equation models of Asian, Asian American, and Pacific Islanders' willingness to seek counseling with a sample of 278 college students. The models represented competing hypotheses regarding the manner in which Asian cultural values, European American cultural values, public stigma, stigma by close others, self-stigma, and attitudes toward seeking professional help related to willingness to seek counseling. We found that Asian and European American cultural values differentially related to willingness to seek counseling indirectly through specific indirect pathways (public stigma, stigma by close others, self-stigma, and attitudes toward seeking professional help). Our results also showed that the magnitude of model-implied relationships did not vary as a function of generational status. Study limitations, future directions for research, and implications for counseling are discussed.

Data characterizing the chloroplast genomes of extinct and endangered Hawaiian endemic mints (Lamiaceae) and their close relatives.

PubMed

Welch, Andreanna J; Collins, Katherine; Ratan, Aakrosh; Drautz-Moses, Daniela I; Schuster, Stephan C; Lindqvist, Charlotte

2016-06-01

These data are presented in support of a plastid phylogenomic analysis of the recent radiation of the Hawaiian endemic mints (Lamiaceae), and their close relatives in the genus Stachys, "The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)" [1]. Here we describe the chloroplast genome sequences for 12 mint taxa. Data presented include summaries of gene content and length for these taxa, structural comparison of the mint chloroplast genomes with published sequences from other species in the order Lamiales, and comparisons of variability among three Hawaiian taxa vs. three outgroup taxa. Finally, we provide a list of 108 primer pairs targeting the most variable regions within this group and designed specifically for amplification of DNA extracted from degraded herbarium material.

The College Experience and Its Effects on Family Closeness and Power.

ERIC Educational Resources Information Center

Grant, Jo Anna; Folwell, Annette L.; Holder, John; Layne, Jill Cole; Garrison, Joel; Wilson, Andria; Bain, Lisa

This study examined the differences in family closeness and power structure between first semester college freshmen and upperclassmen. Fifty-two freshmen and fifty-four upperclassmen completed the Family Systems Test (Gehring & Feldman, 1988) to indicate the closeness and power structure in their immediate families. Aspen-Welch t-tests were used…

Electronic Subband Reconfiguration in a d0-Perovskite Induced by Strain-Driven Structural Transformations

NASA Astrophysics Data System (ADS)

Laukhin, V.; Copie, O.; Rozenberg, M. J.; Weht, R.; Bouzehouane, K.; Reyren, N.; Jacquet, E.; Bibes, M.; Barthélémy, A.; Herranz, G.

2012-11-01

It is well known that transport in lightly n-doped SrTiO3 involves light and heavy electron bands. We have found that upon application of moderate quasi-isotropic pressures, the relative positions of these subbands are changed by a few meV and, eventually, a band inversion occurs at ˜1kbar. Such effects are, however, suppressed in the closely related KTaO3 perovskite. We show that the extremely subtle electronic reconfiguration in SrTiO3 is triggered by strain-induced structural transformations that are accompanied by remarkable mobility enhancements up to about Δμ/μ≈300%. Our results provide a microscopic rationale for the recently discovered transport enhancement under strain and underscore the role of the internal structural degrees of freedom in the modulation of the perovskite electronic properties.

Analysis of network clustering behavior of the Chinese stock market

NASA Astrophysics Data System (ADS)

Chen, Huan; Mai, Yong; Li, Sai-Ping

2014-11-01

Random Matrix Theory (RMT) and the decomposition of correlation matrix method are employed to analyze spatial structure of stocks interactions and collective behavior in the Shanghai and Shenzhen stock markets in China. The result shows that there exists prominent sector structures, with subsectors including the Real Estate (RE), Commercial Banks (CB), Pharmaceuticals (PH), Distillers&Vintners (DV) and Steel (ST) industries. Furthermore, the RE and CB subsectors are mostly anti-correlated. We further study the temporal behavior of the dataset and find that while the sector structures are relatively stable from 2007 through 2013, the correlation between the real estate and commercial bank stocks shows large variations. By employing the ensemble empirical mode decomposition (EEMD) method, we show that this anti-correlation behavior is closely related to the monetary and austerity policies of the Chinese government during the period of study.

Breakfast frequency among adolescents: associations with measures of family functioning.

PubMed

Pedersen, Trine Pagh; Holstein, Bjørn E; Damsgaard, Mogens Trab; Rasmussen, Mette

2016-06-01

To investigate (i) associations between adolescents' frequency of breakfast and family functioning (close relations to parents, quality of family communication and family support) and (ii) if any observed associations between breakfast frequency and family functioning vary by sociodemographic factors. School-based cross-sectional study. Students completed a web-based questionnaire. Associations were estimated by multilevel multivariate logistic regression. Danish arm of the Health Behaviour in School-aged Children study, 2014. Adolescents aged 13 and 15 years (n 3054) from a random sample of forty-one schools. Nearly one-quarter of the adolescents had low breakfast frequency. Low breakfast frequency was associated with low family functioning measured by three dimensions. The OR (95 % CI) of low breakfast frequency was 1·81 (1·40, 2·33) for adolescents who reported no close relations to parents, 2·28 (1·61, 3·22) for adolescents who reported low level of quality of family communication and 2·09 (1·39, 3·15) for adolescents who reported low level of family support. Joint effect analyses suggested that the odds of low breakfast frequency among adolescents with low family functioning compared with high family functioning were highest among adolescents being girls, immigrants and living in other than a traditional family structure. Low breakfast frequency was associated with low family functioning measured by close relations to parents, quality of family communication and family support. Further, analyses suggested that the associations were more pronounced among girls, immigrants and adolescents from other family structure than traditional. The study highlights the importance of the family setting in promoting regular breakfast frequency among adolescents.

Prognosis of Long-Term Load-Bearing Capability in Aerospace Structures: Quantification of Microstructurally Short Crack Growth

DTIC Science & Technology

2013-07-31

and a Voce -Kocks (Kocks 1976; Voce 1955) relation, the first and second terms in Equation 4.3, respectively. Ho and Go in Equation 4.3 are rate...gradient of the plastic deformation gradient, accommodating the evolution of slip close to twin boundaries. It is noteworthy that the Voce -Kocks relation...1956). “The origin of fatigue fracture in copper.” Philosophical Magazine, 1(2), 113–126. Voce , E. (1955). “A practical strain-hardening function

The magnetopause at 5.2 R/E/ on August 4, 1972 - Magnetopause shape and structure

NASA Technical Reports Server (NTRS)

Kaufmann, R. L.; Cahill, L. J., Jr.

1977-01-01

The relatively large magnitude magnetopause field observed in several crossings associated with the ATS 5 and Explorer 45 satellites on August 4, 1972, is used to examine the structure of the magnetopause. The discussion covers magnetopause normals and their intepretation with respect to the shape of the magnetopause and to waves propagating in the magnetopause; magnetopause structure in terms of the field changes observed during magnetopause passages and of the associated magnetopause electric currents interred from the observations; and comparison of the observations with theoretical properties of open and close magnetopause models. Features necessary for comparison of magnetometer observations with pertinent theories are highlighted.

Nambu sigma model and effective membrane actions

NASA Astrophysics Data System (ADS)

Jurčo, Branislav; Schupp, Peter

2012-07-01

We propose an effective action for a p‧-brane with open p-branes ending on it. The action has dual descriptions similar to the commutative and non-commutative ones of the DBI action for D-branes and open strings. The Poisson structure governing the non-commutativity of the D-brane is replaced by a Nambu structure and the open-closed string relations are generalized to the case of p-branes utilizing a novel Nambu sigma model description of p-branes. In the case of an M5-brane our action interpolates between M5-actions already proposed in the literature and matrix-model like actions involving Nambu structures.

Structure Analyses of Highly Symmetric Superstructures Formed by Rodlike Mesogen

NASA Astrophysics Data System (ADS)

Saito, Kazuya; Kutsumizu, Shoichi

Process of structure determination of liquid-crystalline superstructures formed in a mesogenic series, bis(n-alkoxybenzoyl)hydrazine[BABH(n) ; n, the number of carbon atoms in the alkoxy group], is described. The chain-length (n) dependence of relative diffraction intensities from the Ia3d phase resolves the phase problem, leading to the structural description that the molecular centers are on the rods forming two interpenetrating jungle gyms. Theoretical consideration on the stability of superstructures and systematic MEM analysis reveal the coexistence of two aggregation modes (rods forming an extending jungle gym and closed sheets forming spherical shells) for the Im3m phase.

Gradient-driven flux-tube simulations of ion temperature gradient turbulence close to the non-linear threshold

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

Peeters, A. G.; Rath, F.; Buchholz, R.

2016-08-15

It is shown that Ion Temperature Gradient turbulence close to the threshold exhibits a long time behaviour, with smaller heat fluxes at later times. This reduction is connected with the slow growth of long wave length zonal flows, and consequently, the numerical dissipation on these flows must be sufficiently small. Close to the nonlinear threshold for turbulence generation, a relatively small dissipation can maintain a turbulent state with a sizeable heat flux, through the damping of the zonal flow. Lowering the dissipation causes the turbulence, for temperature gradients close to the threshold, to be subdued. The heat flux then doesmore » not go smoothly to zero when the threshold is approached from above. Rather, a finite minimum heat flux is obtained below which no fully developed turbulent state exists. The threshold value of the temperature gradient length at which this finite heat flux is obtained is up to 30% larger compared with the threshold value obtained by extrapolating the heat flux to zero, and the cyclone base case is found to be nonlinearly stable. Transport is subdued when a fully developed staircase structure in the E × B shearing rate forms. Just above the threshold, an incomplete staircase develops, and transport is mediated by avalanche structures which propagate through the marginally stable regions.« less

[A phylogenetic analysis of plant communities of Teberda Biosphere Reserve].

PubMed

Shulakov, A A; Egorov, A V; Onipchenko, V G

2016-01-01

Phylogenetic analysis of communities is based on the comparison of distances on the phylogenetic tree between species of a community under study and those distances in random samples taken out of local flora. It makes it possible to determine to what extent a community composition is formed by more closely related species (i.e., "clustered") or, on the opposite, it is more even and includes species that are less related with each other. The first case is usually interpreted as a result of strong influence caused by abiotic factors, due to which species with similar ecology, a priori more closely related, would remain: In the second case, biotic factors, such as competition, may come to the fore and lead to forming a community out of distant clades due to divergence of their ecological niches: The aim of this' study Was Ad explore the phylogenetic structure in communities of the northwestern Caucasus at two spatial scales - the scale of area from 4 to 100 m2 and the smaller scale within a community. The list of local flora of the alpine belt has been composed using the database of geobotanic descriptions carried out in Teberda Biosphere Reserve at true altitudes exceeding.1800 m. It includes 585 species of flowering plants belonging to 57 families. Basal groups of flowering plants are.not represented in the list. At the scale of communities of three classes, namely Thlaspietea rotundifolii - commumties formed on screes and pebbles, Calluno-Ulicetea - alpine meadow, and Mulgedio-Aconitetea subalpine meadows, have not demonstrated significant distinction of phylogenetic structure. At intra level, for alpine meadows the larger share of closely related species. (clustered community) is detected. Significantly clustered happen to be those communities developing on rocks (class Asplenietea trichomanis) and alpine (class Juncetea trifidi). At the same time, alpine lichen proved to have even phylogenetic structure at the small scale. Alpine (class Salicetea herbaceae) that develop under conditions of winter snow accumulation were more,even at the both.scale, i.e., contained more diverse and distantly related plant species compared with random samples. (Scheuchzerio-Caricetea fuscae) aquatic communities in cold (Montio-Cardaminetea), sedge meadows (Carici rupestris-Kobresietea bellardii), and communities, in which shrubs and predominated (juniper and rhododendron elfin woods, class Loiseleurio-Vaccinietea), have been studied only at the larger scale and showed significant evenness of species composition, i.e., were phylogenetically more diverse compared with random samples.

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

Aripirala, Srinivas; Gonzalez-Pacanowska, Dolores; Oldfield, Eric

Structural insights into L. major farnesyl diphosphate synthase, a key enzyme in the mevalonate pathway, are described. Farnesyl diphosphate synthase (FPPS) is an essential enzyme involved in the biosynthesis of sterols (cholesterol in humans and ergosterol in yeasts, fungi and trypanosomatid parasites) as well as in protein prenylation. It is inhibited by bisphosphonates, a class of drugs used in humans to treat diverse bone-related diseases. The development of bisphosphonates as antiparasitic compounds targeting ergosterol biosynthesis has become an important route for therapeutic intervention. Here, the X-ray crystallographic structures of complexes of FPPS from Leishmania major (the causative agent of cutaneousmore » leishmaniasis) with three bisphosphonates determined at resolutions of 1.8, 1.9 and 2.3 Å are reported. Two of the inhibitors, 1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium (300B) and 3-butyl-1-(2,2-diphosphonoethyl)pyridinium (476A), co-crystallize with the homoallylic substrate isopentenyl diphosphate (IPP) and three Ca{sup 2+} ions. A third inhibitor, 3-fluoro-1-(2-hydroxy-2,2-diphosphonoethyl)pyridinium (46I), was found to bind two Mg{sup 2+} ions but not IPP. Calorimetric studies showed that binding of the inhibitors is entropically driven. Comparison of the structures of L. major FPPS (LmFPPS) and human FPPS provides new information for the design of bisphosphonates that will be more specific for inhibition of LmFPPS. The asymmetric structure of the LmFPPS–46I homodimer indicates that binding of the allylic substrate to both monomers of the dimer results in an asymmetric dimer with one open and one closed homoallylic site. It is proposed that IPP first binds to the open site, which then closes, opening the site on the other monomer, which closes after binding the second IPP, leading to the symmetric fully occupied FPPS dimer observed in other structures.« less

eIF4B stimulates translation of long mRNAs with structured 5′ UTRs and low closed-loop potential but weak dependence on eIF4G

PubMed Central

Sen, Neelam Dabas; Zhou, Fujun; Harris, Michael S.; Ingolia, Nicholas T.

2016-01-01

DEAD-box RNA helicases eukaryotic translation initiation factor 4A (eIF4A) and Ded1 promote translation by resolving mRNA secondary structures that impede preinitiation complex (PIC) attachment to mRNA or scanning. Eukaryotic translation initiation factor 4B (eIF4B) is a cofactor for eIF4A but also might function independently of eIF4A. Ribosome profiling of mutants lacking eIF4B or with impaired eIF4A or Ded1 activity revealed that eliminating eIF4B reduces the relative translational efficiencies of many more genes than does inactivation of eIF4A, despite comparable reductions in bulk translation, and few genes display unusually strong requirements for both factors. However, either eliminating eIF4B or inactivating eIF4A preferentially impacts mRNAs with longer, more structured 5′ untranslated regions (UTRs). These findings reveal an eIF4A-independent role for eIF4B in addition to its function as eIF4A cofactor in promoting PIC attachment or scanning on structured mRNAs. eIF4B, eIF4A, and Ded1 mutations also preferentially impair translation of longer mRNAs in a fashion mitigated by the ability to form closed-loop messenger ribonucleoprotein particles (mRNPs) via eIF4F–poly(A)-binding protein 1 (Pab1) association, suggesting cooperation between closed-loop assembly and eIF4B/helicase functions. Remarkably, depleting eukaryotic translation initiation factor 4G (eIF4G), the scaffold subunit of eukaryotic translation initiation factor 4F (eIF4F), preferentially impacts short mRNAs with strong closed-loop potential and unstructured 5′ UTRs, exactly the opposite features associated with hyperdependence on the eIF4B/helicases. We propose that short, highly efficient mRNAs preferentially depend on the stimulatory effects of eIF4G-dependent closed-loop assembly. PMID:27601676

The role of temporal call structure in species recognition of male Allobates talamancae (Cope, 1875): (Anura: Dendrobatidae).

PubMed

Kollarits, Dennis; Wappl, Christian; Ringler, Max

2017-01-30

Acoustic species recognition in anurans depends on spectral and temporal characteristics of the advertisement call. The recognition space of a species is shaped by the likelihood of heterospecific acoustic interference. The dendrobatid frogs Allobates talamancae (Cope, 1875) and Silverstoneia flotator (Dunn, 1931) occur syntopically in south-west Costa Rica. A previous study showed that these two species avoid acoustic interference by spectral stratification. In this study, the role of the temporal call structure in the advertisement call of A. talamancae was analyzed, in particular the internote-interval duration in providing species specific temporal cues. In playback trials, artificial advertisement calls with internote-intervals deviating up to ± 90 % from the population mean internote-interval were broadcast to vocally active territorial males. The phonotactic reactions of the males indicated that, unlike in closely related species, internote-interval duration is not a call property essential for species recognition in A. talamancae . However, temporal call structure may be used for species recognition when the likelihood of heterospecific interference is high. Also, the close-encounter courtship call of male A. talamancae is described.

Crystal structure of the ATP-gated P2X[subscript 4] ion channel in the closed state

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

Kawate, Toshimitsu; Michel, Jennifer Carlisle; Birdsong, William T.

2009-08-13

P2X receptors are cation-selective ion channels gated by extracellular ATP, and are implicated in diverse physiological processes, from synaptic transmission to inflammation to the sensing of taste and pain. Because P2X receptors are not related to other ion channel proteins of known structure, there is at present no molecular foundation for mechanisms of ligand-gating, allosteric modulation and ion permeation. Here we present crystal structures of the zebrafish P2X{sub 4} receptor in its closed, resting state. The chalice-shaped, trimeric receptor is knit together by subunit-subunit contacts implicated in ion channel gating and receptor assembly. Extracellular domains, rich in {beta}-strands, have largemore » acidic patches that may attract cations, through fenestrations, to vestibules near the ion channel. In the transmembrane pore, the 'gate' is defined by an {approx}8 {angstrom} slab of protein. We define the location of three non-canonical, intersubunit ATP-binding sites, and suggest that ATP binding promotes subunit rearrangement and ion channel opening.« less

Structure of the conversion laws in quantum integrable spin chains with short range interactions

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

Grabowski, M.P.; Mathieu, P.

1995-11-01

The authors present a detailed analysis of the structure of the conservation laws in quantum integrable chains of the XYZ-type and in the Hubbard model. The essential tool for the former class of models is the boost operator, which provides a recursive way of calculating the integrals of motion. With its help, they establish the general form of the XYZ conserved charges in terms of simple polynomials in spin variables and derive recursion relations for the relative coefficients of these polynomials. Although these relations are difficult to solve in general, a subset of the coefficients can be determined. Moreover, formore » two submodels of the XYZ chain, namely the XXX and XY cases, all the charges can be calculated in closed form. Using this approach, the authors rederive the known expressions for the XY charges in a novel way. For the XXX case. a simple description of conserved charges is found in terms of a Catalan tree. This construction is generalized for the su(M) invariant integrable chain. They also investigate the circumstances permitting the existence of a recursive (ladder) operator in general quantum integrable systems. They indicate that a quantum ladder operator can be traced back to the presence of a Hamiltonian mastersymmetry of degree one in the classical continuous version of the model. In this way, quantum chains endowed with a recursive structure can be identified from the properties of their classical relatives. The authors also show that in the quantum continuous limits of the XYZ model, the ladder property of the boost operator disappears. For the Hubbard model they demonstrate the nonexistence of a ladder operator. Nevertheless, the general structure of the conserved charges is indicated, and the expression for the terms linear in the model`s free parameter for all charges is derived in closed form. 62 refs., 4 figs.« less

Tunneling spectroscopy of close-spaced dangling-bond pairs in Si(001):H

PubMed Central

Engelund, Mads; Zuzak, Rafał; Godlewski, Szymon; Kolmer, Marek; Frederiksen, Thomas; García-Lekue, Aran; Sánchez-Portal, Daniel; Szymonski, Marek

2015-01-01

We present a combined experimental and theoretical study of the electronic properties of close-spaced dangling-bond (DB) pairs in a hydrogen-passivated Si(001):H p-doped surface. Two types of DB pairs are considered, called “cross” and “line” structures. Our scanning tunneling spectroscopy (STS) data show that, although the spectra taken over different DBs in each pair exhibit a remarkable resemblance, they appear shifted by a constant energy that depends on the DB-pair type. This spontaneous asymmetry persists after repeated STS measurements. By comparison with density functional theory (DFT) calculations, we demonstrate that the magnitude of this shift and the relative position of the STS peaks can be explained by distinct charge states for each DB in the pair. We also explain how the charge state is modified by the presence of the scanning tunneling microscopy (STM) tip and the applied bias. Our results indicate that, using the STM tip, it is possible to control the charge state of individual DBs in complex structures, even if they are in close proximity. This observation might have important consequences for the design of electronic circuits and logic gates based on DBs in passivated silicon surfaces. PMID:26404520

Solution of cavity resonance and waveguide scattering problems using the eigenmode projection technique

NASA Astrophysics Data System (ADS)

Nasr, Mamdouh H.; Othman, Mohamed A. K.; Eshrah, Islam A.; Abuelfadl, Tamer M.

2017-04-01

New developments in the eigenmode projection technique (EPT) are introduced in solving problems of electromagnetic resonance in closed cavities as well as scattering from discontinuities in guided-wave structures. The EPT invokes the eigenmodes of a canonical predefined cavity in the solution procedure and uses the expansion of these eigenmodes to solve Maxwell's equations, in conjunction with a convenient choice of port boundary conditions. For closed cavities, a new spurious-mode separation method is developed, showing robust and efficient spurious-mode separation. This has been tested using more complex and practical examples demonstrating the powerful use of the presented approach. For waveguide scattering problems, convergence studies are being performed showing stable solutions for a relatively small number of expansion modes, and the proposed method has advantages over conventional solvers in analyzing electromagnetic problems with inhomogeneous materials. These convergence studies also lead to an efficient rule-of-thumb for the number of modes to be used in the simulation. The ability to handle closed and open structures is presented in a unified framework that highlights the generality of the EPT which could be used to analyze and design a variety of microwave components.

THE EFFECT OF RECONNECTION ON THE STRUCTURE OF THE SUN’S OPEN–CLOSED FLUX BOUNDARY

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

Pontin, D. I.; Wyper, P. F., E-mail: dpontin@maths.dundee.ac.uk, E-mail: peter.f.wyper@nasa.gov

2015-05-20

Global magnetic field extrapolations are now revealing the huge complexity of the Sun's corona, and in particular the structure of the boundary between open and closed magnetic flux. Moreover, recent developments indicate that magnetic reconnection in the corona likely occurs in highly fragmented current layers, and that this typically leads to a dramatic increase in the topological complexity beyond that of the equilibrium field. In this paper we use static models to investigate the consequences of reconnection at the open–closed flux boundary (“interchange reconnection”) in a fragmented current layer. We demonstrate that it leads to efficient mixing of magnetic fluxmore » (and therefore plasma) from open and closed field regions. This corresponds to an increase in the length and complexity of the open–closed boundary. Thus, whenever reconnection occurs at a null point or separator of this open–closed boundary, the associated separatrix arc of the so-called S-web in the high corona becomes not a single line but a band of finite thickness within which the open–closed boundary is highly structured. This has significant implications for the acceleration of the slow solar wind, for which the interaction of open and closed field is thought to be important, and may also explain the coronal origins of certain solar energetic particles. The topological structures examined contain magnetic null points, separatrices and separators, and include a model for a pseudo-streamer. The potential for understanding both the large scale morphology and fine structure observed in flare ribbons associated with coronal nulls is also discussed.« less

Rational positive real approximations for LQG optimal compensators arising in active stabilization of flexible structures

NASA Technical Reports Server (NTRS)

Desantis, A.

1994-01-01

In this paper the approximation problem for a class of optimal compensators for flexible structures is considered. The particular case of a simply supported truss with an offset antenna is dealt with. The nonrational positive real optimal compensator transfer function is determined, and it is proposed that an approximation scheme based on a continued fraction expansion method be used. Comparison with the more popular modal expansion technique is performed in terms of stability margin and parameters sensitivity of the relative approximated closed loop transfer functions.

[Demography of aging in Spain].

PubMed

Rubio Herrera, R

1994-01-01

In this article, the demography of the elderly in Spain is scrutinized. The older population from 1960 to 1991 and their presumed development for the period from 2001-2020 is analyzed. According to these data, we attempt to determine the influence on life situation of older people according to several factors, such as changes of family structures and intergenerational relations as well as changes in social stereotypes, expected political and economical developments, and new concepts in medical care. In closing, we raise questions about the necessary future living structures in Spain.

ECOD: An Evolutionary Classification of Protein Domains

PubMed Central

Kinch, Lisa N.; Pei, Jimin; Shi, Shuoyong; Kim, Bong-Hyun; Grishin, Nick V.

2014-01-01

Understanding the evolution of a protein, including both close and distant relationships, often reveals insight into its structure and function. Fast and easy access to such up-to-date information facilitates research. We have developed a hierarchical evolutionary classification of all proteins with experimentally determined spatial structures, and presented it as an interactive and updatable online database. ECOD (Evolutionary Classification of protein Domains) is distinct from other structural classifications in that it groups domains primarily by evolutionary relationships (homology), rather than topology (or “fold”). This distinction highlights cases of homology between domains of differing topology to aid in understanding of protein structure evolution. ECOD uniquely emphasizes distantly related homologs that are difficult to detect, and thus catalogs the largest number of evolutionary links among structural domain classifications. Placing distant homologs together underscores the ancestral similarities of these proteins and draws attention to the most important regions of sequence and structure, as well as conserved functional sites. ECOD also recognizes closer sequence-based relationships between protein domains. Currently, approximately 100,000 protein structures are classified in ECOD into 9,000 sequence families clustered into close to 2,000 evolutionary groups. The classification is assisted by an automated pipeline that quickly and consistently classifies weekly releases of PDB structures and allows for continual updates. This synchronization with PDB uniquely distinguishes ECOD among all protein classifications. Finally, we present several case studies of homologous proteins not recorded in other classifications, illustrating the potential of how ECOD can be used to further biological and evolutionary studies. PMID:25474468

ECOD: an evolutionary classification of protein domains.

PubMed

Cheng, Hua; Schaeffer, R Dustin; Liao, Yuxing; Kinch, Lisa N; Pei, Jimin; Shi, Shuoyong; Kim, Bong-Hyun; Grishin, Nick V

2014-12-01

Understanding the evolution of a protein, including both close and distant relationships, often reveals insight into its structure and function. Fast and easy access to such up-to-date information facilitates research. We have developed a hierarchical evolutionary classification of all proteins with experimentally determined spatial structures, and presented it as an interactive and updatable online database. ECOD (Evolutionary Classification of protein Domains) is distinct from other structural classifications in that it groups domains primarily by evolutionary relationships (homology), rather than topology (or "fold"). This distinction highlights cases of homology between domains of differing topology to aid in understanding of protein structure evolution. ECOD uniquely emphasizes distantly related homologs that are difficult to detect, and thus catalogs the largest number of evolutionary links among structural domain classifications. Placing distant homologs together underscores the ancestral similarities of these proteins and draws attention to the most important regions of sequence and structure, as well as conserved functional sites. ECOD also recognizes closer sequence-based relationships between protein domains. Currently, approximately 100,000 protein structures are classified in ECOD into 9,000 sequence families clustered into close to 2,000 evolutionary groups. The classification is assisted by an automated pipeline that quickly and consistently classifies weekly releases of PDB structures and allows for continual updates. This synchronization with PDB uniquely distinguishes ECOD among all protein classifications. Finally, we present several case studies of homologous proteins not recorded in other classifications, illustrating the potential of how ECOD can be used to further biological and evolutionary studies.

Not Such a Simple Story: Contradictory Evidence from a Review of Story Structure Research for Students At-risk

ERIC Educational Resources Information Center

Faggella-Luby, Michael N.; Drew, Sally Valentino; Schumaker, Jean B.

2015-01-01

The Common Core State Standards and the continued inclusion of students with learning disabilities (LD) in Tier 1 classrooms are changing how close reading of texts occurs in English Language Arts classrooms. Therefore, understanding the potential impact of literacy-related evidence-based practices during Tier 1 instruction that includes students…

L2 Acquisition of Spanish Dative Clitics by English and Dutch Learners

ERIC Educational Resources Information Center

Escobar-Álvarez, M. Ángeles

2017-01-01

This article examines the second language acquisition (SLA) of Spanish dative clitics in clitic doubling (CLD) structures that are closely related to the double object construction (DOC) in English and Dutch. It also addresses the question of how adult English and Dutch speakers learning L2 Spanish in a formal setting develop knowledge and use of…

Collateral Damage

DTIC Science & Technology

1978-10-01

stated, they are, in reality , indexed to a single aspect of the weapon phenomena, e.g., damage levels for airblast-sensitive objects are indexed to...of Burst Propagation Related Airblast Representation Target Altitude Wheather (snow/rain) Terrain Temperature Air Pressure Around Structures 1. d) 3-38...with opaque material. Simply closing a shutter can be quite effective in virtually eliminating all possibility of interior fire starts from a single

1H and 13C NMR spectral assignments of four dammarane triterpenoids from carnauba wax.

PubMed

Cysne, Juliana de Brito; Braz-Filho, Raimundo; Assunção, Marcus Vinícius; Uchoa, Daniel E de Andrade; Silveira, Edilberto R; Pessoa, Otília Deusdênia L

2006-06-01

The phytochemical investigation of carnauba wax led to the isolation of three new dammarane triterpenoids 1, 2 and 4, together with the known triterpene 3. The structures of the new compounds were determined by 1D and 2D NMR spectroscopy and by comparison with published data for closely related compounds. 2006 John Wiley & Sons, Ltd.

Attitudes towards Mathematics at Secondary Level: Development and Structural Validation of the Scale for Assessing Attitudes towards Mathematics in Secondary Education (SAT-MAS)

ERIC Educational Resources Information Center

Yáñez-Marquina, Lara; Villardón-Gallego, Lourdes

2016-01-01

Introduction: In secondary education, students' low achievement and engagement in mathematics are closely related to their attitudes towards the subject. Despite the international body of research, an exhaustive literature review of the existing instruments for measuring it draws attention to the inconsistency in the definition and corresponding…

Comfortable Interpersonal Distance: Aspects of the Interpersonal Behaviour in a Sample of 16-Year-Old Subjects, Males and Females.

ERIC Educational Resources Information Center

Comunian, Anna Laura

According to Duke and Newicki, the distance maintained by a subject towards an approach stimulus is closely related to the internal structures of his personality. The test puts the subject's projective personality and the perception that the group has of the subject into relief. Duke and Newiski's "Comfortable Interpersonal Distance"…

Temporal evolutions and stationary waves for dissipative Benjamin-Ono equation

NASA Astrophysics Data System (ADS)

Feng, Bao-Feng; Kawahara, Takuji

2000-05-01

Initial value problems as well as stationary solitary and periodic waves are investigated for dissipative Benjamin-Ono (DBO) equation. Multi-hump stationary waves and their structures are identified numerically and the stability regions of stationary periodic waves are also examined numerically. These results elucidate a close relation between irregular behaviours in the initial value problem and the multiplicity of stationary waves.

Space and time in the quantum universe.

NASA Astrophysics Data System (ADS)

Smolin, L.

This paper is devoted to the problem of constructing a quantum theory that could describe a closed system - a quantum cosmology. The author argues that this problem is an aspect of a much older problem - that of how to eliminate from the physical theories "ideal elements", which are elements of the mathematical structure whose interpretation requires the existence of things outside the dynamical system described by the theory. This discussion is aimed at uncovering criteria that a theory of quantum cosmology must satisfy, if it is to give physically sensible predictions. The author proposes three such criteria and shows that conventional quantum cosmology can only satisfy them, if there is an intrinsic time coordinate on the phase space of the theory. It is shown that approaches based on correlations in the wave function, that do not use an inner product, cannot satisfy these criteria. As example, the author discusses the problem of quantizing a class of relational dynamical models invented by Barbour and Bertotti. The dynamical structure of these theories is closely analogous to general relativity, and the problem of their measurement theory is also similar. It is concluded that these theories can only be sensibly quantized if they contain an intrinsic time.

Individual and contextual determinants of resident-on-resident abuse in nursing homes: a random sample telephone survey of adults with an older family member in a nursing home.

PubMed

Schiamberg, Lawrence B; von Heydrich, Levente; Chee, Grace; Post, Lori A

2015-01-01

Few empirical investigations of elder abuse in nursing homes address the frequency and determinants of resident-on-resident abuse (RRA). A random sample of 452 adults with an older adult relative, ≥65 years of age, in a nursing home completed a telephone survey regarding elder abuse experienced by that elder family member. Using a Linear Structural Relations (LISREL) modeling design, the study examined the association of nursing home resident demographic characteristics (e.g., age, gender), health and behavioral characteristics (e.g., diagnosis of Alzheimer's Disease, Activities of Daily Living (ADLs), Instrumental Activities of Daily Living (IADLs), types of staff abuse (e.g., physical, emotional), and factors beyond the immediate nursing home setting (e.g., emotional closeness of resident with family members) with RRA. Mplus statistical software was used for structural equation modeling. Main findings indicated that resident-on-resident mistreatment of elderly nursing home residents is associated with the age of the nursing home resident, all forms of staff abuse, all ADLs and IADLs, and emotional closeness of the older adult to the family. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

New open conformation of SMYD3 implicates conformational selection and allostery

PubMed Central

Spellmon, Nicholas; Sun, Xiaonan; Xue, Wen; Holcomb, Joshua; Chakravarthy, Srinivas; Shang, Weifeng; Edwards, Brian; Sirinupong, Nualpun; Li, Chunying; Yang, Zhe

2016-01-01

SMYD3 plays a key role in cancer cell viability, adhesion, migration and invasion. SMYD3 promotes formation of inducible regulatory T cells and is involved in reducing autoimmunity. However, the nearly “closed” substrate-binding site and poor in vitro H3K4 methyltransferase activity have obscured further understanding of this oncogenically related protein. Here we reveal that SMYD3 can adopt an “open” conformation using molecular dynamics simulation and small-angle X-ray scattering. This ligand-binding-capable open state is related to the crystal structure-like closed state by a striking clamshell-like inter-lobe dynamics. The two states are characterized by many distinct structural and dynamical differences and the conformational transition pathway is mediated by a reversible twisting motion of the C-terminal domain (CTD). The spontaneous transition from the closed to open states suggests two possible, mutually non-exclusive models for SMYD3 functional regulation and the conformational selection mechanism and allostery may regulate the catalytic or ligand binding competence of SMYD3. This study provides an immediate clue to the puzzling role of SMYD3 in epigenetic gene regulation. PMID:28050603

Analysis on the urban street network of Korea: Connections between topology and meta-information

NASA Astrophysics Data System (ADS)

Lee, Byoung-Hwa; Jung, Woo-Sung

2018-05-01

Cities consist of infrastructure that enables transportation, which can be considered as topology in abstract terms. Once cities are physically organized in terms of infrastructure, people interact with each other to form the values, which can be regarded as the meta-information of the cities. The topology and meta-information coevolve together as the cities are developed. In this study, we investigate the relationship between the topology and meta-information for a street network, which has aspects of both a complex network and planar graph. The degree of organization of a street structure determines the efficiency and productivity of the city in that they act as blood vessels to transport people, goods, and information. We analyze the topological aspect of a street network using centralities including the betweenness, closeness, straightness, and information. We classify the cities into several groups that share common meta-information based on the centrality, indicating that the topological factor of the street structure is closely related to meta-information through coevolution. We also obtain the coevolution in the planned cities using the regularity. Another footprint is the relation between the street segment length and the population, which shows the sublinear scaling.

Pyrazole amino acids: hydrogen bonding directed conformations of 3-amino-1H-pyrazole-5-carboxylic acid residue.

PubMed

Kusakiewicz-Dawid, Anna; Porada, Monika; Ochędzan-Siodłak, Wioletta; Broda, Małgorzata A; Bujak, Maciej; Siodłak, Dawid

2017-09-01

A series of model compounds containing 3-amino-1H-pyrazole-5-carboxylic acid residue with N-terminal amide/urethane and C-terminal amide/hydrazide/ester groups were investigated by using NMR, Fourier transform infrared, and single-crystal X-ray diffraction methods, additionally supported by theoretical calculations. The studies demonstrate that the most preferred is the extended conformation with torsion angles ϕ and ψ close to ±180°. The studied 1H-pyrazole with N-terminal amide/urethane and C-terminal amide/hydrazide groups solely adopts this energetically favored conformation confirming rigidity of that structural motif. However, when the C-terminal ester group is present, the second conformation with torsion angles ϕ and ψ close to ±180° and 0°, respectively, is accessible. The conformational equilibrium is observed in NMR and Fourier transform infrared studies in solution in polar environment as well as in the crystal structures of other related compounds. The observed conformational preferences are clearly related to the presence of intramolecular interactions formed within the studied residue. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

Substrate-Induced Allosteric Change in the Quaternary Structure of the Spermidine N-Acetyltransferase SpeG.

PubMed

Filippova, Ekaterina V; Weigand, Steven; Osipiuk, Jerzy; Kiryukhina, Olga; Joachimiak, Andrzej; Anderson, Wayne F

2015-11-06

The spermidine N-acetyltransferase SpeG is a dodecameric enzyme that catalyzes the transfer of an acetyl group from acetyl coenzyme A to polyamines such as spermidine and spermine. SpeG has an allosteric polyamine-binding site and acetylating polyamines regulate their intracellular concentrations. The structures of SpeG from Vibrio cholerae in complexes with polyamines and cofactor have been characterized earlier. Here, we present the dodecameric structure of SpeG from V. cholerae in a ligand-free form in three different conformational states: open, intermediate and closed. All structures were crystallized in C2 space group symmetry and contain six monomers in the asymmetric unit cell. Two hexamers related by crystallographic 2-fold symmetry form the SpeG dodecamer. The open and intermediate states have a unique open dodecameric ring. This SpeG dodecamer is asymmetric except for the one 2-fold axis and is unlike any known dodecameric structure. Using a fluorescence thermal shift assay, size-exclusion chromatography with multi-angle light scattering, small-angle X-ray scattering analysis, negative-stain electron microscopy and structural analysis, we demonstrate that this unique open dodecameric state exists in solution. Our combined results indicate that polyamines trigger conformational changes and induce the symmetric closed dodecameric state of the protein when they bind to their allosteric sites. Copyright © 2015. Published by Elsevier Ltd.

Crystallographic and Computational Analyses of AUUCU Repeating RNA That Causes Spinocerebellar Ataxia Type 10 (SCA10).

PubMed

Park, HaJeung; González, Àlex L; Yildirim, Ilyas; Tran, Tuan; Lohman, Jeremy R; Fang, Pengfei; Guo, Min; Disney, Matthew D

2015-06-23

Spinocerebellar ataxia type 10 (SCA10) is caused by a pentanucleotide repeat expansion of r(AUUCU) within intron 9 of the ATXN10 pre-mRNA. The RNA causes disease by a gain-of-function mechanism in which it inactivates proteins involved in RNA biogenesis. Spectroscopic studies showed that r(AUUCU) repeats form a hairpin structure; however, there were no high-resolution structural models prior to this work. Herein, we report the first crystal structure of model r(AUUCU) repeats refined to 2.8 Å and analysis of the structure via molecular dynamics simulations. The r(AUUCU) tracts adopt an overall A-form geometry in which 3 × 3 nucleotide (5')UCU(3')/(3')UCU(5') internal loops are closed by AU pairs. Helical parameters of the refined structure as well as the corresponding electron density map on the crystallographic model reflect dynamic features of the internal loop. The computational analyses captured dynamic motion of the loop closing pairs, which can form single-stranded conformations with relatively low energies. Overall, the results presented here suggest the possibility for r(AUUCU) repeats to form metastable A-from structures, which can rearrange into single-stranded conformations and attract proteins such as heterogeneous nuclear ribonucleoprotein K (hnRNP K). The information presented here may aid in the rational design of therapeutics targeting this RNA.

Crystallographic and Computational Analyses of AUUCU Repeating RNA That Causes Spinocerebellar Ataxia Type 10 (SCA10)

PubMed Central

Park, HaJeung; González, Àlex L.; Yildirim, Ilyas; Tran, Tuan; Lohman, Jeremy R.; Fang, Pengfei; Guo, Min; Disney, Matthew D.

2016-01-01

Spinocerebellar ataxia type 10 (SCA10) is caused by a pentanucleotide repeat expansion of r(AUUCU) within intron 9 of the ATXN10 pre-mRNA. The RNA causes disease by a gain-of-function mechanism in which it inactivates proteins involved in RNA biogenesis. Spectroscopic studies showed that r(AUUCU) repeats form a hairpin structure; however, there were no high-resolution structural models prior to this work. Herein, we report the first crystal structure of model r(AUUCU) repeats refined to 2.8 Å and analysis of the structure via molecular dynamics simulations. The r(AUUCU) tracts adopt an overall A-form geometry in which 3 × 3 nucleotide 5′UCU3′/3′UCU5′ internal loops are closed by AU pairs. Helical parameters of the refined structure as well as the corresponding electron density map on the crystallographic model reflect dynamic features of the internal loop. The computational analyses captured dynamic motion of the loop closing pairs, which can form single-stranded conformations with relatively low energies. Overall, the results presented here suggest the possibility for r(AUUCU) repeats to form metastable A-from structures, which can rearrange into single-stranded conformations and attract proteins such as heterogeneous nuclear ribonucleoprotein K (hnRNP K). The information presented here may aid in the rational design of therapeutics targeting this RNA. PMID:26039897

Substrate-induced allosteric change in the quaternary structure of the spermidine N-acetyltransferase SpeG

DOE PAGES

Filippova, Ekaterina V.; Weigand, Steven J.; Osipiuk, Jerzy; ...

2015-09-26

The spermidine N-acetyltransferase SpeG is a dodecameric enzyme that catalyzes the transfer of an acetyl group from acetyl coenzyme A to polyamines such as spermidine and spermine. SpeG has an allosteric polyamine-binding site and acetylating polyamines regulate their intracellular concentrations. The structures of SpeG from Vibrio cholerae in complexes with polyamines and cofactor have been characterized earlier. Here, we present the dodecameric structure of SpeG from V. cholerae in a ligand-free form in three different conformational states: open, intermediate and closed. All structures were crystallized in C2 space group symmetry and contain six monomers in the asymmetric unit cell. Twomore » hexamers related by crystallographic 2-fold symmetry form the SpeG dodecamer. The open and intermediate states have a unique open dodecameric ring. This SpeG dodecamer is asymmetric except for the one 2-fold axis and is unlike any known dodecameric structure. Using a fluorescence thermal shift assay, size-exclusion chromatography with multi-angle light scattering, small-angle X-ray scattering analysis, negative-stain electron microscopy and structural analysis, we demonstrate that this unique open dodecameric state exists in solution. As a result, our combined results indicate that polyamines trigger conformational changes and induce the symmetric closed dodecameric state of the protein when they bind to their allosteric sites.« less

Closed-Loop Control and Advisory Mode Evaluation of an Artificial Pancreatic β Cell: Use of Proportional–Integral–Derivative Equivalent Model-Based Controllers

PubMed Central

Percival, Matthew W.; Zisser, Howard; Jovanovič, Lois; Doyle, Francis J.

2008-01-01

Background Using currently available technology, it is possible to apply modern control theory to produce a closed-loop artificial β cell. Novel use of established control techniques would improve glycemic control, thereby reducing the complications of diabetes. Two popular controller structures, proportional–integral–derivative (PID) and model predictive control (MPC), are compared first in a theoretical sense and then in two applications. Methods The Bergman model is transformed for use in a PID equivalent model-based controller. The internal model control (IMC) structure, which makes explicit use of the model, is compared with the PID controller structure in the transfer function domain. An MPC controller is then developed as an optimization problem with restrictions on its tuning parameters and is shown to be equivalent to an IMC controller. The controllers are tuned for equivalent performance and evaluated in a simulation study as a closed-loop controller and in an advisory mode scenario on retrospective clinical data. Results Theoretical development shows conditions under which PID and MPC controllers produce equivalent output via IMC. The simulation study showed that the single tuning parameter for the equivalent controllers relates directly to the closed-loop speed of response and robustness, an important result considering system uncertainty. The risk metric allowed easy identification of instances of inadequate control. Results of the advisory mode simulation showed that suitable tuning produces consistently appropriate delivery recommendations. Conclusion The conditions under which PID and MPC are equivalent have been derived. The MPC framework is more suitable given the extensions necessary for a fully closed-loop artificial β cell, such as consideration of controller constraints. Formulation of the control problem in risk space is attractive, as it explicitly addresses the asymmetry of the problem; this is done easily with MPC. PMID:19885240

Phylogenetic analysis and protein structure modelling identifies distinct Ca(2+)/Cation antiporters and conservation of gene family structure within Arabidopsis and rice species.

PubMed

Pittman, Jon K; Hirschi, Kendal D

2016-12-01

The Ca(2+)/Cation Antiporter (CaCA) superfamily is an ancient and widespread family of ion-coupled cation transporters found in nearly all kingdoms of life. In animals, K(+)-dependent and K(+)-indendent Na(+)/Ca(2+) exchangers (NCKX and NCX) are important CaCA members. Recently it was proposed that all rice and Arabidopsis CaCA proteins should be classified as NCX proteins. Here we performed phylogenetic analysis of CaCA genes and protein structure homology modelling to further characterise members of this transporter superfamily. Phylogenetic analysis of rice and Arabidopsis CaCAs in comparison with selected CaCA members from non-plant species demonstrated that these genes form clearly distinct families, with the H(+)/Cation exchanger (CAX) and cation/Ca(2+) exchanger (CCX) families dominant in higher plants but the NCKX and NCX families absent. NCX-related Mg(2+)/H(+) exchanger (MHX) and CAX-related Na(+)/Ca(2+) exchanger-like (NCL) proteins are instead present. Analysis of genomes of ten closely-related rice species and four Arabidopsis-related species found that CaCA gene family structures are highly conserved within related plants, apart from minor variation. Protein structures were modelled for OsCAX1a and OsMHX1. Despite exhibiting broad structural conservation, there are clear structural differences observed between the different CaCA types. Members of the CaCA superfamily form clearly distinct families with different phylogenetic, structural and functional characteristics, and therefore should not be simply classified as NCX proteins, which should remain as a separate gene family.

Response of rocky invertebrate diversity, structure and function to the vertical layering of vegetation

NASA Astrophysics Data System (ADS)

Bustamante, María; Tajadura, Javier; Gorostiaga, José María; Saiz-Salinas, José Ignacio

2014-06-01

Macroalgae comprise a prominent part of the rocky benthos where many invertebrates develop, and are believed to be undergoing severe declines worldwide. In order to investigate how the vegetation structure (crustose, basal and canopy layers) contributes to the diversity, structure and function of benthic invertebrates, a total of 31 subtidal transects were sampled along the northeast Atlantic coast of Spain. Significant positive relationships were found between the canopy layer and faunal abundance, taxonomic diversity and functional group diversity. Canopy forming algae were also related to epiphytic invertebrates, medium size forms, colonial strategy and suspensivores. By contrast, basal algae showed negative relationships with all variables tested except for detritivores. Multivariate multiple regression analyses (DISTLM) point to crustose as well as canopy layers as the best link between seaweeds and invertebrate assemblage structure. A close relationship was found between taxonomic and functional diversities. In general, low levels of taxonomic redundancy were detected for functional groups correlated with vegetation structure. A conceptual model based on the results is proposed, describing distinct stages of invertebrate assemblages in relation to the vertical structure of vegetation.

Theoretical study of the gas-phase structures of sodiated and cesiated leucine and isoleucine: zwitterionic structure disfavored in kinetic method experiments.

PubMed

Rozman, Marko

2005-10-01

The most stable charge-solvated (CS) and zwitterionic (ZW) structures of sodiated and cesiated leucine and isoleucine were studied by density functional theory methods. According to the Boltzmann distribution in gas phase, both forms of LeuNa+ and IleNa+ exist, but in LeuCs+ and IleCs+, the ZW forms are dominant. Results for the sodiated compounds are consistent with the relationship found between decrease in relative stability of CS versus ZW form and aliphatic amino acid side chain length. The observed degeneracy in energy for IleNa+ conformers is at odds with kinetic method results. Additional calculations showed that kinetic method structural determinations for IleNa+ do not reflect relative order of populations in the lowest energy conformers. Since complexation of cationized amino acids into ion-bound dimers disfavors ZW structure by approximately 8 kJ mol(-1), it is suggested that for energy close conformers of sodium-cationized amino acids, the kinetic method may not be reliable for structural determinations. Copyright (c) 2005 John Wiley & Sons, Ltd.

Genetic Diversity and Population Structure of Vibrio cholerae

PubMed Central

Beltrán, Pilar; Delgado, Gabriela; Navarro, Armando; Trujillo, Francisca; Selander, Robert K.; Cravioto, Alejandro

1999-01-01

Multilocus enzyme electrophoresis (MLEE) of 397 Vibrio cholerae isolates, including 143 serogroup reference strains and 244 strains from Mexico and Guatemala, identified 279 electrophoretic types (ETs) distributed in two major divisions (I and II). Linkage disequilibrium was demonstrated in both divisions and in subdivision Ic of division I but not in subdivision Ia, which includes 76% of the ETs. Despite this evidence of relatively frequent recombination, clonal lineages may persist for periods of time measured in at least decades. In addition to the pandemic clones of serogroups O1 and O139, which form a tight cluster of four ETs in subdivision Ia, MLEE analysis identified numerous apparent clonal lineages of non-O1 strains with intercontinental distributions. A clone of serogroup O37 that demonstrated epidemic potential in the 1960s is closely related to the pandemic O1/O139 clones, but the nontoxigenic O1 Inaba El Tor reference strain is not. A strain of serogroup O22, which has been identified as the most likely donor of exogenous rfb region DNA to the O1 progenitor of the O139 clone, is distantly related to the O1/O139 clones. The close evolutionary relationships of the O1, O139, and O37 epidemic clones indicates that new cholera clones are likely to arise by the modification of a lineage that is already epidemic or is closely related to such a clone. PMID:9986816

Genetic diversity and population structure of Vibrio cholerae.

PubMed

Beltrán, P; Delgado, G; Navarro, A; Trujillo, F; Selander, R K; Cravioto, A

1999-03-01

Multilocus enzyme electrophoresis (MLEE) of 397 Vibrio cholerae isolates, including 143 serogroup reference strains and 244 strains from Mexico and Guatemala, identified 279 electrophoretic types (ETs) distributed in two major divisions (I and II). Linkage disequilibrium was demonstrated in both divisions and in subdivision Ic of division I but not in subdivision Ia, which includes 76% of the ETs. Despite this evidence of relatively frequent recombination, clonal lineages may persist for periods of time measured in at least decades. In addition to the pandemic clones of serogroups O1 and O139, which form a tight cluster of four ETs in subdivision Ia, MLEE analysis identified numerous apparent clonal lineages of non-O1 strains with intercontinental distributions. A clone of serogroup O37 that demonstrated epidemic potential in the 1960s is closely related to the pandemic O1/O139 clones, but the nontoxigenic O1 Inaba El Tor reference strain is not. A strain of serogroup O22, which has been identified as the most likely donor of exogenous rfb region DNA to the O1 progenitor of the O139 clone, is distantly related to the O1/O139 clones. The close evolutionary relationships of the O1, O139, and O37 epidemic clones indicates that new cholera clones are likely to arise by the modification of a lineage that is already epidemic or is closely related to such a clone.

Dams and transnational advocacy: Political opportunities in transnational collective action

NASA Astrophysics Data System (ADS)

Fu, Teng

Possible arguments to explain the gradual decline in big dam development and its site transferring from developed to developing countries include technical, economic, and political factors. This study focuses on the political argument---the rise of transnational anti-dam advocacy and its impact on state policy-making. Under what conditions does transnational anti-dam advocacy matter? Under what conditions does transnational advocacy change state dam policies (delay, scale down, or cancel)? It examines the role of transnational anti-dam actors in big dam building in a comparative context in Asia. Applying the social movement theory of political opportunity structure (POS) and using the qualitative case-study method, the study provides both within-case and cross-case analyses. Within-case analysis is utilized to explain the changing dynamics of big dam building in China (Three Gorges Dam and proposed Nu/Salween River dam projects), and to a lesser extent, Sardar Sarovar Project in India and Nam Theun 2 Dam in Laos. Different domestic and international POS (DPOS and IPOS) impact the strategies and outcomes of anti-dam advocacies in these countries. The degree of openness of the POS directly affects the capacity of transnational efforts in influencing state dam policies. The degree of openness or closure is measured by specific laws, institutions, discourse, or elite allies (or the absence of these) for the participation of non-state actors on big dam issues at a particular moment. This degree of openness is relative, varying over time, across countries and regions. This study finds that the impact of transnational anti-dam activism is most effective when both DPOS and IPOS are relatively open. Transnational anti-dam advocacy is least effective in influencing state dam policies when both DPOS and IPOS are relatively closed. Under a relatively open DPOS and closed IPOS, transnational anti-dam advocacy is more likely to successfully change state dam policies and even facilitate the opening of relatively closed IPOS. In contrast, under a relatively closed DPOS and open IPOS, transnational anti-dam advocacy can hardly exist. Without the domestic anti-dam pressure from below, international anti-dam efforts from above are less likely to affect state dam policies or open up closed DPOS.

Related Structure Characters and Stability of Structural Defects in a Metallic Glass

PubMed Central

Niu, Xiaofeng; Feng, Shidong; Pan, Shaopeng

2018-01-01

Structural defects were investigated by a recently proposed structural parameter, quasi-nearest atom (QNA), in a modeled Zr50Cu50 metallic glass through molecular dynamics simulations. More QNAs around an atom usually means that more defects are located near the atom. Structural analysis reveals that the spatial distribution of the numbers of QNAs displays to be clearly heterogeneous. Furthermore, QNA is closely correlated with cluster connections, especially four-atom cluster connections. Atoms with larger coordination numbers usually have less QNAs. When two atoms have the same coordination number, the atom with larger five-fold symmetry has less QNAs. The number of QNAs around an atom changes rather frequently and the change of QNAs might be correlated with the fast relaxation metallic glasses. PMID:29565298

Local dependence in random graph models: characterization, properties and statistical inference

PubMed Central

Schweinberger, Michael; Handcock, Mark S.

2015-01-01

Summary Dependent phenomena, such as relational, spatial and temporal phenomena, tend to be characterized by local dependence in the sense that units which are close in a well-defined sense are dependent. In contrast with spatial and temporal phenomena, though, relational phenomena tend to lack a natural neighbourhood structure in the sense that it is unknown which units are close and thus dependent. Owing to the challenge of characterizing local dependence and constructing random graph models with local dependence, many conventional exponential family random graph models induce strong dependence and are not amenable to statistical inference. We take first steps to characterize local dependence in random graph models, inspired by the notion of finite neighbourhoods in spatial statistics and M-dependence in time series, and we show that local dependence endows random graph models with desirable properties which make them amenable to statistical inference. We show that random graph models with local dependence satisfy a natural domain consistency condition which every model should satisfy, but conventional exponential family random graph models do not satisfy. In addition, we establish a central limit theorem for random graph models with local dependence, which suggests that random graph models with local dependence are amenable to statistical inference. We discuss how random graph models with local dependence can be constructed by exploiting either observed or unobserved neighbourhood structure. In the absence of observed neighbourhood structure, we take a Bayesian view and express the uncertainty about the neighbourhood structure by specifying a prior on a set of suitable neighbourhood structures. We present simulation results and applications to two real world networks with ‘ground truth’. PMID:26560142

Linear decentralized systems with special structure. [for twin lift helicopters

NASA Technical Reports Server (NTRS)

Martin, C. F.

1982-01-01

Certain fundamental structures associated with linear systems having internal symmetries are outlined. It is shown that the theory of finite-dimensional algebras and their representations are closely related to such systems. It is also demonstrated that certain problems in the decentralized control of symmetric systems are equivalent to long-standing problems of linear systems theory. Even though the structure imposed arose in considering the problems of twin-lift helicopters, any large system composed of several identical intercoupled control systems can be modeled by a linear system that satisfies the constraints imposed. Internal symmetry can be exploited to yield new system-theoretic invariants and a better understanding of the way in which the underlying structure affects overall system performance.

Relative Travel Time Tomography for East Asia

NASA Astrophysics Data System (ADS)

Chang, S. J.; CHO, S.

2016-12-01

Japan island region is one of the most seismically active region in the world. As a large number of earthquakes have recently occurred along circum-Pacific belt called the ring of fire, concern over earthquakes is increasing in South Korea close to Japan. In this study, we perform seismic imaging based on relative S-wave travel-times to examine S-wave velocity upper mantle structure of East Asia. We used teleseismic events recorded at the Korea Institute of Geoscience and Mineral Resources (KIGAM) network and F-net network operated by the National Research Institute for Earth Science and Disaster Prevention (NIED). Relative travel-time residuals were obtained by a multi-channel cross-correlation method designed to automatically determine accurate relative phase arrival times. The resulting images show high-velocity anomalies along East and South side of Japan island region. These anomalies may indicate subducting Pacific and Philippine Sea plates, respectively. The velocity structure beneath southwest Japan is revealed very complex because the two slabs interact with each other there. Velocity structure of East Asia is useful to understand the tectonic evolution and the mechanism of earthquakes that occur in this region.

Short-term Rn-222 concentration changes in underground spaces with limited air exchange

NASA Astrophysics Data System (ADS)

Fijałkowska-Lichwa, Lidia; Przylibski, Tadeusz A.

2010-05-01

Authors conducted research on radon concentration in two underground structures located in the vicinity of Kletno (Sudety Mts., SW Poland), which are accessible for visitors. One of these structures is Niedźwiedzia (Bear) Cave, and the second one is the part of former uranium mine - Fluorite Adit. Both selected underground structures are characterized by almost constant temperature, changing within the range from +5 to +7° C and also constant relative humidity, close to 100%. Both these parameters testify that air exchange with the atmosphere is very limited. Air exchange is limited particularly in Niedźwiedzia Cave, which microclimate is protected i.e. by applying of locks at the entrance and exit of tourist route. The measurements were conducted between 16.05.2008. and 15.11.2009., by the use of a new Polish equipment - SRDN-3 devices with semiconductor detector. SRDN-3 device records every hour radon concentration as well as atmospheric parameters - relative humidity and temperature. At the same time authors conducted measurements of basic parameters in the open atmosphere close to Niedźwiedzia Cave. Obtained results of atmospheric parameters measurements may be used for both underground structures; because they are located within the distance of about 1 km. Atmospheric parameters were measured by the use of automatic weather station VantagePro2. On the base of conducted research authors corroborate, that the differences of radon concentration in both underground structures reach three orders of magnitude during a year. In Niedźwiedzia Cave these values are in the range from below 88 Bq/m3 (detection limit of the SRDN-3 device) up to 12 kBq/m3. Related values in Fluorite Adit are between < 88 Bq/m3 and 35 kBq/m3. It was observed also the different course of daily radon concentration changes in both structures. Additionally, authors registered that daily course of radon concentration changes differs due to season of the year. Such changes are observed in both structures. The reasons of these changes are probably connected with the way of air exchange between interior of the structure and the atmosphere. In both cases they are determined by atmospheric air temperature changes in relation with the temperature of the air inside the cave or adit. Authors have been still working on this problem. We can also say, that the character of daily radon concentration changes inside both examined structures differ from typical changes noted in dwelling houses.

Mobile phones and social structures: an exploration of a closed user group in rural Ghana

PubMed Central

2013-01-01

Background In the Millennium Villages Project site of Bonsaaso, Ghana, the Health Team is using a mobile phone closed user group to place calls amongst one another at no cost. Methods In order to determine the utilization and acceptability of the closed user group amongst users, social network analysis and qualitative methods were used. Key informants were identified and interviewed. The key informants also kept prospective call journals. Billing statements and de-identified call data from the closed user group were used to generate data for analyzing the social structure revealed by the network traffic. Results The majority of communication within the closed user group was personal and not for professional purposes. The members of the CUG felt that the group improved their efficiency at work. Conclusions The methods used present an interesting way to investigate the social structure surrounding communication via mobile phones. In addition, the benefits identified from the exploration of this closed user group make a case for supporting mobile phone closed user groups amongst professional groups. PMID:24007331

Clonal sets of a binary relation

NASA Astrophysics Data System (ADS)

Zedam, Lemnaouar; Pérez-Fernández, Raúl; Bouremel, Hassane; De Baets, Bernard

2018-05-01

In a recent paper, we have introduced the notion of clone relation of a given binary relation. Intuitively, two elements are said to be "clones" if they are related in the same way w.r.t. every other element. In this paper, we generalize this notion from pairs of elements to sets of elements of any cardinality, resulting in the introduction of clonal sets. We investigate the most important properties of clonal sets, paying particular attention to the introduction of the clonal closure operator, to the analysis of the (lattice) structure of the set of clonal sets and to a distance metric expressing how close two elements are to being clones.

Transfection of Capsaspora owczarzaki, a close unicellular relative of animals.

PubMed

Parra-Acero, Helena; Ros-Rocher, Núria; Perez-Posada, Alberto; Kożyczkowska, Aleksandra; Sánchez-Pons, Núria; Nakata, Azusa; Suga, Hiroshi; Najle, Sebastián R; Ruiz-Trillo, Iñaki

2018-05-11

How animals emerged from their unicellular ancestor remains a major evolutionary question. New genome data from the closest unicellular relatives of animals has provided important insights into animal origins. We know that the unicellular ancestor of animals had an unexpectedly complex genetic repertoire, including many genes key to animal development and multicellularity. Thus, assessing the function of these genes among unicellular relatives of animals is key to understand how were they co-opted at the onset of Metazoa. However, those analyses have been hampered by the lack of genetic tools. Progress has been made in choanoflagellates and teretosporeans, two of the three lineages closely related to animals, while in filastereans no tools are yet available for functional analysis. Importantly, filastereans possess a striking repertoire of genes involved in transcriptional regulation and other developmental processes. Here, we describe a reliable transfection method for the filasterean Capsaspora owczarzaki We also provide a set of constructs for visualizing subcellular structures in live cells. These tools convert Capsaspora into a unique experimentally tractable organism to address the origin and evolution of animal multicellularity. © 2018. Published by The Company of Biologists Ltd.

Multigene-based analyses on evolutionary phylogeny of two controversial ciliate orders: Pleuronematida and Loxocephalida (Protista, Ciliophora, Oligohymenophorea).

PubMed

Gao, Feng; Katz, Laura A; Song, Weibo

2013-07-01

Relationships among members of the ciliate subclass Scuticociliatia (Ciliophora, Oligohymenophorea) are largely unresolved. Phylogenetic studies of its orders Pleuronematida and Loxocephalida were initially based on small subunit ribosomal RNA gene (SSU-rDNA) analyses of a limited number of taxa. Here we characterized 37 sequences (SSU-rDNA, ITS-5.8S and LSU-rDNA) from 21 taxonomically controversial members of these orders. Phylogenetic trees constructed to assess the inter- and intra-generic relationships of pleuronematids and loxocephalids reveal the following: (1) the order Loxocephalida and its two families Loxocephalidae and Cinetochilidae are not monophyletic when more taxa are added; (2) the core pleuronematids are divided into two fully supported clades, however, the order Pleuronematida is not monophyletic because Cyclidium glaucoma is closer to Thigmotrichida; (3) the family Pleuronematidae and the genus Schizocalyptra are monophyletic, though rDNA sequences of Pleuronema species are highly variable; (4) Pseudoplatynematum and Sathrophilus are closely related to the subclass Astomatia, while Cinetochilum forms a monophyletic group with the subclass Apostomatia; and (5) Hippocomos falls in the order Pleuronematida and is closely related to Eurystomatellidae and Cyclidium plouneouri. Further, in an effort to provide a better resolution of evolutionary relationships, the secondary structures of ITS2 transcripts and the variable region 4 (V4) of the small subunit ribosomal RNA (SSU-rRNA) are predicted, revealing that ITS2 structures are conserved at the order level while V4 region structures are more variable than ITS2 structures. Copyright © 2013 Elsevier Inc. All rights reserved.

Quantification of site-city interaction effects on the response of structure under double resonance condition

NASA Astrophysics Data System (ADS)

Kumar, Neeraj; Narayan, Jay Prakash

2018-01-01

This paper presents the site-city interaction (SCI) effects on the response of closely spaced structures under double resonance condition (F_{02{{D}}}^{{S}} = F_{02{{D}}}^{{B}}), where F_{02{{D}}}^{{S}} and F_{02{{D}}}^{{B}} are fundamental frequencies of 2-D structure and 2-D basin, respectively. This paper also presents the development of empirical relations to predict the F_{02{{D}}}^{{B}} of elliptical and trapezoidal basins for both the polarizations of the S wave. Simulated results revealed that F_{02{{D}}}^{{B}} of a 2-D basin very much depends on its geometry, shape ratio and polarization of the incident S wave. The obtained spectral amplification factor (SAF) at F_{02{{D}}}^{{S}} of a standalone structure in a 2-D basin is greater than that in the 1-D case under double resonance condition. A considerable reduction of the fundamental resonance frequency of structures due to the SCI effects is observed for both the polarizations of the S wave. The SAFs at F_{02{{D}}}^{{S}} of closely spaced structures due to SCI effects is larger in the case of SV than SH waves. A splitting of the fundamental-mode frequency bandwidth along with the drastic decrease of SAF due to the SCI effects is obtained. The findings of this paper raise the question concerning the validity of the predicted response of standalone structure based on soil-structure interaction for the design of structures in a 2-D small basin, in an urban environment.

Structure of alpha-glycerophosphate oxidase from Streptococcus sp.: a template for the mitochondrial alpha-glycerophosphate dehydrogenase.

PubMed

Colussi, Timothy; Parsonage, Derek; Boles, William; Matsuoka, Takeshi; Mallett, T Conn; Karplus, P Andrew; Claiborne, Al

2008-01-22

The FAD-dependent alpha-glycerophosphate oxidase (GlpO) from Enterococcus casseliflavus and Streptococcus sp. was originally studied as a soluble flavoprotein oxidase; surprisingly, the GlpO sequence is 30-43% identical to those of the alpha-glycerophosphate dehydrogenases (GlpDs) from mitochondrial and bacterial sources. The structure of a deletion mutant of Streptococcus sp. GlpO (GlpODelta, lacking a 50-residue insert that includes a flexible surface region) has been determined using multiwavelength anomalous dispersion data and refined at 2.3 A resolution. Using the GlpODelta structure as a search model, we have also determined the intact GlpO structure, as refined at 2.4 A resolution. The first two domains of the GlpO fold are most closely related to those of the flavoprotein glycine oxidase, where they function in FAD binding and substrate binding, respectively; the GlpO C-terminal domain consists of two helix bundles and is not closely related to any known structure. The flexible surface region in intact GlpO corresponds to a segment of missing electron density that links the substrate-binding domain to a betabetaalpha element of the FAD-binding domain. In accordance with earlier biochemical studies (stabilizations of the covalent FAD-N5-sulfite adduct and p-quinonoid form of 8-mercapto-FAD), Ile430-N, Thr431-N, and Thr431-OG are hydrogen bonded to FAD-O2alpha in GlpODelta, stabilizing the negative charge in these two modified flavins and facilitating transfer of a hydride to FAD-N5 (from Glp) as well. Active-site overlays with the glycine oxidase-N-acetylglycine and d-amino acid oxidase-d-alanine complexes demonstrate that Arg346 of GlpODelta is structurally equivalent to Arg302 and Arg285, respectively; in both cases, these residues interact directly with the amino acid substrate or inhibitor carboxylate. The structural and functional divergence between GlpO and the bacterial and mitochondrial GlpDs is also discussed.

Accretion dynamics of EX Lupi in quiescence. The star, the spot, and the accretion column

NASA Astrophysics Data System (ADS)

Sicilia-Aguilar, Aurora; Fang, Min; Roccatagliata, Veronica; Collier Cameron, Andrew; Kóspál, Ágnes; Henning, Thomas; Ábrahám, Peter; Sipos, Nikoletta

2015-08-01

Context. EX Lupi is a young, accreting M0 star and the prototype of EXor variable stars. Its spectrum is very rich in emission lines, including many metallic lines with narrow and broad components. The presence of a close companion has also been proposed, based on radial velocity signatures. Aims: We use the metallic emission lines to study the accretion structures and to test the companion hypothesis. Methods: We analyse 54 spectra obtained during five years of quiescence time. We study the line profile variability and the radial velocity of the narrow and broad metallic emission lines. We use the velocity signatures of different species with various excitation conditions and their time dependency to track the dynamics associated with accretion. Results: We observe periodic velocity variations in the broad and the narrow line components, consistent with rotational modulation. The modulation is stronger for lines with higher excitation potentials (e.g. He II), which are likely produced in a confined area very close to the accretion shock. Conclusions: We propose that the narrow line components are produced in the post-shock region, while the broad components originate in the more extended, pre-shock material in the accretion column. All the emission lines suffer velocity modulation due to the rotation of the star. The broad components are responsible for the line-dependent veiling observed in EX Lupi. We demonstrate that a rotationally modulated line-dependent veiling can explain the radial velocity signature of the photospheric absorption lines, making the close-in companion hypothesis unnecessary. The accretion structure is locked to the star and very stable during the five years of observations. Not all stars with similar spectral types and accretion rates show the same metallic emission lines, which could be related to differences in temperature and density in their accretion structure(s). The contamination of photospheric signatures by accretion-related processes can be turned into a very useful tool for determining the innermost details of the accretion channels in the proximity of the star. The presence of emission lines from very stable accretion columns will nevertheless be a very strong limitation for the detection of companions by radial velocity in young stars, given the similarity of the accretion-related signatures with those produced by a companion. Appendices are available in electronic form at http://www.aanda.org

Signatures of Value Comparison in Ventral Striatum Neurons

PubMed Central

Strait, Caleb E.; Sleezer, Brianna J.; Hayden, Benjamin Y.

2015-01-01

The ventral striatum (VS), like its cortical afferents, is closely associated with processing of rewards, but the relative contributions of striatal and cortical reward systems remains unclear. Most theories posit distinct roles for these structures, despite their similarities. We compared responses of VS neurons to those of ventromedial prefrontal cortex (vmPFC) Area 14 neurons, recorded in a risky choice task. Five major response patterns observed in vmPFC were also observed in VS: (1) offer value encoding, (2) value difference encoding, (3) preferential encoding of chosen relative to unchosen value, (4) a correlation between residual variance in responses and choices, and (5) prominent encoding of outcomes. We did observe some differences as well; in particular, preferential encoding of the chosen option was stronger and started earlier in VS than in vmPFC. Nonetheless, the close match between vmPFC and VS suggests that cortex and its striatal targets make overlapping contributions to economic choice. PMID:26086735

Rapid neo-sex chromosome evolution and incipient speciation in a major forest pest.

PubMed

Bracewell, Ryan R; Bentz, Barbara J; Sullivan, Brian T; Good, Jeffrey M

2017-11-17

Genome evolution is predicted to be rapid following the establishment of new (neo) sex chromosomes, but it is not known if neo-sex chromosome evolution plays an important role in speciation. Here we combine extensive crossing experiments with population and functional genomic data to examine neo-XY chromosome evolution and incipient speciation in the mountain pine beetle. We find a broad continuum of intrinsic incompatibilities in hybrid males that increase in strength with geographic distance between reproductively isolated populations. This striking progression of reproductive isolation is coupled with extensive gene specialization, natural selection, and elevated genetic differentiation on both sex chromosomes. Closely related populations isolated by hybrid male sterility also show fixation of alternative neo-Y haplotypes that differ in structure and male-specific gene content. Our results suggest that neo-sex chromosome evolution can drive rapid functional divergence between closely related populations irrespective of ecological drivers of divergence.

Diagonalizing controller for a superconducting six-axis accelerometer

NASA Astrophysics Data System (ADS)

Bachrach, B.; Canavan, E. R.; Levine, W. S.

A relatively simple MIMO (multiple input, multiple output) controller which converts an instrument with a nondiagonally dominant transfer function matrix into a strongly diagonally dominant device is developed. The instrument, which uses inductance bridges to sense the position of a magnetically levitated superconducting mass, has very lightly damped resonances and fairly strong cross coupling. By taking advantage of the particular structure of the instrument's transfer function matrix, it is possible to develop a relatively simple controller which achieves the desired decoupling. This controller consists of two parts. The first part cancels the nondiagonal terms of the open-loop transfer function matrix, while the second part is simply a set of SISO (single input, single output) controllers. The stability of the closed-loop system is studied using Rosenbrock's INA (inverse Nyguist array) technique, which produces a simple set of conditions guaranteeing stability. Simulation of the closed-loop system indicates that it should easily achieve its performance goals.

Differentiation of closely related isomers: application of data mining techniques in conjunction with variable wavelength infrared multiple photon dissociation mass spectrometry for identification of glucose-containing disaccharide ions.

PubMed

Stefan, Sarah E; Ehsan, Mohammad; Pearson, Wright L; Aksenov, Alexander; Boginski, Vladimir; Bendiak, Brad; Eyler, John R

2011-11-15

Data mining algorithms have been used to analyze the infrared multiple photon dissociation (IRMPD) patterns of gas-phase lithiated disaccharide isomers irradiated with either a line-tunable CO(2) laser or a free electron laser (FEL). The IR fragmentation patterns over the wavelength range of 9.2-10.6 μm have been shown in earlier work to correlate uniquely with the asymmetry at the anomeric carbon in each disaccharide. Application of data mining approaches for data analysis allowed unambiguous determination of the anomeric carbon configurations for each disaccharide isomer pair using fragmentation data at a single wavelength. In addition, the linkage positions were easily assigned. This combination of wavelength-selective IRMPD and data mining offers a powerful and convenient tool for differentiation of structurally closely related isomers, including those of gas-phase carbohydrate complexes.

[Epigenetics of prostate cancer].

PubMed

Yi, Xiao-Ming; Zhou, Wen-Quan

2010-07-01

Prostate cancer is one of the most common malignant tumors in males, and its etiology and pathogenesis remain unclear. Epigenesis is involved in prostate cancer at all stages of the process, and closely related with its growth and metastasis. DNA methylation and histone modification are the most important manifestations of epigenetics in prostate cancer. The mechanisms of carcinogenesis of DNA methylation include whole-genome hypomethylation, aberrant local hypermethylation of promoters and genomic instability. DNA methylation is closely related to the process of prostate cancer, as in DNA damage repair, hormone response, tumor cell invasion/metastasis, cell cycle regulation, and so on. Histone modification causes corresponding changes in chromosome structure and the level of gene transcription, and it may affect the cycle, differentiation and apoptosis of cells, resulting in prostate cancer. Some therapies have been developed targeting the epigenetic changes in prostate cancer, including DNA methyltransferases and histone deacetylase inhibitors, and have achieved certain desirable results.

Localization-delocalization transition in a system of quantum kicked rotors.

PubMed

Creffield, C E; Hur, G; Monteiro, T S

2006-01-20

The quantum dynamics of atoms subjected to pairs of closely spaced delta kicks from optical potentials are shown to be quite different from the well-known paradigm of quantum chaos, the single delta-kick system. We find the unitary matrix has a new oscillating band structure corresponding to a cellular structure of phase space and observe a spectral signature of a localization-delocalization transition from one cell to several. We find that the eigenstates have localization lengths which scale with a fractional power L approximately h(-0.75) and obtain a regime of near-linear spectral variances which approximate the "critical statistics" relation summation2(L) approximately or equal to chi(L) approximately 1/2 (1-nu)L, where nu approximately 0.75 is related to the fractal classical phase-space structure. The origin of the nu approximately 0.75 exponent is analyzed.

Aquaporin structure-function relationships: water flow through plant living cells.

PubMed

Zhao, Chang-Xing; Shao, Hong-Bo; Chu, Li-Ye

2008-04-01

Plant aquaporins play an important role in water uptake and movement-an aquaporin that opens and closes a gate that regulates water movement in and out of cells. Some plant aquaporins also play an important role in response to water stress. Since their discovery, advancing knowledge of their structures and properties led to an understanding of the basic features of the water transport mechanism and increased illumination to water relations. Meanwhile, molecular and functional characterization of aquaporins has revealed the significance of their regulation in response to the adverse environments such as salinity and drought. This paper reviews the structure, species diversity, physiology function, regulation of plant aquaporins, and the relations between environmental factors and plant aquaporins. Complete understanding of aquaporin function and regulation is to integrate those mechanisms in time and space and to well regulate the permeation of water across biological membranes under changing environmental and developmental conditions.

Study of the electronic structure of electron accepting cyano-films: TCNQversusTCNE.

PubMed

Capitán, Maria J; Álvarez, Jesús; Navio, Cristina

2018-04-18

In this article, we perform systematic research on the electronic structure of two closely related organic electron acceptor molecules (TCNQ and TCNE), which are of technological interest due to their outstanding electronic properties. These studies have been performed from the experimental point of view by the use electron spectroscopies (XPS and UPS) and supported theoretically by the use of ab-initio DFT calculations. The cross-check between both molecules allows us to identify the characteristic electronic features of each part of the molecules and their contribution to the final electronic structure. We can describe the nature of the band gap of these materials, and we relate this with the appearance of the shake-up features in the core level spectra. A band bending and energy gap reduction of the aforementioned electronic structure in contact with a metal surface are seen in the experimental results as well in the theoretical calculations. This behavior implies that the TCNQ thin film accepts electrons from the metal substrate becoming a Schottky n-junction.

High-throughput search of ternary chalcogenides for p-type transparent electrodes

PubMed Central

Shi, Jingming; Cerqueira, Tiago F. T.; Cui, Wenwen; Nogueira, Fernando; Botti, Silvana; Marques, Miguel A. L.

2017-01-01

Delafossite crystals are fascinating ternary oxides that have demonstrated transparent conductivity and ambipolar doping. Here we use a high-throughput approach based on density functional theory to find delafossite and related layered phases of composition ABX2, where A and B are elements of the periodic table, and X is a chalcogen (O, S, Se, and Te). From the 15 624 compounds studied in the trigonal delafossite prototype structure, 285 are within 50 meV/atom from the convex hull of stability. These compounds are further investigated using global structural prediction methods to obtain their lowest-energy crystal structure. We find 79 systems not present in the materials project database that are thermodynamically stable and crystallize in the delafossite or in closely related structures. These novel phases are then characterized by calculating their band gaps and hole effective masses. This characterization unveils a large diversity of properties, ranging from normal metals, magnetic metals, and some candidate compounds for p-type transparent electrodes. PMID:28266587

Structure and function of Zika virus NS5 protein: perspectives for drug design.

PubMed

Wang, Boxiao; Thurmond, Stephanie; Hai, Rong; Song, Jikui

2018-05-01

Zika virus (ZIKV) belongs to the positive-sense single-stranded RNA-containing Flaviviridae family. Its recent outbreak and association with human diseases (e.g. neurological disorders) have raised global health concerns, and an urgency to develop a therapeutic strategy against ZIKV infection. However, there is no currently approved antiviral against ZIKV. Here we present a comprehensive overview on recent progress in structure-function investigation of ZIKV NS5 protein, the largest non-structural protein of ZIKV, which is responsible for replication of the viral genome, RNA capping and suppression of host interferon responses. Structural comparison of the N-terminal methyltransferase domain and C-terminal RNA-dependent RNA polymerase domain of ZIKV NS5 with their counterparts from related viruses provides mechanistic insights into ZIKV NS5-mediated RNA replication, and identifies residues critical for its enzymatic activities. Finally, a collection of recently identified small molecule inhibitors against ZIKV NS5 or its closely related flavivirus homologues are also discussed.

Toward elucidating the heat activation mechanism of the TRPV1 channel gating by molecular dynamics simulation.

PubMed

Wen, Han; Qin, Feng; Zheng, Wenjun

2016-12-01

As a key cellular sensor, the TRPV1 cation channel undergoes a gating transition from a closed state to an open state in response to various physical and chemical stimuli including noxious heat. Despite years of study, the heat activation mechanism of TRPV1 gating remains enigmatic at the molecular level. Toward elucidating the structural and energetic basis of TRPV1 gating, we have performed molecular dynamics (MD) simulations (with cumulative simulation time of 3 μs), starting from the high-resolution closed and open structures of TRPV1 solved by cryo-electron microscopy. In the closed-state simulations at 30°C, we observed a stably closed channel constricted at the lower gate (near residue I679), while the upper gate (near residues G643 and M644) is dynamic and undergoes flickery opening/closing. In the open-state simulations at 60°C, we found higher conformational variation consistent with a large entropy increase required for the heat activation, and both the lower and upper gates are dynamic with transient opening/closing. Through ensemble-based structural analyses of the closed state versus the open state, we revealed pronounced closed-to-open conformational changes involving the membrane proximal domain (MPD) linker, the outer pore, and the TRP helix, which are accompanied by breaking/forming of a network of closed/open-state specific hydrogen bonds. By comparing the closed-state simulations at 30°C and 60°C, we observed heat-activated conformational changes in the MPD linker, the outer pore, and the TRP helix that resemble the closed-to-open conformational changes, along with partial formation of the open-state specific hydrogen bonds. Some of the residues involved in the above key hydrogen bonds were validated by previous mutational studies. Taken together, our MD simulations have offered rich structural and dynamic details beyond the static structures of TRPV1, and promising targets for future mutagenesis and functional studies of the TRPV1 channel. Proteins 2016; 84:1938-1949. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Radiating despite a Lack of Character: Ecological Divergence among Closely Related, Morphologically Similar Honeyeaters (Aves: Meliphagidae) Co-occurring in Arid Australian Environments.

PubMed

Miller, Eliot T; Wagner, Sarah K; Harmon, Luke J; Ricklefs, Robert E

2017-02-01

Quantifying the relationship between form and function can inform use of morphology as a surrogate for ecology. How the strength of this relationship varies continentally can inform understanding of evolutionary radiations; for example, does the relationship break down when certain lineages invade and diversify in novel habitats? The 75 species of Australian honeyeaters (Meliphagidae) are morphologically and ecologically diverse, with species feeding on nectar, insects, fruit, and other resources. We investigated Meliphagidae ecomorphology and community structure by (1) quantifying the concordance between morphology and ecology (foraging behavior), (2) estimating rates of trait evolution in relation to the packing of ecological space, and (3) comparing phylogenetic and trait community structure across the broad environmental gradients of the continent. We found that morphology explained 37% of the variance in ecology (and 62% vice versa), and we uncovered well-known bivariate relationships among the multivariate ecomorphological data. Ecological trait diversity declined less rapidly than phylogenetic diversity along a gradient of decreasing precipitation. We employ a new method (trait fields) and extend another (phylogenetic fields) to show that while species in phylogenetically clustered, arid-environment assemblages are similar morphologically, they are as varied in foraging behavior as those from more diverse assemblages. Thus, although closely related and similar morphologically, these arid-adapted species have diverged in ecological space to a similar degree as their mesic counterparts.

Influences of deep learning, need for cognition and preparation time on open- and closed-book test performance.

PubMed

Heijne-Penninga, Marjolein; Kuks, Jan B M; Hofman, W H Adriaan; Cohen-Schotanus, Janke

2010-09-01

The ability to master discipline-specific knowledge is one of the competencies medical students must acquire. In this context, 'mastering' means being able to recall and apply knowledge. A way to assess this competency is to use both open- and closed-book tests. Student performance on both tests can be influenced by the way the student processes information. Deep information processing is expected to influence performance positively. The personal preferences of students in relation to how they process information in general (i.e. their level of need for cognition) may also be of importance. In this study, we examined the inter-relatedness of deep learning, need for cognition and preparation time, and scores on open- and closed-book tests. This study was conducted at the University Medical Centre Groningen. Participants were Year 2 students (n = 423). They were asked to complete a questionnaire on deep information processing, a scale for need for cognition on a questionnaire on intellectualism and, additionally, to write down the time they spent on test preparation. We related these measures to the students' scores on two tests, both consisting of open- and closed-book components and used structural equation modelling to analyse the data. Both questionnaires were completed by 239 students (57%). The results showed that need for cognition positively influenced both open- and closed-book test scores (beta-coefficients 0.05 and 0.11, respectively). Furthermore, study outcomes measured by open-book tests predicted closed-book test results better than the other way around (beta-coefficients 0.72 and 0.11, respectively). Students with a high need for cognition performed better on open- as well as closed-book tests. Deep learning did not influence their performance. Adding open-book tests to the regularly used closed-book tests seems to improve the recall of knowledge that has to be known by heart. Need for cognition may provide a valuable addition to existing theories on learning.

The association between early generative concern and caregiving with friends from early to middle adolescence.

PubMed

Lawford, Heather L; Doyle, Anna-Beth; Markiewicz, Dorothy

2013-12-01

Generativity, defined as concern for future generations, is theorized to become a priority in midlife, preceded by a stage in which intimacy is the central issue. Recent research, however, has found evidence of generativity even in adolescence. This longitudinal study explored the associations between caregiving in friendships, closely related to intimacy, and early generative concern in a young adolescent sample. Given the importance of close friendships in adolescence, it was hypothesized that responsive caregiving in early adolescent friendships would predict later generative concern. Approximately 140 adolescents (56 % female, aged 14 at Time 1) completed questionnaires regarding generative concern and responsive caregiving with friends yearly across 2 years. Structural equation modeling revealed that caregiving predicted generative concern 1 year later but generative concern did not predict later caregiving. These results suggest that caregiving in close friendships plays an important role in the development of adolescents' motivation to contribute to future generations.

Genomic and antigenic characterization of the newly emerging Chinese duck egg-drop syndrome flavivirus: genomic comparison with Tembusu and Sitiawan viruses.

PubMed

Liu, Peipei; Lu, Hao; Li, Shuang; Moureau, Gregory; Deng, Yong-Qiang; Wang, Yongyue; Zhang, Lijiao; Jiang, Tao; de Lamballerie, Xavier; Qin, Cheng-Feng; Gould, Ernest A; Su, Jingliang; Gao, George F

2012-10-01

Duck egg-drop syndrome virus (DEDSV) is a newly emerging pathogenic flavivirus causing avian diseases in China. The infection occurs in laying ducks characterized by a severe drop in egg production with a fatality rate of 5-15 %. The virus was found to be most closely related to Tembusu virus (TMUV), an isolate from mosquitoes in South-east Asia. Here, we have sequenced and characterized the full-length genomes of seven DEDSV strains, including the 5'- and 3'-non-coding regions (NCRs). We also report for the first time the ORF sequences of TMUV and Sitiawan virus (STWV), another closely related flavivirus isolated from diseased chickens. We analysed the phylogenetic and antigenic relationships of DEDSV in relation to the Asian viruses TMUV and STWV, and other representative flaviviruses. Our results confirm the close relationship between DEDSV and TMUV/STWV and we discuss their probable evolutionary origins. We have also characterized the cleavage sites, potential glycosylation sites and unique motifs/modules of these viruses. Additionally, conserved sequences in both 5'- and 3'-NCRs were identified and the predicted secondary structures of the terminal sequences were studied. Antigenic cross-reactivity comparisons of DEDSV with related pathogenic flaviviruses identified a surprisingly close relationship with dengue virus (DENV) and raised the question of whether or not DEDSV may have a potential infectious threat to man. Importantly, DEDSV can be efficiently recognized by a broadly cross-reactive flavivirus mAb, 2A10G6, derived against DENV. The significance of these studies is discussed in the context of the emergence, evolution, epidemiology, antigenicity and pathogenicity of the newly emergent DEDSV.

Stuffed Derivatives of Close-Packed Structures

ERIC Educational Resources Information Center

Douglas, Bodie E.

2007-01-01

Decades ago Buerger described and later Palmer reviewed stuffed silica crystal structures widely used by mineralogists. Many publications and books have discussed common crystal structures in terms of close-packing of one set of atoms or ions (P sites) with other atoms or ions in tetrahedral (T) or octahedral (O) sites. Douglas and Ho described…

Use of the Primitive Unit Cell in Understanding Subtle Features of the Cubic Closest-Packed Structure

ERIC Educational Resources Information Center

Hawkins, John A.; Rittenhouse, Jeffrey L.; Soper, Linda M.; Rittenhouse, Robert C.

2008-01-01

One of the most important crystal structures adopted by metals is characterized by the "abcabc"...stacking of close-packed layers. This structure is commonly referred to in textbooks as the cubic close-packed (ccp) or face-centered cubic (fcc) structure, since the entire lattice can be generated by replication of a face-centered cubic unit cell…

Ab initio study of structural and mechanical property of solid molecular hydrogens

NASA Astrophysics Data System (ADS)

Ye, Yingting; Yang, Li; Yang, Tianle; Nie, Jinlan; Peng, Shuming; Long, Xinggui; Zu, Xiaotao; Du, Jincheng

2015-06-01

Ab initio calculations based on density functional theory (DFT) were performed to investigate the structural and the elastic properties of solid molecular hydrogens (H2). The influence of molecular axes of H2 on structural relative stabilities of hexagonal close-packed (hcp) and face-centered cubic (fcc) structured hydrogen molecular crystals were systematically investigated. Our results indicate that for hcp structures, disordered hydrogen molecule structure is more stable, while for fcc structures, Pa3 hydrogen molecular crystal is most stable. The cohesive energy of fcc H2 crystal was found to be lower than hcp. The mechanical properties of fcc and hcp hydrogen molecular crystals were obtained, with results consistent with previous theoretical calculations. In addition, the effects of zero point energy (ZPE) and van der Waals (vdW) correction on the cohesive energy and the stability of hydrogen molecular crystals were systematically studied and discussed.

Extending CATH: increasing coverage of the protein structure universe and linking structure with function

PubMed Central

Cuff, Alison L.; Sillitoe, Ian; Lewis, Tony; Clegg, Andrew B.; Rentzsch, Robert; Furnham, Nicholas; Pellegrini-Calace, Marialuisa; Jones, David; Thornton, Janet; Orengo, Christine A.

2011-01-01

CATH version 3.3 (class, architecture, topology, homology) contains 128 688 domains, 2386 homologous superfamilies and 1233 fold groups, and reflects a major focus on classifying structural genomics (SG) structures and transmembrane proteins, both of which are likely to add structural novelty to the database and therefore increase the coverage of protein fold space within CATH. For CATH version 3.4 we have significantly improved the presentation of sequence information and associated functional information for CATH superfamilies. The CATH superfamily pages now reflect both the functional and structural diversity within the superfamily and include structural alignments of close and distant relatives within the superfamily, annotated with functional information and details of conserved residues. A significantly more efficient search function for CATH has been established by implementing the search server Solr (http://lucene.apache.org/solr/). The CATH v3.4 webpages have been built using the Catalyst web framework. PMID:21097779

Separation system

DOEpatents

Rubin, Leslie S.

1986-01-01

A separation system for dewatering radioactive waste materials includes a disposal container, drive structure for receiving the container, and means for releasably attaching the container to the drive structure. Separation structure disposed in the container adjacent the inner surface of the side wall structure retains solids while allowing passage of liquids. Inlet port structure in the container top wall is normally closed by first valve structure that is centrifugally actuated to open the inlet port and discharge port structure at the container periphery receives liquid that passes through the separation structure and is normally closed by second valve structure that is centrifugally actuated to open the discharge ports. The container also includes coupling structure for releasable engagement with the centrifugal drive structure. Centrifugal force produced when the container is driven in rotation by the drive structure opens the valve structures, and radioactive waste material introduced into the container through the open inlet port is dewatered, and the waste is compacted. The ports are automatically closed by the valves when the container drum is not subjected to centrifugal force such that containment effectiveness is enhanced and exposure of personnel to radioactive materials is minimized.

Ambivalent Sexism in Close Relationships: (Hostile) Power and (Benevolent) Romance Shape Relationship Ideals

PubMed Central

Lee, Tiane L.; Fiske, Susan T.; Glick, Peter; Chen, Zhixia

2013-01-01

Gender-based structural power and heterosexual dependency produce ambivalent gender ideologies, with hostility and benevolence separately shaping close-relationship ideals. The relative importance of romanticized benevolent versus more overtly power-based hostile sexism, however, may be culturally dependent. Testing this, northeast US (N=311) and central Chinese (N=290) undergraduates rated prescriptions and proscriptions (ideals) for partners and completed Ambivalent Sexism and Ambivalence toward Men Inventories (ideologies). Multiple regressions analyses conducted on group-specific relationship ideals revealed that benevolent ideologies predicted partner ideals, in both countries, especially for US culture’s romance-oriented relationships. Hostile attitudes predicted men’s ideals, both American and Chinese, suggesting both societies’ dominant-partner advantage. PMID:23914004

[Family communication styles, attitude towards institutional authority and adolescents' violent behaviour at school].

PubMed

Estévez López, Estefanía; Murgui Pérez, Sergio; Moreno Ruiz, David; Musitu Ochoa, Gonzalo

2007-02-01

The purpose of present study is to analyse the relationship among certain family and school factors, adolescents' attitude towards institutional authority, and violent behaviour at school. The sample is composed of 1049 adolescents of both sexes and aged from 11 to 16 years old. Statistical analyses were carried out using structural equation modelling. Results indicate a close association between negative communication with father and violent behaviour in adolescence. Moreover, data suggest that teachers' expectations affect students' attitude towards institutional authority, which in turn is closely related to school violence. Finally, findings show an indirect influence of father, mother and teacher in adolescents' violent behaviour, mainly through their effect on family- and school-self-concept.

Upland Hardwood Forests and Related Communities of the Arkansas Ozarks in the Early 19th Century

Treesearch

Thomas L. Foti

2004-01-01

Historic accounts of the 19 th Century Arkansas Ozarks mention such communities as oak forests, pine forests, barrens and prairies. I document the region-wide distribution of these types based on data from the first land survey conducted by the General Land Office (GLO). Structural classes used here include closed forest, open forest, woodland, savanna, open savanna...

[Cross reactivities between food antigens of plant or animal origin].

PubMed

Bakos, N; Nékám, K

2000-03-26

Knowledge about cross reactivities among food proteins of plant or animal origin is getting more and more important. Cross reaction provoking often clinical symptoms may be based on close taxonomical relations or on the presence of "archaic", ubiquiter protein structures preserved during phylogenesis. The most significant cross reactivities characterized by increasing incidence are between pollens and foods of plant origin and between latex and fruits.

Modeling and validating the grabbing forces of hydraulic log grapples used in forest operations

Treesearch

Jingxin Wang; Chris B. LeDoux; Lihai Wang

2003-01-01

The grabbing forces of log grapples were modeled and analyzed mathematically under operating conditions when grabbing logs from compact log piles and from bunch-like log piles. The grabbing forces are closely related to the structural parameters of the grapple, the weight of the grapple, and the weight of the log grabbed. An operational model grapple was designed and...

A new species of Megaperlodes Yokoyama et al. 1990 (Plecoptera, Perlodidae) from the South of the Russian Far East.

PubMed

Teslenko, Valentina A

2015-01-08

A new species of Plecoptera Megaperlodes tiunovi sp. n., from the South of the Russian Far East is described and illustrated. The relationships with its close relatives are discussed. Newly discovered features are added to the diagnosis of the genus Megaperlodes, especially previously overlooked eversible lobes within the paraprocts, egg structure, and wing venation.

Task Design for Students' Work with Basic Theory in Analysis: The Cases of Multidimensional Differentiability and Curve Integrals

ERIC Educational Resources Information Center

Gravesen, Katrine Frovin; Grønbaek, Niels; Winsløw, Carl

2017-01-01

We investigate the challenges students face in the transition from calculus courses, focusing on methods related to the analysis of real valued functions given in closed form, to more advanced courses on analysis where focus is on theoretical structure, including proof. We do so based on task design aiming for a number of generic potentials for…

Closed-loop carrier phase synchronization techniques motivated by likelihood functions

NASA Technical Reports Server (NTRS)

Tsou, H.; Hinedi, S.; Simon, M.

1994-01-01

This article reexamines the notion of closed-loop carrier phase synchronization motivated by the theory of maximum a posteriori phase estimation with emphasis on the development of new structures based on both maximum-likelihood and average-likelihood functions. The criterion of performance used for comparison of all the closed-loop structures discussed is the mean-squared phase error for a fixed-loop bandwidth.

Structural Evidence of a Major Conformational Change Triggered by Substrate Binding in DapE Enzymes: Impact on the Catalytic Mechanism

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

Nocek, Boguslaw; Reidl, Cory; Starus, Anna

In this paper, the X-ray crystal structure of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase from Haemophilus influenzae (HiDapE) bound by the products of hydrolysis, succinic acid and l,l-DAP, was determined at 1.95 Å. Surprisingly, the structure bound to the products revealed that HiDapE undergoes a significant conformational change in which the catalytic domain rotates ~50° and shifts ~10.1 Å (as measured at the position of the Zn atoms) relative to the dimerization domain. This heretofore unobserved closed conformation revealed significant movements within the catalytic domain compared to that of wild-type HiDapE, which results in effectively closing off access to the dinuclearmore » Zn(II) active site with the succinate carboxylate moiety bridging the dinculear Zn(II) cluster in a μ-1,3 fashion forming a bis(μ-carboxylato)dizinc(II) core with a Zn–Zn distance of 3.8 Å. Surprisingly, His194.B, which is located on the dimerization domain of the opposing chain ~10.1 Å from the dinuclear Zn(II) active site, forms a hydrogen bond (2.9 Å) with the oxygen atom of succinic acid bound to Zn2, forming an oxyanion hole. As the closed structure forms upon substrate binding, the movement of His194.B by more than ~10 Å is critical, based on site-directed mutagenesis data, for activation of the scissile carbonyl carbon of the substrate for nucleophilic attack by a hydroxide nucleophile. Employing the HiDapE product-bound structure as the starting point, a reverse engineering approach called product-based transition-state modeling provided structural models for each major catalytic step. Finally, these data provide insight into the catalytic reaction mechanism and also the future design of new, potent inhibitors of DapE enzymes.« less

Structural Evidence of a Major Conformational Change Triggered by Substrate Binding in DapE Enzymes: Impact on the Catalytic Mechanism

DOE PAGES

Nocek, Boguslaw; Reidl, Cory; Starus, Anna; ...

2017-12-22

In this paper, the X-ray crystal structure of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase from Haemophilus influenzae (HiDapE) bound by the products of hydrolysis, succinic acid and l,l-DAP, was determined at 1.95 Å. Surprisingly, the structure bound to the products revealed that HiDapE undergoes a significant conformational change in which the catalytic domain rotates ~50° and shifts ~10.1 Å (as measured at the position of the Zn atoms) relative to the dimerization domain. This heretofore unobserved closed conformation revealed significant movements within the catalytic domain compared to that of wild-type HiDapE, which results in effectively closing off access to the dinuclearmore » Zn(II) active site with the succinate carboxylate moiety bridging the dinculear Zn(II) cluster in a μ-1,3 fashion forming a bis(μ-carboxylato)dizinc(II) core with a Zn–Zn distance of 3.8 Å. Surprisingly, His194.B, which is located on the dimerization domain of the opposing chain ~10.1 Å from the dinuclear Zn(II) active site, forms a hydrogen bond (2.9 Å) with the oxygen atom of succinic acid bound to Zn2, forming an oxyanion hole. As the closed structure forms upon substrate binding, the movement of His194.B by more than ~10 Å is critical, based on site-directed mutagenesis data, for activation of the scissile carbonyl carbon of the substrate for nucleophilic attack by a hydroxide nucleophile. Employing the HiDapE product-bound structure as the starting point, a reverse engineering approach called product-based transition-state modeling provided structural models for each major catalytic step. Finally, these data provide insight into the catalytic reaction mechanism and also the future design of new, potent inhibitors of DapE enzymes.« less

Structural Evidence of a Major Conformational Change Triggered by Substrate Binding in DapE Enzymes: Impact on the Catalytic Mechanism.

PubMed

Nocek, Boguslaw; Reidl, Cory; Starus, Anna; Heath, Tahirah; Bienvenue, David; Osipiuk, Jerzy; Jedrzejczak, Robert; Joachimiak, Andrzej; Becker, Daniel P; Holz, Richard C

2018-02-06

The X-ray crystal structure of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase from Haemophilus influenzae (HiDapE) bound by the products of hydrolysis, succinic acid and l,l-DAP, was determined at 1.95 Å. Surprisingly, the structure bound to the products revealed that HiDapE undergoes a significant conformational change in which the catalytic domain rotates ∼50° and shifts ∼10.1 Å (as measured at the position of the Zn atoms) relative to the dimerization domain. This heretofore unobserved closed conformation revealed significant movements within the catalytic domain compared to that of wild-type HiDapE, which results in effectively closing off access to the dinuclear Zn(II) active site with the succinate carboxylate moiety bridging the dinculear Zn(II) cluster in a μ-1,3 fashion forming a bis(μ-carboxylato)dizinc(II) core with a Zn-Zn distance of 3.8 Å. Surprisingly, His194.B, which is located on the dimerization domain of the opposing chain ∼10.1 Å from the dinuclear Zn(II) active site, forms a hydrogen bond (2.9 Å) with the oxygen atom of succinic acid bound to Zn2, forming an oxyanion hole. As the closed structure forms upon substrate binding, the movement of His194.B by more than ∼10 Å is critical, based on site-directed mutagenesis data, for activation of the scissile carbonyl carbon of the substrate for nucleophilic attack by a hydroxide nucleophile. Employing the HiDapE product-bound structure as the starting point, a reverse engineering approach called product-based transition-state modeling provided structural models for each major catalytic step. These data provide insight into the catalytic reaction mechanism and also the future design of new, potent inhibitors of DapE enzymes.

On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase

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

Brokaw, Jason B.; Chu, Jhih-wei

2010-11-17

We characterized the conformational change of adenylate kinase (AK) between open and closed forms by conducting five all-atom molecular-dynamics simulations, each of 100 ns duration. Different initial structures and substrate binding configurations were used to probe the pathways of AK conformational change in explicit solvent, and no bias potential was applied. A complete closed-to-open and a partial open-to-closed transition were observed, demonstrating the direct impact of substrate-mediated interactions on shifting protein conformation. The sampled configurations suggest two possible pathways for connecting the open and closed structures of AK, affirming the prediction made based on available x-ray structures and earlier worksmore » of coarse-grained modeling. The trajectories of the all-atom molecular-dynamics simulations revealed the complexity of protein dynamics and the coupling between different domains during conformational change. Calculations of solvent density and density fluctuations surrounding AK did not show prominent variation during the transition between closed and open forms. Finally, we characterized the effects of local unfolding of an important hinge near Pro177 on the closed-to-open transition of AK and identified a novel mechanism by which hinge unfolding modulates protein conformational change. The local unfolding of Pro177 hinge induces alternative tertiary contacts that stabilize the closed structure and prevent the opening transition.« less

Elementary Students' Effortful Control and Academic Achievement: The Mediating Role of Teacher-Student Relationship Quality

PubMed Central

Hernández, Maciel M.; Valiente, Carlos; Eisenberg, Nancy; Berger, Rebecca H.; Spinrad, Tracy L.; VanSchyndel, Sarah K.; Silva, Kassondra M.; Southworth, Jody; Thompson, Marilyn S.

2017-01-01

This study evaluated the association between effortful control in kindergarten and academic achievement one year later (N = 301), and whether teacher–student closeness and conflict in kindergarten mediated the association. Parents, teachers, and observers reported on children's effortful control, and teachers reported on their perceived levels of closeness and conflict with students. Students completed the passage comprehension and applied problems subtests of the Woodcock–Johnson tests of achievement, as well as a behavioral measure of effortful control. Analytical models predicting academic achievement were estimated using a structural equation model framework. Effortful control positively predicted academic achievement even when controlling for prior achievement and other covariates. Mediation hypotheses were tested in a separate model; effortful control positively predicted teacher–student closeness and strongly, negatively predicted teacher–student conflict. Teacher–student closeness and effortful control, but not teacher–student conflict, had small, positive associations with academic achievement. Effortful control also indirectly predicted higher academic achievement through its positive effect on teacher–student closeness and via its positive relation to early academic achievement. The findings suggest that teacher–student closeness is one mechanism by which effortful control is associated with academic achievement. Effortful control was also a consistent predictor of academic achievement, beyond prior achievement levels and controlling for teacher–student closeness and conflict, with implications for intervention programs on fostering regulation and achievement concurrently. PMID:28684888

Elementary Students' Effortful Control and Academic Achievement: The Mediating Role of Teacher-Student Relationship Quality.

PubMed

Hernández, Maciel M; Valiente, Carlos; Eisenberg, Nancy; Berger, Rebecca H; Spinrad, Tracy L; VanSchyndel, Sarah K; Silva, Kassondra M; Southworth, Jody; Thompson, Marilyn S

This study evaluated the association between effortful control in kindergarten and academic achievement one year later ( N = 301), and whether teacher-student closeness and conflict in kindergarten mediated the association. Parents, teachers, and observers reported on children's effortful control, and teachers reported on their perceived levels of closeness and conflict with students. Students completed the passage comprehension and applied problems subtests of the Woodcock-Johnson tests of achievement, as well as a behavioral measure of effortful control. Analytical models predicting academic achievement were estimated using a structural equation model framework. Effortful control positively predicted academic achievement even when controlling for prior achievement and other covariates. Mediation hypotheses were tested in a separate model; effortful control positively predicted teacher-student closeness and strongly, negatively predicted teacher-student conflict. Teacher-student closeness and effortful control, but not teacher-student conflict, had small, positive associations with academic achievement. Effortful control also indirectly predicted higher academic achievement through its positive effect on teacher-student closeness and via its positive relation to early academic achievement. The findings suggest that teacher-student closeness is one mechanism by which effortful control is associated with academic achievement. Effortful control was also a consistent predictor of academic achievement, beyond prior achievement levels and controlling for teacher-student closeness and conflict, with implications for intervention programs on fostering regulation and achievement concurrently.

Effect of foaming temperature on the mechanical properties of produced closed-cell A356Aluminum foams with melting method

NASA Astrophysics Data System (ADS)

Movahedi, N.; Mirbagheri, S. M. H.; Hoseini, S. R.

2014-07-01

In this study an attempt was carried out to determine the effect of production temperature on the mechanical properties and energy absorption behavior of closed-cell A356 alloy foams under uniaxial compression test. For this purpose, three different A356 alloy closed-cell foams were synthesized at three different casting temperatures, 650 °C, 675 °C and 700 °C by adding the same amounts of granulated calcium as thickening and TiH2 as blowing agent. The samples were characterized by SEM to study the pore morphology at different foaming temperatures. Compression tests of the A356 foams were carried out to assess their mechanical properties and energy absorption behavior. The results indicated that increasing the foaming temperature from 650 °C to 675 °C and 700 °C reduces the relative density of closed cell A356 alloys by 18.3% and 38% respectively and consequently affects the compressive strength and energy absorption of cellular structures by changing them from equiaxed polyhedral closed cells to distorted cells. Also at 700 °C foaming temperature, growth of micro-pores and coalescence with other surrounding pores leads to several big voids.

Factor structure of the Psychiatric Diagnostic Screening Questionnaire (PDSQ), a screening questionnaire for DSM-IV axis I disorders.

PubMed

Sheeran, T; Zimmerman, M

2004-03-01

We examined the factor structure of the Psychiatric Diagnostic Screening Questionnaire (PDSQ), a 125-item self-report scale that screens for 15 of the most common Axis I psychiatric disorders for which patients seek treatment in outpatient settings. The sample consisted of 2440 psychiatric outpatients. Thirteen factors were extracted. Ten mapped directly onto the DSM-IV diagnosis for which they were designed and one represented suicidal ideation. The remaining two factors reflected closely related disorders: Panic Disorder/Agoraphobia, and Somatization/Hypochondriasis. A psychosis factor was not extracted. Overall, the factor structure of the PDSQ was consistent with the DSM-IV nosology upon which it was developed.

Germ layer differentiation during early hindgut and cloaca formation in rabbit and pig embryos

PubMed Central

Hassoun, Romia; Schwartz, Peter; Rath, Detlef; Viebahn, Christoph; Männer, Jörg

2010-01-01

Relative to recent advances in understanding molecular requirements for endoderm differentiation, the dynamics of germ layer morphology and the topographical distribution of molecular factors involved in endoderm formation at the caudal pole of the embryonic disc are still poorly defined. To discover common principles of mammalian germ layer development, pig and rabbit embryos at late gastrulation and early neurulation stages were analysed as species with a human-like embryonic disc morphology, using correlative light and electron microscopy. Close intercellular contact but no direct structural evidence of endoderm formation such as mesenchymal–epithelial transition between posterior primitive streak mesoderm and the emerging posterior endoderm were found. However, a two-step process closely related to posterior germ layer differentiation emerged for the formation of the cloacal membrane: (i) a continuous mesoderm layer and numerous patches of electron-dense flocculent extracellular matrix mark the prospective region of cloacal membrane formation; and (ii) mesoderm cells and all extracellular matrix including the basement membrane are lost locally and close intercellular contact between the endoderm and ectoderm is established. The latter process involves single cells at first and then gradually spreads to form a longitudinally oriented seam-like cloacal membrane. These gradual changes were found from gastrulation to early somite stages in the pig, whereas they were found from early somite to mid-somite stages in the rabbit; in both species cloacal membrane formation is complete prior to secondary neurulation. The results highlight the structural requirements for endoderm formation during development of the hindgut and suggest new mechanisms for the pathogenesis of common urogenital and anorectal malformations. PMID:20874819

Excitations and relaxation dynamics in multiferroic GeV4S8 studied by terahertz and dielectric spectroscopy

NASA Astrophysics Data System (ADS)

Reschke, S.; Wang, Zhe; Mayr, F.; Ruff, E.; Lunkenheimer, P.; Tsurkan, V.; Loidl, A.

2017-10-01

We report on THz time-domain spectroscopy on multiferroic GeV4S8 , which undergoes orbital ordering at a Jahn-Teller transition at 30.5 K and exhibits antiferromagnetic order below 14.6 K. The THz experiments are complemented by dielectric experiments at audio and radio frequencies. We identify a low-lying excitation close to 0.5 THz, which is only weakly temperature dependent and probably corresponds to a molecular excitation within the electronic level scheme of the V4 clusters. In addition, we detect complex temperature-dependent behavior of a low-lying phononic excitation, closely linked to the onset of orbitally driven ferroelectricity. In the high-temperature cubic phase, which is paramagnetic and orbitally disordered, this excitation is of relaxational character becomes an overdamped Lorentzian mode in the orbitally ordered phase below the Jahn-Teller transition, and finally appears as well-defined phonon excitation in the antiferromagnetic state. Abrupt changes in the real and imaginary parts of the complex dielectric permittivity show that orbital ordering appears via a structural phase transition with strong first-order character and that the onset of antiferromagnetic order is accompanied by significant structural changes, which are of first-order character, too. Dielectric spectroscopy documents that at low frequencies, significant dipolar relaxations are present in the orbitally ordered, paramagnetic phase only. In contrast to the closely related GaV4S8 , this relaxation dynamics that most likely mirrors coupled orbital and polar fluctuations does not seem to be related to the dynamic processes detected in the THz regime.

Environmental, health and economic conditions perceived by 50 rural communities in Bangladesh.

PubMed

Ohtsuka, Ryutaro; Inaoka, Tsukasa; Moji, Kazuhiko; Karim, Enamul; Yoshinaga, Mari

2002-12-01

For randomly selected 50 villages in Bangladesh, an interview survey with a structured questionnaire was conducted to reveal their perception on the environmental, health and economic conditions at present and for the past 10-year change. The eight following items were analyzed in this paper: air pollution and water pollution, which represent environmental conditions with close relation to health conditions, soil degradation and deforestation, which represent environmental conditions with close relation to economic conditions, epidemic diseases and malnutrition, which represent health conditions, and poverty and jobless, which represent economic conditions. Among the 50 villages, deforestation was most frequently perceived serious at present and worsened in the past 10 years. Of the remaining seven items, those related to economic conditions were more seriously perceived than those related to health and environmental conditions. As revealed by the cluster analysis for the inter-item relations, epidemic diseases, which formed the same cluster with the environmental items, were recognized less serious whereas malnutrition, which formed the same cluster with the economic items, was recognized more serious. These findings are useful not only for rural development programs but also for mitigation programs toward health and environmental hazards in Bangladesh.

Supramolecular order and structural dynamics: A STM study of 2H-tetraphenylporphycene on Cu(111)

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

Stark, Michael; Träg, Johannes; Ditze, Stefanie

2015-03-14

The adsorption of 2H-tetraphenylporphycene (2HTPPc) on Cu(111) was investigated by scanning tunneling microscopy (STM). At medium coverages, supramolecular ordered islands are observed. The individual 2HTPPc molecules appear as two pairs of intense protrusions which are separated by an elongated depression. In the islands, the molecules are organized in rows oriented along one of the close packed Cu(111) substrate rows; the structure is stabilized by T-type interactions of the phenyl substituents of neighboring molecules. Two types of rows are observed, namely, highly ordered rows in which all molecules exhibit the same orientation, and less ordered rows in which the molecules exhibitmore » two perpendicular orientations. Altogether, three different azimuthal orientations of 2HTPPc are observed within one domain, all of them rotated by 15° ± 1° relative to one closed packed Cu direction. The highly ordered rows are always separated by either one or two less ordered rows, with the latter structure being the thermodynamically more stable one. The situation in the islands is highly dynamic, such that molecules in the less ordered rows occasionally change orientation, also complete highly ordered rows can move. The supramolecular order and structural dynamics are discussed on the basis of the specific molecule-substrate and molecule-molecule interactions.« less

The syntactic organization of pasta-eating and the structure of reach movements in the head-fixed mouse.

PubMed

Whishaw, Ian Q; Faraji, Jamshid; Kuntz, Jessica R; Mirza Agha, Behroo; Metz, Gerlinde A S; Mohajerani, Majid H

2017-09-08

Mice are adept in the use of their hands for activities such as feeding, which has led to their use in investigations of the neural basis of skilled-movements. We describe the syntactic organization of pasta-eating and the structure of hand movements used for pasta manipulation by the head-fixed mouse. An ethogram of mice consuming pieces of spaghetti reveals that they eat in bite/chew bouts. A bout begins with pasta lifted to the mouth and then manipulated with hand movements into a preferred orientation for biting. Manipulation involves many hand release-reach movements, each with a similar structure. A hand is advanced from a digit closed and flexed (collect) position to a digit extended and open position (overgrasp) and then to a digit closed and flexed (grasp) position. Reach distance, hand shaping, and grasp patterns featuring precision grasps or whole hand grasps are related. To bite, mice display hand preference and asymmetric grasps; one hand (guide grasp) directs food into the mouth and the other stabilizes the pasta for biting. When chewing after biting, the hands hold the pasta in a symmetric resting position. Pasta-eating is organized and features structured hand movements and so lends itself to the neural investigation of skilled-movements.

ON THE RELATIONSHIP BETWEEN SUNSPOT STRUCTURE AND MAGNETIC FIELD CHANGES ASSOCIATED WITH SOLAR FLARES

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

Song, Y. L.; Zhang, M., E-mail: ylsong@bao.ac.cn

Many previous studies have shown that magnetic fields and sunspot structures present rapid and irreversible changes associated with solar flares. In this paper, we first use five X-class flares observed by Solar Dynamics Observatory /Helioseismic and Magnetic Imager to show that not only do magnetic fields and sunspot structures show rapid, irreversible changes, but also that these changes are closely related both spatially and temporally. The magnitudes of the correlation coefficients between the temporal variations of the horizontal magnetic field and sunspot intensity are all larger than 0.90, with a maximum value of 0.99 and an average value of 0.96.more » Then, using four active regions during quiescent periods, three observed and one simulated, we show that in sunspot penumbra regions there also exists a close correlation between sunspot intensity and horizontal magnetic field strength in addition to the well-known correlation between sunspot intensity and the normal magnetic field strength. By connecting these two observational phenomena, we show that the sunspot structure change and magnetic field change are two facets of the same phenomena of solar flares; one change might be induced by the change of the other due to a linear correlation between sunspot intensity and magnetic field strength out of a local force balance.« less

Turbulent structure of stably stratified inhomogeneous flow

NASA Astrophysics Data System (ADS)

Iida, Oaki

2018-04-01

Effects of buoyancy force stabilizing disturbances are investigated on the inhomogeneous flow where disturbances are dispersed from the turbulent to non-turbulent field in the direction perpendicular to the gravity force. Attaching the fringe region, where disturbances are excited by the artificial body force, a Fourier spectral method is used for the inhomogeneous flow stirred at one side of the cuboid computational box. As a result, it is found that the turbulent kinetic energy is dispersed as layered structures elongated in the streamwise direction through the vibrating motion. A close look at the layered structures shows that they are flanked by colder fluids at the top and hotter fluids at the bottom, and hence vertically compressed and horizontally expanded by the buoyancy related to the countergradient heat flux, though they are punctuated by the vertical expansion of fluids at the forefront of the layered structures, which is related to the downgradient heat flux, indicating that the layered structures are gravity currents. However, the phase between temperature fluctuations and vertical velocity is shifted by π/2 rad, indicating that temperature fluctuations are generated by the propagation of internal gravity waves.

Impact of clay mineral, wood sawdust or root organic matter on the bacterial and fungal community structures in two aged PAH-contaminated soils.

PubMed

Cébron, Aurélie; Beguiristain, Thierry; Bongoua-Devisme, Jeanne; Denonfoux, Jérémie; Faure, Pierre; Lorgeoux, Catherine; Ouvrard, Stéphanie; Parisot, Nicolas; Peyret, Pierre; Leyval, Corinne

2015-09-01

The high organic pollutant concentration of aged polycyclic aromatic hydrocarbon (PAH)-contaminated wasteland soils is highly recalcitrant to biodegradation due to its very low bioavailability. In such soils, the microbial community is well adapted to the pollution, but the microbial activity is limited by nutrient availability. Management strategies could be applied to modify the soil microbial functioning as well as the PAH contamination through various amendment types. The impact of amendment with clay minerals (montmorillonite), wood sawdust and organic matter plant roots on microbial community structure was investigated on two aged PAH-contaminated soils both in laboratory and 1-year on-site pot experiments. Total PAH content (sum of 16 PAHs of the US-EPA list) and polar polycyclic aromatic compounds (pPAC) were monitored as well as the available PAH fraction using the Tenax method. The bacterial and fungal community structures were monitored using fingerprinting thermal gradient gel electrophoresis (TTGE) method. The abundance of bacteria (16S rRNA genes), fungi (18S rRNA genes) and PAH degraders (PAH-ring hydroxylating dioxygenase and catechol dioxygenase genes) was followed through qPCR assays. Although the treatments did not modify the total and available PAH content, the microbial community density, structure and the PAH degradation potential changed when fresh organic matter was provided as sawdust and under rhizosphere influence, while the clay mineral only increased the percentage of catechol-1,2-dioxygenase genes. The abundance of bacteria and fungi and the percentage of fungi relative to bacteria were enhanced in soil samples supplemented with wood sawdust and in the plant rhizospheric soils. Two distinct fungal populations developed in the two soils supplemented with sawdust, i.e. fungi related to Chaetomium and Neurospora genera and Brachyconidiellopsis and Pseudallescheria genera, in H and NM soils respectively. Wood sawdust amendment favoured the development of PAH-degrading bacteria holding Gram-negative PAH-ring hydroxylating dioxygenase, catechol-1,2-dioxygenase and catechol-2,3-dioxygenase genes. Regarding the total community structure, bacteria closely related to Thiobacillus (β-Proteobacteria) and Steroidobacter (γ-Proteobacteria) genera were favoured by wood sawdust amendment. In both soils, plant rhizospheres induced the development of fungi belonging to Ascomycota and related to Alternaria and Fusarium genera. Bacteria closely related to Luteolibacter (Verrucomicrobia) and Microbacterium (Actinobacteria) were favoured in alfalfa and ryegrass rhizosphere.

Brain Events Underlying Episodic Memory Changes in Aging: A Longitudinal Investigation of Structural and Functional Connectivity.

PubMed

Fjell, Anders M; Sneve, Markus H; Storsve, Andreas B; Grydeland, Håkon; Yendiki, Anastasia; Walhovd, Kristine B

2016-03-01

Episodic memories are established and maintained by close interplay between hippocampus and other cortical regions, but degradation of a fronto-striatal network has been suggested to be a driving force of memory decline in aging. We wanted to directly address how changes in hippocampal-cortical versus striatal-cortical networks over time impact episodic memory with age. We followed 119 healthy participants (20-83 years) for 3.5 years with repeated tests of episodic verbal memory and magnetic resonance imaging for quantification of functional and structural connectivity and regional brain atrophy. While hippocampal-cortical functional connectivity predicted memory change in young, changes in cortico-striatal functional connectivity were related to change in recall in older adults. Within each age group, effects of functional and structural connectivity were anatomically closely aligned. Interestingly, the relationship between functional connectivity and memory was strongest in the age ranges where the rate of reduction of the relevant brain structure was lowest, implying selective impacts of the different brain events on memory. Together, these findings suggest a partly sequential and partly simultaneous model of brain events underlying cognitive changes in aging, where different functional and structural events are more or less important in various time windows, dismissing a simple uni-factorial view on neurocognitive aging. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Emergence of scale-free close-knit friendship structure in online social networks.

PubMed

Cui, Ai-Xiang; Zhang, Zi-Ke; Tang, Ming; Hui, Pak Ming; Fu, Yan

2012-01-01

Although the structural properties of online social networks have attracted much attention, the properties of the close-knit friendship structures remain an important question. Here, we mainly focus on how these mesoscale structures are affected by the local and global structural properties. Analyzing the data of four large-scale online social networks reveals several common structural properties. It is found that not only the local structures given by the indegree, outdegree, and reciprocal degree distributions follow a similar scaling behavior, the mesoscale structures represented by the distributions of close-knit friendship structures also exhibit a similar scaling law. The degree correlation is very weak over a wide range of the degrees. We propose a simple directed network model that captures the observed properties. The model incorporates two mechanisms: reciprocation and preferential attachment. Through rate equation analysis of our model, the local-scale and mesoscale structural properties are derived. In the local-scale, the same scaling behavior of indegree and outdegree distributions stems from indegree and outdegree of nodes both growing as the same function of the introduction time, and the reciprocal degree distribution also shows the same power-law due to the linear relationship between the reciprocal degree and in/outdegree of nodes. In the mesoscale, the distributions of four closed triples representing close-knit friendship structures are found to exhibit identical power-laws, a behavior attributed to the negligible degree correlations. Intriguingly, all the power-law exponents of the distributions in the local-scale and mesoscale depend only on one global parameter, the mean in/outdegree, while both the mean in/outdegree and the reciprocity together determine the ratio of the reciprocal degree of a node to its in/outdegree. Structural properties of numerical simulated networks are analyzed and compared with each of the four real networks. This work helps understand the interplay between structures on different scales in online social networks.

Emergence of Scale-Free Close-Knit Friendship Structure in Online Social Networks

PubMed Central

Cui, Ai-Xiang; Zhang, Zi-Ke; Tang, Ming; Hui, Pak Ming; Fu, Yan

2012-01-01

Although the structural properties of online social networks have attracted much attention, the properties of the close-knit friendship structures remain an important question. Here, we mainly focus on how these mesoscale structures are affected by the local and global structural properties. Analyzing the data of four large-scale online social networks reveals several common structural properties. It is found that not only the local structures given by the indegree, outdegree, and reciprocal degree distributions follow a similar scaling behavior, the mesoscale structures represented by the distributions of close-knit friendship structures also exhibit a similar scaling law. The degree correlation is very weak over a wide range of the degrees. We propose a simple directed network model that captures the observed properties. The model incorporates two mechanisms: reciprocation and preferential attachment. Through rate equation analysis of our model, the local-scale and mesoscale structural properties are derived. In the local-scale, the same scaling behavior of indegree and outdegree distributions stems from indegree and outdegree of nodes both growing as the same function of the introduction time, and the reciprocal degree distribution also shows the same power-law due to the linear relationship between the reciprocal degree and in/outdegree of nodes. In the mesoscale, the distributions of four closed triples representing close-knit friendship structures are found to exhibit identical power-laws, a behavior attributed to the negligible degree correlations. Intriguingly, all the power-law exponents of the distributions in the local-scale and mesoscale depend only on one global parameter, the mean in/outdegree, while both the mean in/outdegree and the reciprocity together determine the ratio of the reciprocal degree of a node to its in/outdegree. Structural properties of numerical simulated networks are analyzed and compared with each of the four real networks. This work helps understand the interplay between structures on different scales in online social networks. PMID:23272067

Sinorhizobium meliloti Phage ΦM9 Defines a New Group of T4 Superfamily Phages with Unusual Genomic Features but a Common T=16 Capsid

PubMed Central

Johnson, Matthew C.; Tatum, Kelsey B.; Lynn, Jason S.; Brewer, Tess E.; Lu, Stephen; Washburn, Brian K.

2015-01-01

ABSTRACT Relatively little is known about the phages that infect agriculturally important nitrogen-fixing rhizobial bacteria. Here we report the genome and cryo-electron microscopy structure of the Sinorhizobium meliloti-infecting T4 superfamily phage ΦM9. This phage and its close relative Rhizobium phage vB_RleM_P10VF define a new group of T4 superfamily phages. These phages are distinctly different from the recently characterized cyanophage-like S. meliloti phages of the ΦM12 group. Structurally, ΦM9 has a T=16 capsid formed from repeating units of an extended gp23-like subunit that assemble through interactions between one subunit and the adjacent E-loop insertion domain. Though genetically very distant from the cyanophages, the ΦM9 capsid closely resembles that of the T4 superfamily cyanophage Syn9. ΦM9 also has the same T=16 capsid architecture as the very distant phage SPO1 and the herpesviruses. Despite their overall lack of similarity at the genomic and structural levels, ΦM9 and S. meliloti phage ΦM12 have a small number of open reading frames in common that appear to encode structural proteins involved in interaction with the host and which may have been acquired by horizontal transfer. These proteins are predicted to encode tail baseplate proteins, tail fibers, tail fiber assembly proteins, and glycanases that cleave host exopolysaccharide. IMPORTANCE Despite recent advances in the phylogenetic and structural characterization of bacteriophages, only a small number of phages of plant-symbiotic nitrogen-fixing soil bacteria have been studied at the molecular level. The effects of phage predation upon beneficial bacteria that promote plant growth remain poorly characterized. First steps in understanding these soil bacterium-phage dynamics are genetic, molecular, and structural characterizations of these groups of phages. The T4 superfamily phages are among the most complex phages; they have large genomes packaged within an icosahedral head and a long, contractile tail through which the DNA is delivered to host cells. This phylogenetic and structural study of S. meliloti-infecting T4 superfamily phage ΦM9 provides new insight into the diversity of this family. The comparison of structure-related genes in both ΦM9 and S. meliloti-infecting T4 superfamily phage ΦM12, which comes from a completely different lineage of these phages, allows the identification of host infection-related factors. PMID:26311868

Quantum theory of the structure and bonding in proteins. Part 11. A simplified method and its application to the α-amino-isobutyric acid residue

NASA Astrophysics Data System (ADS)

Peters, David; Peters, Jane

Information about the preferred conformation of the α-amino-isobutyric acid residue (α-AIB) is obtained without explicit computation of its wave function. The conformation of lowest energy of this residue is close to the usual helical conformation and so the residue may occur at the 2 position of a type I or I' bend or in either position of a type III or III' bend. The available experimental information refers to a β bend formed from α-AIB-PRO and then the theory and experiment agree that the only possibility is a type III bend. It is predicted that a β sheet structure may be formed at rather higher energy and in the planar and not the pleated form. There is no apparent reason why this residue should not form an α helix. The simplified method used here is closely related to the partitioned potential energy methods which are widely used in this subject.

Quantization, Frobenius and Bi algebras from the Categorical Framework of Quantum Mechanics to Natural Language Semantics

NASA Astrophysics Data System (ADS)

Sadrzadeh, Mehrnoosh

2017-07-01

Compact Closed categories and Frobenius and Bi algebras have been applied to model and reason about Quantum protocols. The same constructions have also been applied to reason about natural language semantics under the name: ``categorical distributional compositional'' semantics, or in short, the ``DisCoCat'' model. This model combines the statistical vector models of word meaning with the compositional models of grammatical structure. It has been applied to natural language tasks such as disambiguation, paraphrasing and entailment of phrases and sentences. The passage from the grammatical structure to vectors is provided by a functor, similar to the Quantization functor of Quantum Field Theory. The original DisCoCat model only used compact closed categories. Later, Frobenius algebras were added to it to model long distance dependancies such as relative pronouns. Recently, bialgebras have been added to the pack to reason about quantifiers. This paper reviews these constructions and their application to natural language semantics. We go over the theory and present some of the core experimental results.

Molecular Simulation Uncovers the Conformational Space of the λ Cro Dimer in Solution

PubMed Central

Ahlstrom, Logan S.; Miyashita, Osamu

2011-01-01

The significant variation among solved structures of the λ Cro dimer suggests its flexibility. However, contacts in the crystal lattice could have stabilized a conformation which is unrepresentative of its dominant solution form. Here we report on the conformational space of the Cro dimer in solution using replica exchange molecular dynamics in explicit solvent. The simulated ensemble shows remarkable correlation with available x-ray structures. Network analysis and a free energy surface reveal the predominance of closed and semi-open dimers, with a modest barrier separating these two states. The fully open conformation lies higher in free energy, indicating that it requires stabilization by DNA or crystal contacts. Most NMR models are found to be unstable conformations in solution. Intersubunit salt bridging between Arg4 and Glu53 during simulation stabilizes closed conformations. Because a semi-open state is among the low-energy conformations sampled in simulation, we propose that Cro-DNA binding may not entail a large conformational change relative to the dominant dimer forms in solution. PMID:22098751

Structure of the charge density wave in cuprate superconductors: Lessons from NMR

NASA Astrophysics Data System (ADS)

Atkinson, W. A.; Ufkes, S.; Kampf, A. P.

2018-03-01

Using a mix of numerical and analytic methods, we show that recent NMR 17O measurements provide detailed information about the structure of the charge-density wave (CDW) phase in underdoped YBa2Cu3O6 +x . We perform Bogoliubov-de Gennes (BdG) calculations of both the local density of states and the orbitally resolved charge density, which are closely related to the magnetic and electric quadrupole contributions to the NMR spectrum, using a microscopic model that was shown previously to agree closely with x-ray experiments. The BdG results reproduce qualitative features of the experimental spectrum extremely well. These results are interpreted in terms of a generic "hot-spot" model that allows one to trace the origins of the NMR line shapes. We find that four quantities—the orbital character of the Fermi surface at the hot spots, the Fermi surface curvature at the hot spots, the CDW correlation length, and the magnitude of the subdominant CDW component—are key in determining the line shapes.

The fundamental closed-form solution of control-related states of kth order S3PR system with left-side non-sharing resource places of Petri nets

NASA Astrophysics Data System (ADS)

Chao, Daniel Yuh; Yu, Tsung Hsien

2016-01-01

Due to the state explosion problem, it has been unimaginable to enumerate reachable states for Petri nets. Chao broke the barrier earlier by developing the very first closed-form solution of the number of reachable and other states for marked graphs and the kth order system. Instead of using first-met bad marking, we propose 'the moment to launch resource allocation' (MLR) as a partial deadlock avoidance policy for a large, real-time dynamic resource allocation system. Presently, we can use the future deadlock ratio of the current state as the indicator of MLR due to which the ratio can be obtained real-time by a closed-form formula. This paper progresses the application of an MLR concept one step further on Gen-Left kth order systems (one non-sharing resource place in any position of the left-side process), which is also the most fundamental asymmetric net structure, by the construction of the system's closed-form solution of the control-related states (reachable, forbidden, live and deadlock states) with a formula depending on the parameters of k and the location of the non-sharing resource. Here, we kick off a new era of real-time, dynamic resource allocation decisions by constructing a generalisation formula of kth order systems (Gen-Left) with r* on the left side but at arbitrary locations.

Structural and Cultural Factors in Successful Aging Among Older Hispanics

PubMed Central

Angel, Ronald J.

2014-01-01

Successful or healthful aging are terms that draw attention to life course issues related to individual, physical, and psychologic development and maturation, but they also draw attention to the material basis of successful aging and the social structures that determine one’s place in the social hierarchy. This article focuses on barriers to optimal aging for Hispanics, especially those of Mexican origin, and argues that cultural factors and social class are closely associated. The reduction of health disparities and equity in medical and long-term care requires an understanding of both cultural and material sources of differential health levels. PMID:19065093

Undistorted 3D microstructures in SU8 formed through two-photon polymerization

NASA Astrophysics Data System (ADS)

Ohlinger, Kris; Lin, Yuankun; Poole, Zsolt; Chen, Kevin P.

2011-09-01

This paper presents the wavelength dependence of two-photon polymerization in SU-8 between 720-780 nm. The study is performed by microstructuring SU-8 through a single-shot exposure of SU-8 to 140 fs tunable laser pulses with 80 MHz repetition rate, or by laser direct writing. Two-photon absorption is closely related to one-photon absorption in pristine SU-8. By careful design of the neighboring micro-structures, or by varying wet-processing parameters during development, undistorted and unbended 3D micro-structures have been fabricated through direct laser writing.

SAFETY SYSTEM FOR CONTROL ROD

DOEpatents

Paget, J.A.

1963-05-14

A structure for monitoring the structural continuity of a control rod foi a neutron reactor is presented. A electric conductor readily breakable under mechanical stress is fastened along the length of the control rod at a plurality of positions and forms a closed circuit with remote electrical components responsive to an open circuit. A portion of the conductor between the control rod and said components is helically wound to allow free and normally unrestricted movement of the segment of conductor secured to the control rod relative to the remote components. Any break in the circuit is indicative of control rod breakage. (AEC)

Atomic force microscope studies of fullerene films - Highly stable C60 fcc (311) free surfaces

NASA Technical Reports Server (NTRS)

Snyder, Eric J.; Tong, William M.; Williams, R. S.; Anz, Samir J.; Anderson, Mark S.

1991-01-01

Atomic force microscopy and X-ray diffractometry were used to study 1500 A-thick films of pure C60 grown by sublimation in ultrahigh vacuum onto a CaF2 (111) substrte. Topographs of the films did not reveal the expected close-packed structures, but they showed instead large regions that correspond to a face-centered cubic (311) surface and distortions of this surface. The open (311) structure may have a relatively low free energy because the low packing density contributes to a high entropy of the exposed surface.

Lattice dynamics of the lanthanides: Samarium at high pressure

NASA Astrophysics Data System (ADS)

Olijnyk, H.; Jephcoat, A. P.

2005-02-01

Sm was studied by Raman spectroscopy at pressures up to 20 GPa. The Raman-active phonon modes, both of the Sm-type phase and the dhcp phase, show a frequency decrease as pressure increases. There is evidence that the entire structural sequence hcp → Sm-type → dhcp → fcc under pressure for the individual regular lanthanides is associated with softening of certain acoustic and optical-phonon modes as well as elastic anomalies. Comparison is made to corresponding transitions between close-packed lattices in other metals and possible relations to the lanthanide's electronic structure are addressed.

A controller design approach for large flexible space structures

NASA Technical Reports Server (NTRS)

Joshi, S. M.

1981-01-01

A controller design approach for large space structures is presented, which consists of a primary attitude controller and a secondary or damping enhancement controller. The secondary controller, which uses several Annular Momentum Control Device (AMCD's), is shown to make the closed loop system asymptotically stable under relatively simple conditions. The primary controller using torque actuators (or AMCD's) and colocated attitude and rate sensors is shown to be stable. It is shown that the same AMCD's can be used for simultaneous actuation of primary and secondary controllers. Numerical results are obtained for a large, thin, completely free plate model.

Closed-loop transfer recovery with observer-based controllers. I - Analysis. II - Design

NASA Technical Reports Server (NTRS)

Chen, Ben M.; Saberi, Ali; Ly, Uy-Loi

1992-01-01

A detailed study is presented of three fundamental issues related to the problem of closed-loop transfer (CLT) recovery. The first issues concerns what can and cannot be achieved for a given system and for an arbitrary target CLT function (TCLTF). The second issue involves developing necessary and/or sufficient conditions for a TCLTF to be recoverable either exactly or approximately. The third issue involves the necessary and/or sufficient conditions on a given system such that it has at least one recoverable TCLTF. The results of the analysis identify some fundamental limitations of the given system as a consequence of its structural properties which enables designers to appreciate at the outset different design limitations incurred in the synthesis of output-feedback controllers. Then, the actual design of full-order or reduced-order observer-based controllers is addressed which will achieve as close as possibly the desired TCLTF. Three design methods are considered: (1) the ATEA method, (2) a method that minimizes the H2-norm of a recovery matrix, and (3) a method that minimizes the respective H(infinity) norm. The relative merits of the methods are discussed.

2D and 3D imaging of the gas phase close to an operating model catalyst by planar laser induced fluorescence

NASA Astrophysics Data System (ADS)

Blomberg, Sara; Zhou, Jianfeng; Gustafson, Johan; Zetterberg, Johan; Lundgren, Edvin

2016-11-01

In recent years, efforts have been made in catalysis related surface science studies to explore the possibilities to perform experiments at conditions closer to those of a technical catalyst, in particular at increased pressures. Techniques such as high pressure scanning tunneling/atomic force microscopy (HPSTM/AFM), near ambient pressure x-ray photoemission spectroscopy (NAPXPS), surface x-ray diffraction (SXRD) and polarization-modulation infrared reflection absorption spectroscopy (PM-IRAS) at semi-realistic conditions have been used to study the surface structure of model catalysts under reaction conditions, combined with simultaneous mass spectrometry (MS). These studies have provided an increased understanding of the surface dynamics and the structure of the active phase of surfaces and nano particles as a reaction occurs, providing novel information on the structure/activity relationship. However, the surface structure detected during the reaction is sensitive to the composition of the gas phase close to the catalyst surface. Therefore, the catalytic activity of the sample itself will act as a gas-source or gas-sink, and will affect the surface structure, which in turn may complicate the assignment of the active phase. For this reason, we have applied planar laser induced fluorescence (PLIF) to the gas phase in the vicinity of an active model catalysts. Our measurements demonstrate that the gas composition differs significantly close to the catalyst and at the position of the MS, which indeed should have a profound effect on the surface structure. However, PLIF applied to catalytic reactions presents several beneficial properties in addition to investigate the effect of the catalyst on the effective gas composition close to the model catalyst. The high spatial and temporal resolution of PLIF provides a unique tool to visualize the on-set of catalytic reactions and to compare different model catalysts in the same reactive environment. The technique can be applied to a large number of molecules thanks to the technical development of lasers and detectors over the last decades, and is a complementary and visual alternative to traditional MS to be used in environments difficult to asses with MS. In this article we will review general considerations when performing PLIF experiments, our experimental set-up for PLIF and discuss relevant examples of PLIF applied to catalysis.

Structural comparison of nickel electrodes and precursor phases

NASA Technical Reports Server (NTRS)

Cornilsen, Bahne C.; Shan, Xiaoyin; Loyselle, Patricia

1989-01-01

A summary of previous Raman spectroscopic results and a discussion of important structural differences in the various phases of active mass and active mass precurors are presented. Raman spectra provide unique signatures for these phases, and allow one to distinguish each phase, even when the compound is amorphous to X-rays (i.e., does not scatter X-rays because of a lack of order and/or small particle size). The structural changes incurred during formation, charge and discharge, cobalt addition, and aging will be discussed and related to electrode properties. Important structural differences include NiO2 layer stacking, nonstoichiometry (especially cation-deficit nonstoichiometry), disorder, dopant content, and water content. The results indicate that optimal nickel active mass is non-close packed and nonstoichiometric. The formation process transforms precursor phases into this structure. Therefore, the precursor disorder, or lack thereof, influences this final active mass structure and the rate of formation. Aging processes induce structural change which is believed to be detrimental. The role of cobalt addition can be appreciated in terms of structures favored or stabilized by the dopant. In recent work, the in situ Raman technique to characterize the critical structural parameters was developed. An in situ method relates structure, electrochemistry, and preparation. In situ Raman spectra of cells during charge and discharge, either during cyclic voltammetry or under constant current conditions were collected. With the structure-preparation knowledge and the in situ Raman tool, it will be possible to define the structure-property-preparation relations in more detail. This instrumentation has application to a variety of electrode systems.

Manipulation of morphology and structure of the top of GaAs nanowires grown by molecular-beam epitaxy

NASA Astrophysics Data System (ADS)

Li, Lixia; Pan, Dong; Yu, Xuezhe; So, Hyok; Zhao, Jianhua

2017-10-01

Self-catalyzed GaAs nanowires (NWs) are grown on Si (111) substrates by molecular-beam epitaxy. The effect of different closing sequences of the Ga and As cell shutters on the morphology and structural phase of GaAs NWs is investigated. For the sequences of closing the Ga and As cell shutters simultaneously or closing the As cell shutter 1 min after closing the Ga cell shutter, the NWs grow vertically to the substrate surface. In contrast, when the As cell shutter is closed first, maintaining the Ga flux is found to be critical for the following growth of GaAs NWs, which can change the growth direction from [111] to < 11\\bar{1}> . The evolution of the morphology and structural phase transition at the tips of these GaAs NWs confirm that the triple-phase-line shift mode is at work even for the growth with different cell shutter closing sequences. Our work will provide new insights for better understanding of the growth mechanism and realizing of the morphology and structure control of the GaAs NWs. Project supported partly by the MOST of China (No. 2015CB921503), the National Natural Science Foundation of China (Nos. 61504133, 61334006, 61404127), and Youth Innovation Promotion Association, CAS (No. 2017156).

Robust Stabilization Control Based on Guardian Maps Theory for a Longitudinal Model of Hypersonic Vehicle

PubMed Central

Liu, Mengying; Sun, Peihua

2014-01-01

A typical model of hypersonic vehicle has the complicated dynamics such as the unstable states, the nonminimum phases, and the strong coupling input-output relations. As a result, designing a robust stabilization controller is essential to implement the anticipated tasks. This paper presents a robust stabilization controller based on the guardian maps theory for hypersonic vehicle. First, the guardian maps theories are provided to explain the constraint relations between the open subsets of complex plane and the eigenvalues of the state matrix of closed-loop control system. Then, a general control structure in relation to the guardian maps theories is proposed to achieve the respected design demands. Furthermore, the robust stabilization control law depending on the given general control structure is designed for the longitudinal model of hypersonic vehicle. Finally, a simulation example is provided to verify the effectiveness of the proposed methods. PMID:24795535

Robust stabilization control based on guardian maps theory for a longitudinal model of hypersonic vehicle.

PubMed

Liu, Yanbin; Liu, Mengying; Sun, Peihua

2014-01-01

A typical model of hypersonic vehicle has the complicated dynamics such as the unstable states, the nonminimum phases, and the strong coupling input-output relations. As a result, designing a robust stabilization controller is essential to implement the anticipated tasks. This paper presents a robust stabilization controller based on the guardian maps theory for hypersonic vehicle. First, the guardian maps theories are provided to explain the constraint relations between the open subsets of complex plane and the eigenvalues of the state matrix of closed-loop control system. Then, a general control structure in relation to the guardian maps theories is proposed to achieve the respected design demands. Furthermore, the robust stabilization control law depending on the given general control structure is designed for the longitudinal model of hypersonic vehicle. Finally, a simulation example is provided to verify the effectiveness of the proposed methods.

Liquid-to-liquid crossover in the GaIn eutectic alloy

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

Yu, Q.; Wang, X. D.; Su, Y.

Liquid-liquid crossover is promising and closely related to the atomic dynamics during heating and cooling processes. Here we reveal a reversible structural crossover in the liquid Ga85.8In14.2 eutectic alloys by using in situ synchrotron x-ray diffraction and ab initio molecular dynamics simulation. A kink always appears on the temperature dependent behaviors of density, ratio of the second peak position to the first in the pair correlation function, coordination number, heat capacity, free energy, and atomic diffusivity in the temperature range of about 400–550 K. It is likely ascribed to atomic rearrangements of Ga and In atoms from a relative randommore » packing at high temperatures to a relative nonuniform packing at low temperatures, in which In atoms prefer to have more In neighbors. This observation will promote more understanding of the liquid structure of eutectic alloys« less

Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations.

PubMed

Golebiowski, Jérôme; Antonczak, Serge; Fernandez-Carmona, Juan; Condom, Roger; Cabrol-Bass, Daniel

2004-12-01

Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the loop of an RNA in complementary interaction with HIV-1 TAR. The simulations reveal that the mismatch GA base, mediated by a water molecule, leads to a complex that presents the best compromise between flexibility and energetic contributions. The mismatch CU base pair, in spite of the presence of an inserted water molecule, is too short to achieve a tight interaction at the closing-loop junction and seems to force TAR to reorganize upon binding. An energetic analysis has allowed us to quantify the strength of the interactions of the closing and the loop-loop pairs throughout the simulations. Although the water-mediated GA closing base pair presents an interaction energy similar to that found on fully geometry-optimized structure, the water-mediated CU closing base pair energy interaction reaches less than half the optimal value.

VNTR internal structure mapping at the {alpha}-globin 3{prime}HVR locus reveals a hierachy of related lineages in oceania

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

Martinson, J.J.; Clegg, J.B.; Boyce, A.J.

1994-09-01

Analysis of the {alpha}-globin gene complex in Oceania has revealed many different rearrangements which remove one of the adult globin genes. Frequencies of these deletion chromosomes are elevated by malarial resistance conferred by the resulting {alpha}-thalassaemia. One particular deletion chromosome, designated -{alpha}{sup 3.7}III, is found at high levels in Melanesia and Polynesia: RFLP haplotype analysis shows that this deletion is always found on chromosomes bearing the IIIa haplotype and is likely to be the product of one single rearrangement event. A subset of the -{alpha}{sup 3.7}III chromosomes carries a more recent mutation which generates the haemoglobin variant HbJ{sup Tongariki}. Wemore » have characterized the allelic variation at the 3{prime}HVR VNTR locus located 6 kb from the globin genes in each of these groups of chromosomes. We have determined the internal structure of these alleles by RFLP mapping of PCR-amplified DNA: within each group, the allelic diversity results from the insertion and/or deletion of small {open_quotes}motifs{close_quotes} of up to 6 adjacent repeats. Mapping of 3{prime}HVR alleles associated with other haplotypes reveals that these are composed of repeat arrays that are substantially different to those derived from IIIa chromosomes, indicating that interchromosomal recombination between heterologous haplotypes does not account for any of the diversity seen to date. We have recently shown that allelic size variation at the two VNTR loci flanking the {alpha}-globin complex is very closely linked to the haplotypes known to be present at this locus. Here we show that, within a haplotype, VNTR alleles are very closely related to each other on the basis of internal structure and demonstrate that intrachromosomal mutation processes involving small numbers of tandem repeats are the main cause of variation at this locus.« less

Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open ↔ Closed Transitions

PubMed Central

Beckstein, Oliver; Denning, Elizabeth J.; Perilla, Juan R.; Woolf, Thomas B.

2009-01-01

Adenylate kinase (AdK), a phosphotransferase enzyme, plays an important role in cellular energy homeostasis. It undergoes a large conformational change between an open and a closed state, even in the absence of substrate. We investigate the apo-AdK transition at the atomic level both with free energy calculations and our new dynamic importance sampling (DIMS) molecular dynamics (MD) method. DIMS is shown to sample biologically relevant conformations as verified by comparing an ensemble of hundreds of DIMS transitions to AdK crystal structure intermediates. The simulations reveal in atomic detail how hinge regions partially and intermittently unfold during the transition. Conserved salt bridges are seen to have important structural and dynamic roles; in particular four ionic bonds are identified that open in a sequential, zipper-like fashion and thus dominate the free energy landscape of the transition. Transitions between the closed and open conformations only have to overcome moderate free energy barriers. Unexpectedly, the closed and open state encompass broad free energy basins that contain conformations differing in domain hinge motions by up to 40°. The significance of these extended states is discussed in relation to recent experimental FRET measurements. Taken together, these results demonstrate how a small number of cooperative key interactions can shape the overall dynamics of an enzyme and suggest an “all-or-nothing” mechanism for the opening and closing of AdK. Our efficient DIMS-MD computer simulation approach can provide a detailed picture of a functionally important macromolecular transition and thus help to interpret and suggest experiments to probe the conformational landscape of dynamic proteins such as AdK. PMID:19751742

Verbal and non-verbal intelligence changes in the teenage brain.

PubMed

Ramsden, Sue; Richardson, Fiona M; Josse, Goulven; Thomas, Michael S C; Ellis, Caroline; Shakeshaft, Clare; Seghier, Mohamed L; Price, Cathy J

2011-10-19

Intelligence quotient (IQ) is a standardized measure of human intellectual capacity that takes into account a wide range of cognitive skills. IQ is generally considered to be stable across the lifespan, with scores at one time point used to predict educational achievement and employment prospects in later years. Neuroimaging allows us to test whether unexpected longitudinal fluctuations in measured IQ are related to brain development. Here we show that verbal and non-verbal IQ can rise or fall in the teenage years, with these changes in performance validated by their close correlation with changes in local brain structure. A combination of structural and functional imaging showed that verbal IQ changed with grey matter in a region that was activated by speech, whereas non-verbal IQ changed with grey matter in a region that was activated by finger movements. By using longitudinal assessments of the same individuals, we obviated the many sources of variation in brain structure that confound cross-sectional studies. This allowed us to dissociate neural markers for the two types of IQ and to show that general verbal and non-verbal abilities are closely linked to the sensorimotor skills involved in learning. More generally, our results emphasize the possibility that an individual's intellectual capacity relative to their peers can decrease or increase in the teenage years. This would be encouraging to those whose intellectual potential may improve, and would be a warning that early achievers may not maintain their potential.

Permeability estimations and frictional flow features passing through porous media comprised of structured microbeads

NASA Astrophysics Data System (ADS)

Shin, C.

2017-12-01

Permeability estimation has been extensively researched in diverse fields; however, methods that suitably consider varying geometries and changes within the flow region, for example, hydraulic fracture closing for several years, are yet to be developed. Therefore, in the present study a new permeability estimation method is presented based on the generalized Darcy's friction flow relation, in particular, by examining frictional flow parameters and characteristics of their variations. For this examination, computational fluid dynamics (CFD) simulations of simple hydraulic fractures filled with five layers of structured microbeads and accompanied by geometry changes and flow transitions are performed. Consequently, it was checked whether the main structures and shapes of each flow path are preserved, even for geometry variations within porous media. However, the scarcity and discontinuity of streamlines increase dramatically in the transient- and turbulent-flow regions. The quantitative and analytic examinations of the frictional flow features were also performed. Accordingly, the modified frictional flow parameters were successfully presented as similarity parameters of porous flows. In conclusion, the generalized Darcy's friction flow relation and friction equivalent permeability (FEP) equation were both modified using the similarity parameters. For verification, the FEP values of the other aperture models were estimated and then it was checked whether they agreed well with the original permeability values. Ultimately, the proposed and verified method is expected to efficiently estimate permeability variations in porous media with changing geometric factors and flow regions, including such instances as hydraulic fracture closings.

Denitrification potential under different fertilization regimes is closely coupled with changes in the denitrifying community in a black soil.

PubMed

Yin, Chang; Fan, Fenliang; Song, Alin; Cui, Peiyuan; Li, Tingqiang; Liang, Yongchao

2015-07-01

Preferable inorganic fertilization over the last decades has led to fertility degradation of black soil in Northeast China. However, how fertilization regimes impact denitrification and its related bacterial community in this soil type is still unclear. Here, taking advantage of a suit of molecular ecological tools in combination of assaying the potential denitrification (DP), we explored the variation of activity, community structure, and abundance of nirS and nirK denitrifiers under four different fertilization regimes, namely no fertilization control (N0M0), organic pig manure (N0M1), inorganic fertilization (N1M0), and combination of inorganic fertilizer and pig manure (N1M1). The results indicated that organic fertilization increased DP, but inorganic fertilization had no impacts. The increase of DP was mirrored by the shift of nirS denitrifiers' community structure but not by that of nirK denitrifiers'. Furthermore, the change of DP coincided with the variation of abundances of both denitrifiers. Shifts of community structure and abundance of nirS and nirK denitrifiers were correlated with the change of soil pH, total nitrogen (TN), organic matter (OM), C:P, total phosphorus (TP), and available phosphorus (Olsen P). Our results suggest that the change of DP under these four fertilization regimes was closely related to the shift of denitrifying bacteria communities resulting from the variation of properties in the black soil tested.

Characterization of eubacterial and archaeal community diversity in the pit mud of Chinese Luzhou-flavor liquor by nested PCR-DGGE.

PubMed

Ding, Xiao-Fei; Wu, Chong-De; Zhang, Li-Qiang; Zheng, Jia; Zhou, Rong-Qing

2014-02-01

The aim of this study was to investigate and compare the microbial community structures of eubacteria and archaea in the pit mud of Chinese Luzhou-flavor liquor from the wall (C(w)) and bottom (C(b)) of cellar through nested PCR-denaturing gradient gel electrophoresis (DGGE). The Shannon-Wiener index (H) calculated from the DGGE profiles showed that the community diversities of eubacteria and archaea in samples from C(b) were almost higher than that from C(w). In addition, cluster analysis of the DGGE profiles revealed that some differences were found in the microbial community structure in samples from different locations. The closely relative microorganisms of all eubacterial 16S rRNA gene sequences fell into four phyla (Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria), including 12 genera and 2 uncultured eubacteria. Moreover, 37.1% eubacteria were affiliated with Clostridium. Particularly, genus Acinetobacter was absent in all samples from C(b) but present in all samples from C(w). The closely relative microorganisms of all archaeal 16S rRNA gene sequences fell into four genera, which included Methanobrevibacter, Methanoculleus, Methanobacterium and Methanosaeta, while the dominant archaea in samples from C(w) and C(b) were similar. Results presented in this study provide further understanding of the spatial differences in microbial community structure in the pit mud, and is of great importance for the production and quality improvement of Luzhou-flavor liquor.

Hollow V(2)O(5) nanoparticles (fullerene-like analogues) prepared by laser ablation.

PubMed

Levi, Roi; Bar-Sadan, Maya; Albu-Yaron, Ana; Popovitz-Biro, Ronit; Houben, Lothar; Shahar, Chen; Enyashin, Andrey; Seifert, Gotthard; Prior, Yehiam; Tenne, Reshef

2010-08-18

Nanoparticles of materials with layered structure are able to spontaneously form closed-cage nanostructures such as nested fullerene-like nanoparticles and nanotubes. This propensity has been demonstrated in a large number of compounds such as WS(2), NiCl(2), and others. Layered metal oxides possess a higher ionic character and consequently are stiffer and cannot be evenly folded. Vanadium pentoxide (V(2)O(5)), a layered metal oxide, has received much attention due to its attractive qualities in numerous applications such as catalysis and electronic and optical devices and as an electrode material for lithium rechargeable batteries. The synthesis by pulsed laser ablation (PLA) of V(2)O(5) hollow nanoparticles, which are closely (nearly) associated with inorganic "fullerene-like" (NIF-V(2)O(5)) nanoparticles, but not quite as perfect, is reported in the present work. The relation between the PLA conditions and the NIF-V(2)O(5) morphology is elucidated. A new mechanism leading to hollow nanostructure via crystallization of lower density amorphous nanoparticles is proposed. Transmission electron microscopy (TEM) is used extensively in conjunction with structural modeling of the NIF-V(2)O(5) in order to study the complex 3-D structure of the NIF-V(2)O(5) nanoparticles. This structure was shown to be composed of facets with their low-energy surfaces pointing outward and seamed by defective domains. These understandings are used to formulate a formation mechanism and may improve the function of V(2)O(5) in its many uses through additional morphological control. Furthermore, this study outlines which properties are required from layered compounds to fold into perfectly closed-cage IF nanoparticles.

Comparing photonic band structure calculation methods for diamond and pyrochlore crystals.

PubMed

Vermolen, E C M; Thijssen, J H J; Moroz, A; Megens, M; van Blaaderen, A

2009-04-27

The photonic band diagrams of close-packed colloidal diamond and pyrochlore structures, have been studied using Korringa-Kohn-Rostoker (KKR) and plane-wave calculations. In addition, the occurrence of a band gap has been investigated for the binary Laves structures and their constituent large- and small-sphere substructures. It was recently shown that these Laves structures give the possibility to fabricate the diamond and pyrochlore structures by self-organization. The comparison of the two calculation methods opens the possibility to study the validity and the convergence of the results, which have been an issue for diamond-related structures in the past. The KKR calculations systematically give a lower value for the gap width than the plane-wave calculations. This difference can partly be ascribed to a convergence issue in the plane-wave code when a contact point of two spheres coincides with the grid.

Comparison of structural performance of one- and two-bay rotary joints for truss applications

NASA Technical Reports Server (NTRS)

Vail, J. Douglas; Lake, Mark S.

1991-01-01

The structural performance of one- and two-bay large-diameter discrete-bearing rotary joints was addressed for application to truss-beam structures such as the Space Station Freedom. Finite element analyses are performed to determine values for rotary joint parameters that give the same bending vibration frequency as the parent truss beam. The structural masses and maximum internal loads of these joints are compared to determine their relative structural efficiency. Results indicate that no significant difference exists in the masse of one- and two-bay rotary joints. This conclusion is reinforced with closed-form calculations of rotary joint structural efficiency in extension. Also, transition truss-member loads are higher in the one-bay rotary joint. However, because of the increased buckling strength of these members, the external load-carrying capability of the one-bay concept is higher than that of the two-bay concept.

Structural and functional measures of social relationships and quality of life among older adults: does chronic disease status matter?

PubMed

Liao, Jing; Brunner, Eric J

2016-01-01

To evaluate the relative importance of structural and functional social relationships for quality of life (QoL) and the extent to which diagnosed chronic disease modifies these associations. Multivariate linear regression was used to investigate time-lagged associations between structural and functional measures of social relationships and QoL assessed 5 years apart by CASP-19, in 5925 Whitehall II participants (mean age 61, SD 6.0). Chronic disease was clinically verified coronary heart disease, stroke, diabetes or cancer. Social relationships-QoL associations were consistent across disease status (P-values for interaction: 0.15-0.99). Larger friend network (β = 1.9, 95% CI 1.5-2.3), having a partner (β = 1.2, 95% CI 0.5-1.7), higher confiding support (β = 2.2, 95% CI 1.8-2.7) and lower negative aspects of close relationships (β = 3.3, 95% CI 2.8-3.8) were independently related to improved QoL in old age. The estimated difference in QoL due to social relationships was equivalent to up to 0.5 SD of the CASP-19 score and was stronger than the effect of chronic disease (coronary heart disease β = 2.0, 95% CI 1.4-2.6). We found that beneficial aspects of social relationships in relation to QoL were, in order of importance: avoiding negative aspects of close relationships, having confiding support, having a wide network of friends and having a partner. These associations were not modified by chronic disease. Thus, despite inevitable physical deterioration, we may be able to enhance a satisfying late life by optimizing our social relationships.

The socio-genetics of a complex society: female gelada relatedness patterns mirror association patterns in a multilevel society.

PubMed

Snyder-Mackler, Noah; Alberts, Susan C; Bergman, Thore J

2014-12-01

Multilevel societies with fission-fusion dynamics--arguably the most complex animal societies--are defined by two or more nested levels of organization. The core of these societies are modular social units that regularly fission and fuse with one another. Despite convergent evolution in disparate taxa, we know strikingly little about how such societies form and how fitness benefits operate. Understanding the kinship structure of complex societies could inform us about the origins of the social structure as well as about the potential for individuals in these societies to accrue indirect fitness benefits. Here, we combined genetic and behavioural data on geladas (Theropithecus gelada), an Old World Monkey, to complete the most comprehensive socio-genetic analysis of a multilevel society to date. In geladas, individuals in the core social 'units', associate at different frequencies to form 'teams', 'bands' and, the largest aggregations, 'communities'. Units were composed of closely related females, and females remained with their close kin during permanent fissions of units. Interestingly, female-female relatedness also significantly predicted between-unit, between-team and between-band association patterns, while male-male relatedness did not. Thus, it is likely that the socio-genetic structure of gelada society results from females maintaining associations with their female relatives during successive unit fissions--possibly in an attempt to balance the direct and indirect fitness benefits of group living. Overall, the persistence of associations among related females across generations appears to drive the formation of higher levels of gelada society, suggesting that females seek kin for inclusive fitness benefits at multiple levels of gelada society. © 2014 John Wiley & Sons Ltd.

Descriptions of carbon isotopes within the energy density functional theory

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

Ismail, Atef; Cheong, Lee Yen; Yahya, Noorhana

2014-10-24

Within the energy density functional (EDF) theory, the structure properties of Carbon isotopes are systematically studied. The shell model calculations are done for both even-A and odd-A nuclei, to study the structure of rich-neutron Carbon isotopes. The EDF theory indicates the single-neutron halo structures in {sup 15}C, {sup 17}C and {sup 19}C, and the two-neutron halo structures in {sup 16}C and {sup 22}C nuclei. It is also found that close to the neutron drip-line, there exist amazing increase in the neutron radii and decrease on the binding energies BE, which are tightly related with the blocking effect and correspondingly themore » blocking effect plays a significant role in the shell model configurations.« less

Chronological age and its impact on associative learning proficiency and brain structure in middle adulthood.

PubMed

Diwadkar, Vaibhav A; Bellani, Marcella; Ahmed, Rizwan; Dusi, Nicola; Rambaldelli, Gianluca; Perlini, Cinzia; Marinelli, Veronica; Ramaseshan, Karthik; Ruggeri, Mirella; Bambilla, Paolo

2016-01-15

The rate of biological change in middle-adulthood is relatively under-studied. Here, we used behavioral testing in conjunction with structural magnetic resonance imaging to examine the effects of chronological age on associative learning proficiency and on brain regions that previous functional MRI studies have closely related to the domain of associative learning. Participants (n=66) completed a previously established associative learning paradigm, and consented to be scanned using structural magnetic resonance imaging. Age-related effects were investigated both across sub-groups in the sample (younger vs. older) and across the entire sample (using regression approaches). Chronological age had substantial effects on learning proficiency (independent of IQ and Education Level), with older adults showing a decrement compared to younger adults. In addition, decreases in estimated gray matter volume were observed in multiple brain regions including the hippocampus and the dorsal prefrontal cortex, both of which are strongly implicated in associative learning. The results suggest that middle adulthood may be a more dynamic period of life-span change than previously believed. The conjunctive application of narrowly focused tasks, with conjointly acquired structural MRI data may allow us to enrich the search for, and the interpretation of, age-related changes in cross-sectional samples. Copyright © 2015 Elsevier B.V. All rights reserved.

ANTIGENIC STRUCTURE OF THE ACTINOMYCETALES VII.

PubMed Central

Kwapinski, J. B.

1964-01-01

Kwapinski, J. B. (The University of New England, Armidale, Australia). Antigenic structure of the Actinomycetales. VII. Chemical and serological similarities of cell walls from 100 Actinomycetales strains. J. Bacteriol. 88:1211–1219. 1964.—Cell walls prepared mechanically from 100 strains of Actinomycetales were studied by chromatographic and serological methods. The cell walls of Actinomyces were found to be serologically related to those of the corynebacteria and to some strains of mycobacteria and nocardiae. The cell walls of nocardiae appeared to be more closely related to those of the mycobacteria, Streptomyces, Micromonospora, and Waksmania. The cell walls of Micromonospora and Waksmania showed certain serological similarities to those of Thermoactinomyces and nocardiae. Micropolyspora was antigenically different from other species of the Actinomycetales. Three serological groups of mycobacteria and four groups of nocardiae were distinguished. PMID:14234773

Probing the determinants of protein stability: comparison of class A beta-lactamases.

PubMed Central

Vanhove, M; Houba, S; b1motte-Brasseur, J; Frère, J M

1995-01-01

Five class A beta-lactamases produced by various mesophilic bacterial species have been compared. Although closely related in primary and overall structures, these enzymes exhibit very different stabilities. In order to investigate the factors responsible for these differences, several features deduced from the amino acid composition and three-dimensional structures were studied for the five proteins. This analysis revealed that higher stability appeared to correlate with increased numbers of intramolecular hydrogen bonds and of salt bridges. By contrast, the global hydrophobicity of the protein seemed to play a relatively minor role. A strongly unfavourable balance between charged residues and the presence of a cis-peptide bond preceding a non-proline residue might also contribute to the particularly low stability of two of the enzymes. PMID:8948443

Characteristics of 5M modulated martensite in Ni-Mn-Ga magnetic shape memory alloys

NASA Astrophysics Data System (ADS)

Ćakır, A.; Acet, M.; Righi, L.; Albertini, F.; Farle, M.

2015-09-01

The applicability of the magnetic shape memory effect in Ni-Mn-based martensitic Heusler alloys is closely related to the nature of the crystallographically modulated martensite phase in these materials. We study the properties of modulated phases as a function of temperature and composition in three magnetic shape memory alloys Ni49.8Mn25.0Ga25.2, Ni49.8Mn27.1Ga23.1 and Ni49.5Mn28.6Ga21.9. The effect of substituting Ga for Mn leads to an anisotropic expansion of the lattice, where the b-parameter of the 5M modulated structure increases and the a and c-parameters decrease with increasing Ga concentration. The modulation vector is found to be both temperature and composition dependent. The size of the modulation vector corresponds to an incommensurate structure for Ni49.8Mn25.0Ga25.2 at all temperatures. For the other samples the modulation is incommensurate at low temperatures but reaches a commensurate value of q ≈ 0.400 close to room temperature. The results show that commensurateness of the 5M modulated structure is a special case of incommensurate 5M at a particular temperature.

Fifty years of coiled-coils and alpha-helical bundles: a close relationship between sequence and structure.

PubMed

Parry, David A D; Fraser, R D Bruce; Squire, John M

2008-09-01

alpha-Helical coiled coils are remarkable for the diversity of related conformations that they adopt in both fibrous and globular proteins, and for the range of functions that they exhibit. The coiled coils are based on a heptad (7-residue), hendecad (11-residue) or a related quasi-repeat of apolar residues in the sequences of the alpha-helical regions involved. Most of these, however, display one or more sequence discontinuities known as stutters or stammers. The resulting coiled coils vary in length, in the number of chains participating, in the relative polarity of the contributing alpha-helical regions (parallel or antiparallel), and in the pitch length and handedness of the supercoil (left- or right-handed). Functionally, the concept that a coiled coil can act only as a static rod is no longer valid, and the range of roles that these structures have now been shown to exhibit has expanded rapidly in recent years. An important development has been the recognition that the delightful simplicity that exists between sequence and structure, and between structure and function, allows coiled coils with specialized features to be designed de novo.

Host ecology and variation in helminth community structure in Mastomys rodents from Senegal.

PubMed

Brouat, C; Kane, M; Diouf, M; Bâ, K; Sall-Dramé, R; Duplantier, J M

2007-03-01

We studied patterns of variation in parasite communities of 2 closely related species of Mastomys rodents. These 2 species live in sympatry in South-eastern Senegal, but differ drastically in their habitat choice. We asked (a) whether the host species have the same parasites; (b) whether there is any observable pattern relative to the host species/habitat type in the structure of parasite communities; (c) whether the variability in parasite community for each host species is related to habitat characteristics. We analysed 220 and 264 individuals of each host species, sampled respectively in 10 and 11 trap sites. Twenty parasite taxa were recorded, and the majority were nematodes. Between-host species comparisons showed that helminth communities were slightly more diversified in M. natalensis. Many parasite species were found in both Mastomys. However, various helminth taxa varied in frequency and abundance between host species. Within each host species, helminth diversity, prevalence and/or abundance of some parasites were correlated with habitat or host population factors that may influence parasite life-cycles, such as village structure, or the presence/absence of a pool. Our results suggest that habitat characteristics have a strong impact on helminth community structure.

CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments.

PubMed

Zhou, Carol L Ecale

2015-01-01

In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many multiple sequence alignment derived from a set of structure or sequence alignments, and a need was evident for creating such a tool for combining pairwise structure alignments that would allow for insertion of gaps in the reference structure. This report describes a new Python code, CombAlign, which takes as input a set of pairwise sequence alignments (which may be structure based) and generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA). The use and utility of CombAlign was demonstrated by generating gapped MSSAs using sets of pairwise structure-based sequence alignments between structure models of the matrix protein (VP40) and pre-small/secreted glycoprotein (sGP) of Reston Ebolavirus and the corresponding proteins of several other filoviruses. The gapped MSSAs revealed structure-based residue-residue correspondences, which enabled identification of structurally similar versus differing regions in the Reston proteins compared to each of the other corresponding proteins. CombAlign is a new Python code that generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA) given a set of pairwise sequence alignments (which may be structure based). CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related proteins. CombAlign was developed in Python 2.6, and the source code is available for download from the GitHub code repository.

Noah’s Ark Conservation Will Not Preserve Threatened Ecological Communities under Climate Change

PubMed Central

Harris, Rebecca Mary Bernadette; Carter, Oberon; Gilfedder, Louise; Porfirio, Luciana Laura; Lee, Greg; Bindoff, Nathaniel Lee

2015-01-01

Background Effective conservation of threatened ecological communities requires knowledge of where climatically suitable habitat is likely to persist into the future. We use the critically endangered Lowland Grassland community of Tasmania, Australia as a case study to identify options for management in cases where future climatic conditions become unsuitable for the current threatened community. Methods We model current and future climatic suitability for the Lowland Themeda and the Lowland Poa Grassland communities, which make up the listed ecological community. We also model climatic suitability for the structurally dominant grass species of these communities, and for closely related grassland and woodland communities. We use a dynamically downscaled regional climate model derived from six CMIP3 global climate models, under the A2 SRES emissions scenario. Results All model projections showed a large reduction in climatically suitable area by mid-century. Outcomes are slightly better if closely related grassy communities are considered, but the extent of suitable area is still substantially reduced. Only small areas within the current distribution are projected to remain climatically suitable by the end of the century, and very little of that area is currently in good condition. Conclusions As the climate becomes less suitable, a gradual change in the species composition, structure and habitat quality of the grassland communities is likely. Conservation management will need to focus on maintaining diversity, structure and function, rather than attempting to preserve current species composition. Options for achieving this include managing related grassland types to maintain grassland species at the landscape-scale, and maximising the resilience of grasslands by reducing further fragmentation, weed invasion and stress from other land uses, while accepting that change is inevitable. Attempting to maintain the status quo by conserving the current structure and composition of Lowland Grassland communities is unlikely to be a viable management option in the long term. PMID:25881302

Noah's Ark conservation will not preserve threatened ecological communities under climate change.

PubMed

Harris, Rebecca Mary Bernadette; Carter, Oberon; Gilfedder, Louise; Porfirio, Luciana Laura; Lee, Greg; Bindoff, Nathaniel Lee

2015-01-01

Effective conservation of threatened ecological communities requires knowledge of where climatically suitable habitat is likely to persist into the future. We use the critically endangered Lowland Grassland community of Tasmania, Australia as a case study to identify options for management in cases where future climatic conditions become unsuitable for the current threatened community. We model current and future climatic suitability for the Lowland Themeda and the Lowland Poa Grassland communities, which make up the listed ecological community. We also model climatic suitability for the structurally dominant grass species of these communities, and for closely related grassland and woodland communities. We use a dynamically downscaled regional climate model derived from six CMIP3 global climate models, under the A2 SRES emissions scenario. All model projections showed a large reduction in climatically suitable area by mid-century. Outcomes are slightly better if closely related grassy communities are considered, but the extent of suitable area is still substantially reduced. Only small areas within the current distribution are projected to remain climatically suitable by the end of the century, and very little of that area is currently in good condition. As the climate becomes less suitable, a gradual change in the species composition, structure and habitat quality of the grassland communities is likely. Conservation management will need to focus on maintaining diversity, structure and function, rather than attempting to preserve current species composition. Options for achieving this include managing related grassland types to maintain grassland species at the landscape-scale, and maximising the resilience of grasslands by reducing further fragmentation, weed invasion and stress from other land uses, while accepting that change is inevitable. Attempting to maintain the status quo by conserving the current structure and composition of Lowland Grassland communities is unlikely to be a viable management option in the long term.

CONTINUITY AND CHANGE IN THE AMERICAN CLASS STRUCTURE: WORKPLACE OWNERSHIP AND AUTHORITY RELATIONS FROM 1972 TO 2010.

PubMed

Wodtke, Geoffrey T

2015-12-01

This study investigates changes in the American class structure-defined in terms of workplace ownership and authority relations-and trends in status group disparities in class attainment from 1972 to 2010. Although theory and prior research suggest a variety of appreciable changes in class structure and class attainment, data from the General Social Survey indicate that the sizes of different classes remained fairly stable during this time period and that status group disparities in access to ownership and authority persisted largely intact. The 1970s witnessed a decline in the proportion of workers and growth in the proportion of managers and proprietors, but these trends reversed in the 1980s. As a result, by the late 2000s, the ownership and authority structure of the U.S. economy closely resembled that of the early 1970s. Racial and gender disparities in class attainment also did not change significantly over time: blacks and women remained underrepresented (relative to whites and men) in positions of ownership and authority throughout this period. Even after controlling for an extensive set of human capital characteristics, family constraints, and structural economic factors, there is little evidence of status group integration across these key dimensions of economic power.

Healthier Students Are Better Learners: A Missing Link in School Reforms to Close the Achievement Gap. Equity Matters. Research Review No. 6

ERIC Educational Resources Information Center

Basch, Charles E.

2010-01-01

No matter how well teachers are prepared to teach, no matter what accountability measures are put in place, no matter what governing structures are established for schools, educational progress will be profoundly limited if students are not "motivated and able to learn". Health-related problems play a major role in limiting the motivation and…

Aeruginascin, a trimethylammonium analogue of psilocybin from the hallucinogenic mushroom Inocybe aeruginascens.

PubMed

Jensen, Niels; Gartz, Jochen; Laatsch, Hartmut

2006-06-01

The hallucinogenic mushroom Inocybe aeruginascens contains several typical Psilocybe alkaloids including psilocybin. We have now elucidated the structure of a further indole derivative named aeruginascin as the quaternary ammonium compound N, N, N-trimethyl-4-phosphoryloxytryptamine. Aeruginascin is closely related to the frog skin toxin bufotenidine (5-HTQ), a potent 5-HT3 receptor agonist, and has been found exclusively in Inocybe aeruginascens so far.

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

PubMed Central

Bushley, Kathryn E.; Ohm, Robin A.; Otillar, Robert; Martin, Joel; Schackwitz, Wendy; Grimwood, Jane; MohdZainudin, NurAinIzzati; Xue, Chunsheng; Wang, Rui; Manning, Viola A.; Dhillon, Braham; Tu, Zheng Jin; Steffenson, Brian J.; Salamov, Asaf; Sun, Hui; Lowry, Steve; LaButti, Kurt; Han, James; Copeland, Alex; Lindquist, Erika; Barry, Kerrie; Schmutz, Jeremy; Baker, Scott E.; Ciuffetti, Lynda M.; Grigoriev, Igor V.; Zhong, Shaobin; Turgeon, B. Gillian

2013-01-01

The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five percent of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25× higher than those between inbred lines and 50× lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP–encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence. PMID:23357949

Diversity in 113 cowpea [Vigna unguiculata (L) Walp] accessions assessed with 458 SNP markers.

PubMed

Egbadzor, Kenneth F; Ofori, Kwadwo; Yeboah, Martin; Aboagye, Lawrence M; Opoku-Agyeman, Michael O; Danquah, Eric Y; Offei, Samuel K

2014-01-01

Single Nucleotide Polymorphism (SNP) markers were used in characterization of 113 cowpea accessions comprising of 108 from Ghana and 5 from abroad. Leaf tissues from plants cultivated at the University of Ghana were genotyped at KBioscience in the United Kingdom. Data was generated for 477 SNPs, out of which 458 revealed polymorphism. The results were used to analyze genetic dissimilarity among the accessions using Darwin 5 software. The markers discriminated among all of the cowpea accessions and the dissimilarity values which ranged from 0.006 to 0.63 were used for factorial plot. Unexpected high levels of heterozygosity were observed on some of the accessions. Accessions known to be closely related clustered together in a dendrogram drawn with WPGMA method. A maximum length sub-tree which comprised of 48 core accessions was constructed. The software package structure was used to separate accessions into three groups, and the programme correctly identified varieties that were known hybrids. The hybrids were those accessions with numerous heterozygous loci. The structure plot showed closely related accessions with similar genome patterns. The SNP markers were more efficient in discriminating among the cowpea germplasm than morphological, seed protein polymorphism and simple sequence repeat studies reported earlier on the same collection.

Purification and characterization of multiple forms of the pineapple-stem-derived cysteine proteinases ananain and comosain.

PubMed Central

Napper, A D; Bennett, S P; Borowski, M; Holdridge, M B; Leonard, M J; Rogers, E E; Duan, Y; Laursen, R A; Reinhold, B; Shames, S L

1994-01-01

A mixture of ananain (EC 3.4.22.31) and comosain purified from crude pineapple stem extract was found to contain numerous closely related enzyme forms. Chromatographic separation of the major enzyme forms was achieved after treatment of the mixture with thiol-modifying reagents: reversible modification with 2-hydroxyethyl disulphide provided enzyme for kinetic studies, and irreversible alkylation with bromotrifluoroacetone or iodoacetamide gave enzyme for structural analyses by 19F-n.m.r. and electrospray mass spectrometry respectively. Structural and kinetic analyses revealed comosain to be closely related to stem bromelain (EC 3.4.22.32), whereas ananain differed markedly from both comosain and stem bromelain. Nevertheless, differences were seen between comosain and stem bromelain in amino acid composition and kinetic specificity towards the epoxide inhibitor E-64. Differences between five isolatable alternative forms of ananain were characterized by amidolytic activity, thiol stoichiometry and accurate mass determinations. Three of the enzyme forms displayed ananain-like amidolytic activity, whereas the other two forms were inactive. Thiol-stoichiometry determinations revealed that the active enzyme forms contained one free thiol, whereas the inactive forms lacked the reactive thiol required for enzyme activity. M.s. provided direct evidence for oxidation of the active-site thiol to the corresponding sulphinic acid. Images Figure 3 Figure 4 PMID:8053898

The CCK(-like) receptor in the animal kingdom: functions, evolution and structures.

PubMed

Staljanssens, Dorien; Azari, Elnaz Karimian; Christiaens, Olivier; Beaufays, Jérôme; Lins, Laurence; Van Camp, John; Smagghe, Guy

2011-03-01

In this review, the cholecystokinin (CCK)(-like) receptors throughout the animal kingdom are compared on the level of physiological functions, evolutionary basis and molecular structure. In vertebrates, the CCK receptor is an important member of the G-protein coupled receptors as it is involved in the regulation of many physiological functions like satiety, gastrointestinal motility, gastric acid secretion, gall bladder contraction, pancreatic secretion, panic, anxiety and memory and learning processes. A homolog for this receptor is also found in nematodes and arthropods, called CK receptor and sulfakinin (SK) receptor, respectively. These receptors seem to have evolved from a common ancestor which is probably still closely related to the nematode CK receptor. The SK receptor is more closely related to the CCK receptor and seems to have similar functions. A molecular 3D-model for the CCK receptor type 1 has been built together with the docking of the natural ligands for the CCK and SK receptors in the CCK receptor type 1. These molecular models can help to study ligand-receptor interactions, that can in turn be useful in the development of new CCK(-like) receptor agonists and antagonists with beneficial health effects in humans or potential for pest control. Copyright © 2010 Elsevier Inc. All rights reserved.

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

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

Condon, Bradford J.; Leng, Yueqiang; Wu, Dongliang

The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five of each genome differs between strains of the same species,more » while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25 higher than those between inbred lines and 50 lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.« less

Thermal vibrations and polymorphic β → γ transition in cerium

NASA Astrophysics Data System (ADS)

Agafonov, S. S.; Blanter, M. S.; Glazkov, V. P.; Somenkov, V. A.; Shushunov, M. N.

2010-10-01

Method of neutron diffraction was used to determine the temperature dependence of the Debye-Waller factor and the related thermal atomic displacements for two polymorphic modifications of cerium, namely, for β-Ce with a double hexagonal closed-packed (dhcp) structure and for γ-Ce with a face-centered cubic (fcc) structure. It has been shown that the phase transition does not lead to substantial changes in the root-mean-square thermal atomic displacements and that the Debye temperatures of the two modifications are close: 131 K for β-Ce and 127 K for γ-Ce. However, the relative (with respect to the lattice parameters) displacements along the axes change considerably. The transition from the anisotropic hexagonal to the isotropic cubic modification leads, because of a redistribution of thermal atomic displacements along the crystallographic axes, to a decrease in the maximum values of these quantities and to a weakening of their temperature dependence. It has also been shown that a change in the thermal atomic vibrations and in the vibrational contribution to the entropy of the polymorphic transformations is connected with the sign of the volume effect of the transformation (stronger upon a positive effect and weaker, upon a negative one). The reasons for this behavior are discussed.

Application of close-range terrestrial photogrammetry to bridge structures : final report.

DOT National Transportation Integrated Search

1985-01-01

A field application of close-range terrestrial photogrammetry to the measurement of small order of magnitude structural displacements and differences in elevation was conducted. A Jena UMK 10/1318 camera was used to take the photographs used in the e...

Passivity-based control of linear time-invariant systems modelled by bond graph

NASA Astrophysics Data System (ADS)

Galindo, R.; Ngwompo, R. F.

2018-02-01

Closed-loop control systems are designed for linear time-invariant (LTI) controllable and observable systems modelled by bond graph (BG). Cascade and feedback interconnections of BG models are realised through active bonds with no loading effect. The use of active bonds may lead to non-conservation of energy and the overall system is modelled by proposed pseudo-junction structures. These structures are build by adding parasitic elements to the BG models and the overall system may become singularly perturbed. The structures for these interconnections can be seen as consisting of inner structures that satisfy energy conservation properties and outer structures including multiport-coupled dissipative fields. These fields highlight energy properties like passivity that are useful for control design. In both interconnections, junction structures and dissipative fields for the controllers are proposed, and passivity is guaranteed for the closed-loop systems assuring robust stability. The cascade interconnection is applied to the structural representation of closed-loop transfer functions, when a stabilising controller is applied to a given nominal plant. Applications are given when the plant and the controller are described by state-space realisations. The feedback interconnection is used getting necessary and sufficient stability conditions based on the closed-loop characteristic polynomial, solving a pole-placement problem and achieving zero-stationary state error.

Co-evolution in a landrace meta-population: two closely related pathogens interacting with the same host can lead to different adaptive outcomes.

PubMed

Rau, Domenico; Rodriguez, Monica; Leonarda Murgia, Maria; Balmas, Virgilio; Bitocchi, Elena; Bellucci, Elisa; Nanni, Laura; Attene, Giovanna; Papa, Roberto

2015-08-07

We examined the local adaptation patterns in a system comprising several interconnected heterogeneous plant populations from which populations of two phylogenetically closely related pathogens were also sampled. The host is Hordeum vulgare (cultivated barley); the pathogens are Pyrenophora teres f. teres (net form) and Pyrenophora teres f. maculata (spot form), the causal agents of barley net blotch. We integrated two approaches, the comparison between the population structures of the host and the pathogens, and a cross-inoculation test. We demonstrated that two closely related pathogens with very similar niche specialisation and life-styles can give rise to different co-evolutionary outcomes on the same host. Indeed, we detected local adaptation for the net form of the pathogen but not for the spot form. We also provided evidence that an a-priori well-known resistance quantitative-trait-locus on barley chromosome 6H is involved in the co-evolutionary 'arms race' between the plant and the net-form pathogen. Moreover, data suggested latitudinal clines of host resistance and that different ecological conditions can result in differential selective pressures at different sites. Our data are of interest for on-farm conservation of plant genetic resources, as also in establishing efficient breeding programs and strategies for deployment of resistance genes of P. teres.

Co-evolution in a landrace meta-population: two closely related pathogens interacting with the same host can lead to different adaptive outcomes

PubMed Central

Rau, Domenico; Rodriguez, Monica; Leonarda Murgia, Maria; Balmas, Virgilio; Bitocchi, Elena; Bellucci, Elisa; Nanni, Laura; Attene, Giovanna; Papa, Roberto

2015-01-01

We examined the local adaptation patterns in a system comprising several interconnected heterogeneous plant populations from which populations of two phylogenetically closely related pathogens were also sampled. The host is Hordeum vulgare (cultivated barley); the pathogens are Pyrenophora teres f. teres (net form) and Pyrenophora teres f. maculata (spot form), the causal agents of barley net blotch. We integrated two approaches, the comparison between the population structures of the host and the pathogens, and a cross-inoculation test. We demonstrated that two closely related pathogens with very similar niche specialisation and life-styles can give rise to different co-evolutionary outcomes on the same host. Indeed, we detected local adaptation for the net form of the pathogen but not for the spot form. We also provided evidence that an a-priori well-known resistance quantitative-trait-locus on barley chromosome 6H is involved in the co-evolutionary ‘arms race’ between the plant and the net-form pathogen. Moreover, data suggested latitudinal clines of host resistance and that different ecological conditions can result in differential selective pressures at different sites. Our data are of interest for on-farm conservation of plant genetic resources, as also in establishing efficient breeding programs and strategies for deployment of resistance genes of P. teres. PMID:26248796

"Who'll do all these if I'm not around?": Bonding social capital and health and well-being of inpatients.

PubMed

Amoah, Padmore Adusei; Koduah, Adwoa Owusuaa; Gyasi, Razak Mohammed

2018-12-01

Although social capital influences health-related decisions and behavioural patterns in many developing countries, minimal attention has been paid to the nuances of its effect on healthcare. This paper examines how bonding social capital affects healthcare delivery for inpatients in Ghana. Semi-structured in-depth interviews were used and thematic analysis method employed to analyse the data. Interviews were conducted with health professionals and relatives and close friends of inpatients in three public health facilities in Ashanti region. Relatives and close friends of inpatients were a critical source of instrumental support such as provision of meals, laundry services, running errands and financial assistance as well as emotional support. These functions-that were both 'expected' and 'encouraged'- reduced the burden on the health facilities, which apparently had limited resources to offer adequate care. However, the relatives of inpatients sometimes inadvertently obstructed efficient healthcare delivery through actions such as extending 'unapproved' alternative care to patients. Moreover, the process of contributing towards health and well-being of the sick exposed the relatives to health risks due to poor living conditions. A well-defined and befitting role must be devised for at least an immediate social relation of inpatients to improve the positive effects of bonding social capital on healthcare delivery.

Albumin Antioxidant Response to Stress in Diabetic Nephropathy Progression

PubMed Central

Medina-Navarro, Rafael; Corona-Candelas, Itzia; Barajas-González, Saúl; Díaz-Flores, Margarita; Durán-Reyes, Genoveva

2014-01-01

Background A new component of the protein antioxidant capacity, designated Response Surplus (RS), was recently described. A major feature of this component is the close relationship between protein antioxidant capacity and molecular structure. Oxidative stress is associated with renal dysfunction in patients with renal failure, and plasma albumin is the target of massive oxidation in nephrotic syndrome and diabetic nephropathy. The aim of the present study was to explore the albumin redox state and the RS component of human albumin isolated from diabetic patients with progressive renal damage. Methods/Principal Findings Serum aliquots were collected and albumin isolated from 125 diabetic patients divided into 5 groups according to their estimated glomerular filtration rate (GFR). In addition to clinical and biochemical variables, the albumin redox state, including antioxidant capacity, thiol group content, and RS component, were evaluated. The albumin antioxidant capacity and thiol group content were reciprocally related to the RS component in association with GFR reduction. The GFR decline and RS component were significantly negatively correlated (R = –0.83, p<0.0001). Age, creatinine, thiol groups, and antioxidant capacity were also significantly related to the GFR decline (R = –0.47, p<0.001; R = –0.68, p<0.0001; R = 0.44, p<0.001; and R = 0.72, p<0.0001). Conclusion/Significance The response of human albumin to stress in relation to the progression of diabetic renal disease was evaluated. The findings confirm that the albumin molecular structure is closely related to its redox state, and is a key factor in the progression of diabetes nephropathy. PMID:25187963

Chimeric β-Lactamases: Global Conservation of Parental Function and Fast Time-Scale Dynamics with Increased Slow Motions

PubMed Central

Clouthier, Christopher M.; Morin, Sébastien; Gobeil, Sophie M. C.; Doucet, Nicolas; Blanchet, Jonathan; Nguyen, Elisabeth; Gagné, Stéphane M.; Pelletier, Joelle N.

2012-01-01

Enzyme engineering has been facilitated by recombination of close homologues, followed by functional screening. In one such effort, chimeras of two class-A β-lactamases – TEM-1 and PSE-4 – were created according to structure-guided protein recombination and selected for their capacity to promote bacterial proliferation in the presence of ampicillin (Voigt et al., Nat. Struct. Biol. 2002 9:553). To provide a more detailed assessment of the effects of protein recombination on the structure and function of the resulting chimeric enzymes, we characterized a series of functional TEM-1/PSE-4 chimeras possessing between 17 and 92 substitutions relative to TEM-1 β-lactamase. Circular dichroism and thermal scanning fluorimetry revealed that the chimeras were generally well folded. Despite harbouring important sequence variation relative to either of the two ‘parental’ β-lactamases, the chimeric β-lactamases displayed substrate recognition spectra and reactivity similar to their most closely-related parent. To gain further insight into the changes induced by chimerization, the chimera with 17 substitutions was investigated by NMR spin relaxation. While high order was conserved on the ps-ns timescale, a hallmark of class A β-lactamases, evidence of additional slow motions on the µs-ms timescale was extracted from model-free calculations. This is consistent with the greater number of resonances that could not be assigned in this chimera relative to the parental β-lactamases, and is consistent with this well-folded and functional chimeric β-lactamase displaying increased slow time-scale motions. PMID:23284969

A hetero-micro-seeding strategy for readily crystallizing closely related protein variants.

PubMed

Islam, Mohammad M; Kuroda, Yutaka

2017-11-04

Protein crystallization remains difficult to rationalize and screening for optimal crystallization conditions is a tedious and time consuming procedure. Here, we report a hetero-micro-seeding strategy for producing high resolution crystals of closely related protein variants, where micro crystals from a readily crystallized variant are used as seeds to develop crystals of other variants less amenable to crystallization. We applied this strategy to Bovine Pancreatic Trypsin Inhibitor (BPTI) variants, which would not crystallize using standard crystallization practice. Out of six variants in our analysis, only one called BPTI-[5,55]A14G formed well behaving crystals; and the remaining five (A14GA38G, A14GA38V, A14GA38L, A14GA38I, and A14GA38K) could be crystallized only using micro-seeds from the BPTI-[5,55]A14G crystal. All hetero-seeded crystals diffracted at high resolution with minimum mosaicity, retaining the same space group and cell dimension. Moreover, hetero-micro-seeding did not introduce any biases into the mutant's structure toward the seed structure, as demonstrated by A14GA38I structures solved using micro-seeds from A14GA38G, A14GA38L and A14GA38I. Though hetero-micro-seeding is a simple and almost naïve strategy, this is the first direct demonstration of its workability. We believe that hetero-micro-seeding, which is contrasting with the popular idea that crystallization requires highly purified proteins, could contribute a new tool for rapidly solving protein structures in mutational analysis studies. Copyright © 2017 Elsevier Inc. All rights reserved.

Multiple genome alignment for identifying the core structure among moderately related microbial genomes.

PubMed

Uchiyama, Ikuo

2008-10-31

Identifying the set of intrinsically conserved genes, or the genomic core, among related genomes is crucial for understanding prokaryotic genomes where horizontal gene transfers are common. Although core genome identification appears to be obvious among very closely related genomes, it becomes more difficult when more distantly related genomes are compared. Here, we consider the core structure as a set of sufficiently long segments in which gene orders are conserved so that they are likely to have been inherited mainly through vertical transfer, and developed a method for identifying the core structure by finding the order of pre-identified orthologous groups (OGs) that maximally retains the conserved gene orders. The method was applied to genome comparisons of two well-characterized families, Bacillaceae and Enterobacteriaceae, and identified their core structures comprising 1438 and 2125 OGs, respectively. The core sets contained most of the essential genes and their related genes, which were primarily included in the intersection of the two core sets comprising around 700 OGs. The definition of the genomic core based on gene order conservation was demonstrated to be more robust than the simpler approach based only on gene conservation. We also investigated the core structures in terms of G+C content homogeneity and phylogenetic congruence, and found that the core genes primarily exhibited the expected characteristic, i.e., being indigenous and sharing the same history, more than the non-core genes. The results demonstrate that our strategy of genome alignment based on gene order conservation can provide an effective approach to identify the genomic core among moderately related microbial genomes.

Experimental identification of closely spaced modes using NExT-ERA

NASA Astrophysics Data System (ADS)

Hosseini Kordkheili, S. A.; Momeni Massouleh, S. H.; Hajirezayi, S.; Bahai, H.

2018-01-01

This article presents a study on the capability of the time domain OMA method, NExT-ERA, to identify closely spaced structural dynamic modes. A survey in the literature reveals that few experimental studies have been conducted on the effectiveness of the NExT-ERA methodology in case of closely spaced modes specifically. In this paper we present the formulation for NExT-ERA. This formulation is then implemented in an algorithm and a code, developed in house to identify the modal parameters of different systems using their generated time history data. Some numerical models are firstly investigated to validate the code. Two different case studies involving a plate with closely spaced modes and a pulley ring with greater extent of closeness in repeated modes are presented. Both structures are excited by random impulses under the laboratory condition. The resulting time response acceleration data are then used as input in the developed code to extract modal parameters of the structures. The accuracy of the results is checked against those obtained from experimental tests.

Electronic structures of Al-Si clusters and the magic number structure Al8Si4

NASA Astrophysics Data System (ADS)

Du, Ning; Su, Mingzhi; Chen, Hongshan

2018-02-01

The low-energy structures of Al8Sim (m = 1-6) have been determined by using the genetic algorithm combined with density functional theory and the Second-order Moller-Plesset perturbation theory (MP2) models. The results show that the close-packed structures are preferable in energy for Al-Si clusters and in most cases there exist a few isomers with close energies. The valence molecular orbitals, the orbital level structures and the electron localisation function (ELF) consistently demonstrate that the electronic structures of Al-Si clusters can be described by the jellium model. Al8Si4 corresponds to a magic number structure with pronounced stability and large energy gap; the 40 valence electrons form closed 1S21P61D102S21F142P6 shells. The ELF attractors also suggest weak covalent Si-Si, Si-Al and Al-Al bonding, and doping Si in aluminium clusters promotes the covalent interaction between Al atoms.

Laboratory Detection of HSiCN and HSiNC

NASA Astrophysics Data System (ADS)

Sanz, M. Eugenia; McCarthy, Michael C.; Thaddeus, Patrick

2002-09-01

Two new silicon-bearing molecules, the closed-shell asymmetric tops cyanosilylene HSiCN and its isomer HSiNC, have been detected in a laboratory discharge by molecular beam Fourier transform microwave spectroscopy. The rotational spectra of the normal and deuterated isotopic species of both molecules have been analyzed to derive precise spectroscopic constants, which allow the astronomically most interesting transitions up to 120 GHz to be calculated to an accuracy better than 1 km s-1 in equivalent radial velocity. Both molecules are good candidates for astronomical detection, closely related in structure and composition to known astronomical molecules, and they are highly polar, with estimated dipole moments of 3.5 D for HSiCN and 2.5 D for HSiNC.

Cognitive factors in the close visual and magnetic particle inspection of welds underwater.

PubMed

Leach, J; Morris, P E

1998-06-01

Underwater close visual inspection (CVI) and magnetic particle inspection (MPI) are major components of the commercial diver's job of nondestructive testing and the maintenance of subsea structures. We explored the accuracy of CVI in Experiment 1 and that of MPI in Experiment 2 and observed high error rates (47% and 24%, respectively). Performance was strongly correlated with embedded figures and visual search tests and was unrelated to length of professional diving experience, formal inspection qualification, or age. Cognitive tests of memory for designs, spatial relations, dotted outlines, and block design failed to correlate with performance. Actual or potential applications of this research include more reliable inspection reporting, increased effectiveness from current inspection techniques, and directions for the refinement of subsea inspection equipment.

Stability of cavitation structures in a thin liquid layer.

PubMed

Wu, Pengfei; Bai, Lixin; Lin, Weijun; Yan, Jiuchun

2017-09-01

The inception and evolution of acoustic cavitation structures in thin liquid layers under different conditions and perturbations are investigated experimentally with high speed photography. The stability and characterization of cavitation structures are quantified by image analysis methods. It is found that cavitation structures (shape of bubble cloud and number of bubbles) are stable under unaltered experimental conditions, and the cavitation bubble cloud will return to the original structure and remain stable even in the face of large perturbations. When the experimental conditions are altered (for example, acoustic intensity, cavitation nuclei, boundary), the cavitation structures will vary correspondingly. Further analysis implies that the stability of cavitation structures is closely related to the number of bubbles in the cavitation bubble cloud. There are two mechanisms acting simultaneously in the cavitation bubble cloud evolution, one "bubble production" and the other "bubble disappearance". We propose that the two mechanisms acting together constitute the most likely explanation for the stability of cavitation structures and their transformation. Copyright © 2017 Elsevier B.V. All rights reserved.

Complete Mitochondrial Genomes of New Zealand’s First Dogs

PubMed Central

Greig, Karen; Boocock, James; Prost, Stefan; Horsburgh, K. Ann; Jacomb, Chris; Walter, Richard; Matisoo-Smith, Elizabeth

2015-01-01

Dogs accompanied people in their migrations across the Pacific Ocean and ultimately reached New Zealand, which is the southern-most point of their oceanic distribution, around the beginning of the fourteenth century AD. Previous ancient DNA analyses of mitochondrial control region sequences indicated the New Zealand dog population included two lineages. We sequenced complete mitochondrial genomes of fourteen dogs from the colonisation era archaeological site of Wairau Bar and found five closely-related haplotypes. The limited number of mitochondrial lineages present at Wairau Bar suggests that the founding population may have comprised only a few dogs; or that the arriving dogs were closely related. For populations such as that at Wairau Bar, which stemmed from relatively recent migration events, control region sequences have insufficient power to address questions about population structure and founding events. Sequencing mitogenomes provided the opportunity to observe sufficient diversity to discriminate between individuals that would otherwise be assigned the same haplotype and to clarify their relationships with each other. Our results also support the proposition that at least one dispersal of dogs into the Pacific was via a south-western route through Indonesia. PMID:26444283

A distributed finite-element modeling and control approach for large flexible structures

NASA Technical Reports Server (NTRS)

Young, K. D.

1989-01-01

An unconventional framework is described for the design of decentralized controllers for large flexible structures. In contrast to conventional control system design practice which begins with a model of the open loop plant, the controlled plant is assembled from controlled components in which the modeling phase and the control design phase are integrated at the component level. The developed framework is called controlled component synthesis (CCS) to reflect that it is motivated by the well developed Component Mode Synthesis (CMS) methods which were demonstrated to be effective for solving large complex structural analysis problems for almost three decades. The design philosophy behind CCS is also closely related to that of the subsystem decomposition approach in decentralized control.

Future of the world's automobile industry

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

Kagawa, T.

1989-03-01

The author feels that the Japanese automobile industry is approaching a turning point. But it is not enough to refer only to the changing structure of the Japanese automobile industry when similar structural changes are taking place on a worldwide scale. Therefore he first comments on the current state of the automobile industry of the world, and then reviews the reasons for the gap between automobile production and demand and the historical background of this phenomenon. Then, finally, he discusses the current progress of and future challenges in the structural adjustment of the global automobile industry. He notes the verymore » close relation of the battery industry to the automobile industry, and hopes the former will prosper hand in hand with the latter. 6 tables.« less

Discrete and continuum links to a nonlinear coupled transport problem of interacting populations

NASA Astrophysics Data System (ADS)

Duong, M. H.; Muntean, A.; Richardson, O. M.

2017-07-01

We are interested in exploring interacting particle systems that can be seen as microscopic models for a particular structure of coupled transport flux arising when different populations are jointly evolving. The scenarios we have in mind are inspired by the dynamics of pedestrian flows in open spaces and are intimately connected to cross-diffusion and thermo-diffusion problems holding a variational structure. The tools we use include a suitable structure of the relative entropy controlling TV-norms, the construction of Lyapunov functionals and particular closed-form solutions to nonlinear transport equations, a hydrodynamics limiting procedure due to Philipowski, as well as the construction of numerical approximates to both the continuum limit problem in 2D and to the original interacting particle systems.

Structural investigations in helium charged titanium films using grazing incidence XRD and EXAFS spectroscopy

NASA Astrophysics Data System (ADS)

Wan, Chubin; Zhou, Xiaosong; Wang, Yuting; Li, Shina; Ju, Xin; Peng, Shuming

2014-01-01

The crystal structure and local atomic arrangements surrounding Ti atoms were determined for He-charged hexagonal close-packed (hcp) Ti films and measured at glancing angles by synchrotron radiation X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy, respectively. The charged specimens were prepared by direct current magnetron sputtering with a He/Ar mixture. He atoms with a relatively medium concentration (He/Ti atomic ratio as high as 17 at.%) were incorporated evenly in the deposited films. XRD results showed the changes in the peak intensities in Ti films with different He contents. EXAFS Fourier Transform analysis indicated that the average Ti-Ti distance decreased significantly, and proved the existence of phase transition.

AB INITIO Investigations of the Magnetism in Diluted Magnetic Semiconductor Fe-DOPED GaN

NASA Astrophysics Data System (ADS)

Cheng, Jie; Zhou, Jing; Xu, Wei; Dong, Peng

2014-01-01

In this paper, we present a first principle investigation on Fe-doped GaN with wurtzite and zinc-blend structure using full potential density functional calculations. Data point out that the magnetic behavior of Fe-doped GaN system is strongly dependent on Fe doping configurations. In agreement with the experimental reports, and independently by doping, antiferromagnetism occurs in the zinc-blend structure, while in the wurtzite structure ferromagnetism depends on the Fe doping configurations. Detailed analyses combined with density of state calculations support the assignment that the ferromagnetism is closely related to the impurity band at the origin of the hybridization of Fe 3d and N 2p states in the Fe-doped GaN of wurtzite phase.

Structure and Evolution of Insect Sperm: New Interpretations in the Age of Phylogenomics.

PubMed

Dallai, Romano; Gottardo, Marco; Beutel, Rolf Georg

2016-01-01

This comprehensive review of the structure of sperm in all orders of insects evaluates phylogenetic implications, with the background of a phylogeny based on transcriptomes. Sperm characters strongly support several major branches of the phylogeny of insects-for instance, Cercophora, Dicondylia, and Psocodea-and also different infraordinal groups. Some closely related taxa, such as Trichoptera and Lepidoptera (Amphiesmenoptera), differ greatly in sperm structure. Sperm characters are very conservative in some groups (Heteroptera, Odonata) but highly variable in others, including Zoraptera, a small and morphologically uniform group with a tremendously accelerated rate of sperm evolution. Unusual patterns such as sperm dimorphism, the formation of bundles, or aflagellate and immotile sperm have evolved independently in several groups.

System for plotting subsoil structure and method therefor

NASA Technical Reports Server (NTRS)

Narasimhan, K. Y.; Nathan, R.; Parthasarathy, S. P. (Inventor)

1980-01-01

Data for use in producing a tomograph of subsoil structure between boreholes is derived by pacing spaced geophones in one borehole, on the Earth surface if desired, and by producing a sequence of shots at spaced apart locations in the other borehole. The signals, detected by each of the geophones from the various shots, are processed either on a time of arrival basis, or on the basis of signal amplitude, to provide information of the characteristics of a large number of incremental areas between the boreholes. Such information is useable to produce a tomograph of the subsoil structure between the boreholes. By processing signals of relatively high frequencies, e.g., up to 100 Hz, and by closely spacing the geophones, a high resolution tomograph can be produced.

Pre-marital genetic counselling to consanguineous couples: attitudes, beliefs and decisions among counselled, noncounselled and unrelated couples in Israel.

PubMed

Shiloh, S; Reznik, H; Bat-Miriam-Katznelson, M; Goldman, B

1995-11-01

Semi-structured interviews were conducted with 65 Israeli subjects who received genetic counselling while considering marriage to a close relative, 40 subjects married to a close relative who did not receive pre-marital genetic counselling, and 125 controls married to a nonrelative and never having considered marrying a relative. It was found that 72% of the consanguineous couples who received pre-marital genetic counselling proceeded with their plans and married their relative; 86% of them reported that the counselling influenced their final decision to some degree. Counsellees' appraisals of genetic counselling revealed unfulfilled expectations to obtain more definitive answers, and mixed reactions to the nondirective approach applied by the counsellors. Comparisons between consanguineous and control couples revealed different views about consanguinity in general, and genetic risks in particular. Consanguineous couples, unlike controls, perceived consanguinity as an ordinary form of marriage, and had more favorable attitudes towards it. Compared to the noncounselled consanguineous group, consanguineous couples who received pre-marital genetic counselling had fewer children, estimated their genetic risk as lower but its subjective significance as higher, and perceived genetic disorders as more severe. The implications of these results are discussed from both theoretical and practical standpoints.

Digital control algorithms for microgravity isolation systems

NASA Technical Reports Server (NTRS)

Sinha, Alok; Wang, Yung-Peng

1992-01-01

New digital control algorithms were developed to achieve the desired acceleration transmissibility function. The attractive electromagnets have been taken as actuators. The relative displacement and the acceleration of the mass were used as feedback signals. Two approaches were developed to find that controller transfer function in Z-domain, which yields the desired transmissibility at each frequency. In the first approach, the controller transfer function is obtained by assuming that the desired transmissibility is known in Z-domain. Since the desired transmissibility H sub d(S) = 1/(tauS+1)(exp 2) is given in S-domain, the first task is to obtain the desired transmissibility in Z-domain. There are three methods to perform this task: bilinear transformation, and backward and forward rectangular rules. The bilinear transformation and backward rectangular rule lead to improper controller transfer functions, which are physically not realizable. The forward rectangular rule does lead to a physically realizable controller. However, this controller is found to be marginally stable because of a pole at Z=1. In order to eliminate this pole, a hybrid control structure is proposed. Here the control input is composed of two parts: analog and digital. The analog input simply represents the velocity (or the integral of acceleration) feedback; and the digital controller which uses only relative displacement signal, is then obtained to achieve the desired closed-loop transfer function. The stability analysis indicates that the controller transfer function is stable for typical values of sampling period. In the second approach, the aforementioned hybrid control structure is again used. First, an analog controller transfer function corresponding to relative displacement feedback is obtained to achieve the transmissibility as 1/(tauS+1)(exp 2). Then the transfer function for the digital control input is obtained by discretizing this analog controller transfer function via bilinear transformation. The stability of the resulting Z-domain closed loop system is analyzed. Also, the frequency response of the Z-domain closed-loop transfer function is determined to evaluate the performance of the control system.

Co-Conserved MAPK Features Couple D-Domain Docking Groove to Distal Allosteric Sites via the C-Terminal Flanking Tail

PubMed Central

Nguyen, Tuan; Ruan, Zheng; Oruganty, Krishnadev; Kannan, Natarajan

2015-01-01

Mitogen activated protein kinases (MAPKs) form a closely related family of kinases that control critical pathways associated with cell growth and survival. Although MAPKs have been extensively characterized at the biochemical, cellular, and structural level, an integrated evolutionary understanding of how MAPKs differ from other closely related protein kinases is currently lacking. Here, we perform statistical sequence comparisons of MAPKs and related protein kinases to identify sequence and structural features associated with MAPK functional divergence. We show, for the first time, that virtually all MAPK-distinguishing sequence features, including an unappreciated short insert segment in the β4-β5 loop, physically couple distal functional sites in the kinase domain to the D-domain peptide docking groove via the C-terminal flanking tail (C-tail). The coupling mediated by MAPK-specific residues confers an allosteric regulatory mechanism unique to MAPKs. In particular, the regulatory αC-helix conformation is controlled by a MAPK-conserved salt bridge interaction between an arginine in the αC-helix and an acidic residue in the C-tail. The salt-bridge interaction is modulated in unique ways in individual sub-families to achieve regulatory specificity. Our study is consistent with a model in which the C-tail co-evolved with the D-domain docking site to allosterically control MAPK activity. Our study provides testable mechanistic hypotheses for biochemical characterization of MAPK-conserved residues and new avenues for the design of allosteric MAPK inhibitors. PMID:25799139

Interactions between plants and primates shape community diversity in a rainforest in Madagascar.

PubMed

Herrera, James P

2016-07-01

Models of ecological community assembly predict how communities of interacting organisms may be shaped by abiotic and biotic factors. Competition and environmental filtering are the predominant factors hypothesized to explain community assembly. This study tested the effects of habitat, phylogenetic and phenotypic trait predictors on species co-occurrence patterns and abundances, with the endemic primates of Madagascar as an empirical system. The abundance of 11 primate species was estimated along gradients of elevation, food resource abundance and anthropogenic habitat disturbance at local scales in south-east Madagascar. Community composition was compared to null models to test for phylogenetic and functional structure, and the effects of phylogenetic relatedness of co-occurring species, their trait similarity and environmental variables on species' abundances were tested using mixed models and quantile regressions. Resource abundance was the strongest predictor of community structure. Where food tree abundance was high, closely related species with similar traits dominated communities. High-elevation communities with lower food tree abundance consisted of species that were distantly related and had divergent traits. Closely related species had dissimilar abundances where they co-occurred, partially driven by trait dissimilarity, indicating character displacement. By integrating local-scale variation in primate community composition, evolutionary relatedness and functional diversity, this study found strong evidence that community assembly in this system can be explained by competition and character displacement along ecological gradients. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

Basement involved thrusts from Northwestern Maracaibo Basin

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

Audemard, F.

1993-02-01

The interpretation of seismic reflection profiles from northwestern Maracaibo Basin, north of the Palmar River, suggests a late Neogene age for all the structures located within the north-northeast trends of anticlinal belts. These folded structures appear to be ramp anticlines generated from basement involved thrusts. Such detachments are intercepted by conjugate systems of low-angle decollements decoupled from the thick shaly intervals of Cretaceous and Eocene age. The resulting configuration of these fault systems are related to a mechanic of deformation referred as [open quotes]fish tail[close quotes]. This structural style favors the superposition of structural traps at different levels. The superposedmore » reservoirs from La Paz, Mara, Sibucara, Mara Oeste, and Ensenada among others constitute superb examples of this style of deformation. Similar anticlinal structures are also observed to the southeast of the Basin in the Ceuta-Tomoporo area.« less

Structural insights into substrate specificity of Feruloyl-CoA 6’-Hydroxylase from Arabidopsis thaliana

DOE PAGES

Sun, Xinxiao; Zhou, Dayong; Kandavelu, Palani; ...

2015-05-20

Coumarins belong to an important class of plant secondary metabolites. Feruloyl-CoA 6’-hydroxylase (F6’H), a 2-oxoglutarate dependent dioxygenase (2OGD), catalyzes a pivotal step in the biosynthesis of a simple coumarin scopoletin. In this study, we determined the 3-dimensional structure of the F6’H1 apo enzyme by X-ray crystallography. It is the first reported structure of a 2OGD enzyme involved in coumarin biosynthesis and closely resembles the structure of Arabidopsis thaliana anthocyanidin synthase. To better understand the mechanism of enzyme catalysis and substrate specificity, we also generated a homology model of a related ortho-hydroxylase (C 2’H) from sweet potato. By comparing these twomore » structures, we targeted two amino acid residues and verified their roles in substrate binding and specificity by site-directed mutagenesis.« less

Structural insights into substrate specificity of Feruloyl-CoA 6’-Hydroxylase from Arabidopsis thaliana

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

Sun, Xinxiao; Zhou, Dayong; Kandavelu, Palani

Coumarins belong to an important class of plant secondary metabolites. Feruloyl-CoA 6’-hydroxylase (F6’H), a 2-oxoglutarate dependent dioxygenase (2OGD), catalyzes a pivotal step in the biosynthesis of a simple coumarin scopoletin. In this study, we determined the 3-dimensional structure of the F6’H1 apo enzyme by X-ray crystallography. It is the first reported structure of a 2OGD enzyme involved in coumarin biosynthesis and closely resembles the structure of Arabidopsis thaliana anthocyanidin synthase. To better understand the mechanism of enzyme catalysis and substrate specificity, we also generated a homology model of a related ortho-hydroxylase (C 2’H) from sweet potato. By comparing these twomore » structures, we targeted two amino acid residues and verified their roles in substrate binding and specificity by site-directed mutagenesis.« less

Generating a New Higher-Dimensional Coupled Integrable Dispersionless System: Algebraic Structures, Bäcklund Transformation and Hidden Structural Symmetries

NASA Astrophysics Data System (ADS)

Souleymanou, Abbagari; Thomas, B. Bouetou; Timoleon, C. Kofane

2013-08-01

The prolongation structure methodologies of Wahlquist—Estabrook [H.D. Wahlquist and F.B. Estabrook, J. Math. Phys. 16 (1975) 1] for nonlinear differential equations are applied to a more general set of coupled integrable dispersionless system. Based on the obtained prolongation structure, a Lie-Algebra valued connection of a closed ideal of exterior differential forms related to the above system is constructed. A Lie-Algebra representation of some hidden structural symmetries of the previous system, its Bäcklund transformation using the Riccati form of the linear eigenvalue problem and their general corresponding Lax-representation are derived. In the wake of the previous results, we extend the above prolongation scheme to higher-dimensional systems from which a new (2 + 1)-dimensional coupled integrable dispersionless system is unveiled along with its inverse scattering formulation, which applications are straightforward in nonlinear optics where additional propagating dimension deserves some attention.

Structural Basis for Sialoglycan Binding by the Streptococcus sanguinis SrpA Adhesin*♦

PubMed Central

Bensing, Barbara A.; Loukachevitch, Lioudmila V.; McCulloch, Kathryn M.; Yu, Hai; Vann, Kendra R.; Wawrzak, Zdzislaw; Anderson, Spencer; Chen, Xi; Sullam, Paul M.; Iverson, T. M.

2016-01-01

Streptococcus sanguinis is a leading cause of infective endocarditis, a life-threatening infection of the cardiovascular system. An important interaction in the pathogenesis of infective endocarditis is attachment of the organisms to host platelets. S. sanguinis expresses a serine-rich repeat adhesin, SrpA, similar in sequence to platelet-binding adhesins associated with increased virulence in this disease. In this study, we determined the first crystal structure of the putative binding region of SrpA (SrpABR) both unliganded and in complex with a synthetic disaccharide ligand at 1.8 and 2.0 Å resolution, respectively. We identified a conserved Thr-Arg motif that orients the sialic acid moiety and is required for binding to platelet monolayers. Furthermore, we propose that sequence insertions in closely related family members contribute to the modulation of structural and functional properties, including the quaternary structure, the tertiary structure, and the ligand-binding site. PMID:26833566

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

Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding.

PubMed

Tomić, A; Berynskyy, M; Wade, R C; Tomić, S

2015-11-01

The experimentally determined structures of human dipeptidyl peptidase III (DPP III) for the wild-type protein and for the complex of its E451A mutant with the peptide substrate, tynorphin, differ significantly in their overall shape. The two domains of the enzyme are separated by a wide cleft in the structure of the ligand-free enzyme, while in the ligand-bound mutant they are very close to each other, and the protein structure is extremely compact. Here, we applied a range of molecular dynamics simulation techniques to investigate the DPP III conformational landscape and the influence of ligand binding on the protein structure and dynamics. We used conventional, accelerated and steered methods to simulate DPP III and its complexes with tynorphin and with the preferred, synthetic, substrate Arg-Arg-2-naphthylamide. We found that DPP III can adopt a number of different forms in solution. The compact forms are more stable, but the open and partially closed states, spanning a wide range of conformations, can more effectively recognize the substrate which preferentially binds to the five-stranded β-core of the lower DPP III domain. The simulations indicated the existence of a dynamic equilibrium between open and semi-closed states and revealed two ways that the protein can close, leading to two distinct compact structures. The way in which the protein closes depends on the presence of the ligand.

Carbon cycling at the tipping point: Does ecosystem structure predict resistance to disturbance?

NASA Astrophysics Data System (ADS)

Gough, C. M.; Bond-Lamberty, B. P.; Stuart-Haentjens, E.; Atkins, J.; Haber, L.; Fahey, R. T.

2017-12-01

Ecosystems worldwide are subjected to disturbances that reshape their physical and biological structure and modify biogeochemical processes, including carbon storage and cycling rates. Disturbances, including those from insect pests, pathogens, and extreme weather, span a continuum of severity and, accordingly, may have different effects on carbon cycling processes. Some ecosystems resist biogeochemical changes following disturbance, until a critical threshold of severity is exceeded. The ecosystem properties underlying such functional resistance, and signifying when a tipping point will occur, however, are almost entirely unknown. Here, we present observational and experimental results from forests in the Great Lakes region, showing ecosystem structure is closely coupled with carbon cycling responses to disturbance, with shifts in structure predicting thresholds of and, in some cases, increases in carbon storage. We find, among forests in the region, that carbon storage regularly exhibits a non-linear threshold response to increasing disturbance levels, but the severity at which a threshold is reached varies among disturbed forests. More biologically and structurally complex forest ecosystems sometimes exhibit greater functional resistance than simpler forests, and consequently may have a higher disturbance severity threshold. Counter to model predictions but consistent with some theoretical frameworks, empirical data show moderate levels of disturbance may increase ecosystem complexity to a point, thereby increasing rates of carbon storage. Disturbances that increase complexity therefore may stimulate carbon storage, while severe disturbances at or beyond thresholds may simplify structure, leading to carbon storage declines. We conclude that ecosystem structural attributes are closely coupled with biogeochemical thresholds across disturbance severity gradients, suggesting that improved predictions of disturbance-related changes in the carbon cycle require better representation of ecosystem structure in models.

Mechanical properties of additively manufactured octagonal honeycombs.

PubMed

Hedayati, R; Sadighi, M; Mohammadi-Aghdam, M; Zadpoor, A A

2016-12-01

Honeycomb structures have found numerous applications as structural and biomedical materials due to their favourable properties such as low weight, high stiffness, and porosity. Application of additive manufacturing and 3D printing techniques allows for manufacturing of honeycombs with arbitrary shape and wall thickness, opening the way for optimizing the mechanical and physical properties for specific applications. In this study, the mechanical properties of honeycomb structures with a new geometry, called octagonal honeycomb, were investigated using analytical, numerical, and experimental approaches. An additive manufacturing technique, namely fused deposition modelling, was used to fabricate the honeycomb from polylactic acid (PLA). The honeycombs structures were then mechanically tested under compression and the mechanical properties of the structures were determined. In addition, the Euler-Bernoulli and Timoshenko beam theories were used for deriving analytical relationships for elastic modulus, yield stress, Poisson's ratio, and buckling stress of this new design of honeycomb structures. Finite element models were also created to analyse the mechanical behaviour of the honeycombs computationally. The analytical solutions obtained using Timoshenko beam theory were close to computational results in terms of elastic modulus, Poisson's ratio and yield stress, especially for relative densities smaller than 25%. The analytical solutions based on the Timoshenko analytical solution and the computational results were in good agreement with experimental observations. Finally, the elastic properties of the proposed honeycomb structure were compared to those of other honeycomb structures such as square, triangular, hexagonal, mixed, diamond, and Kagome. The octagonal honeycomb showed yield stress and elastic modulus values very close to those of regular hexagonal honeycombs and lower than the other considered honeycombs. Copyright © 2016 Elsevier B.V. All rights reserved.

Outline-based morphometrics, an overlooked method in arthropod studies?

PubMed

Dujardin, Jean-Pierre; Kaba, D; Solano, P; Dupraz, M; McCoy, K D; Jaramillo-O, N

2014-12-01

Modern methods allow a geometric representation of forms, separating size and shape. In entomology, as well as in many other fields involving arthropod studies, shape variation has proved useful for species identification and population characterization. In medical entomology, it has been applied to very specific questions such as population structure, reinfestation of insecticide-treated areas and cryptic species recognition. For shape comparisons, great importance is given to the quality of landmarks in terms of comparability. Two conceptually and statistically separate approaches are: (i) landmark-based morphometrics, based on the relative position of a few anatomical "true" or "traditional" landmarks, and (ii) outline-based morphometrics, which captures the contour of forms through a sequence of close "pseudo-landmarks". Most of the studies on insects of medical, veterinary or economic importance make use of the landmark approach. The present survey makes a case for the outline method, here based on elliptic Fourier analysis. The collection of pseudo-landmarks may require the manual digitization of many points and, for this reason, might appear less attractive. It, however, has the ability to compare homologous organs or structures having no landmarks at all. This strength offers the possibility to study a wider range of anatomical structures and thus, a larger range of arthropods. We present a few examples highlighting its interest for separating close or cryptic species, or characterizing conspecific geographic populations, in a series of different vector organisms. In this simple application, i.e. the recognition of close or cryptic forms, the outline approach provided similar scores as those obtained by the landmark-based approach. Copyright © 2014 Elsevier B.V. All rights reserved.

In Vivo Measurement of Pediatric Vocal Fold Motion Using Structured Light Laser Projection

PubMed Central

Patel, Rita R.; Donohue, Kevin D.; Lau, Daniel; Unnikrishnan, Harikrishnan

2013-01-01

Summary Objective The aim of the study was to present the development of a miniature structured light laser projection endoscope and to quantify vocal fold length and vibratory features related to impact stress of the pediatric glottis using high-speed imaging. Study Design The custom-developed laser projection system consists of a green laser with a 4-mm diameter optics module at the tip of the endoscope, projecting 20 vertical laser lines on the glottis. Measurements of absolute phonatory vocal fold length, membranous vocal fold length, peak amplitude, amplitude-to-length ratio, average closing velocity, and impact velocity were obtained in five children (6–9 years), two adult male and three adult female participants without voice disorders, and one child (10 years) with bilateral vocal fold nodules during modal phonation. Results Independent measurements made on the glottal length of a vocal fold phantom demonstrated a 0.13 mm bias error with a standard deviation of 0.23 mm, indicating adequate precision and accuracy for measuring vocal fold structures and displacement. First, in vivo measurements of amplitude-to-length ratio, peak closing velocity, and impact velocity during phonation in pediatric population and a child with vocal fold nodules are reported. Conclusion The proposed laser projection system can be used to obtain in vivo measurements of absolute length and vibratory features in children and adults. Children have large amplitude-to-length ratio compared with typically developing adults, whereas nodules result in larger peak amplitude, amplitude-to-length ratio, average closing velocity, and impact velocity compared with typically developing children. PMID:23809569

Receiving power through confirmation: the meaning of close relatives for people who have been critically ill.

PubMed

Engström, Asa; Söderberg, Siv

2007-09-01

This paper is a report of a study to elucidate the meaning of close relatives for people who have been critically ill and received care in an intensive care unit. Falling critically ill can bring about a difficult change in life. In previous reports such events are described as frightening experiences, and close relatives are described as an important source of support in this difficult situation. A purposive sample of 10 adults, eight men and two women, narrated how they experienced their close relatives during and after the time they were critically ill. The data were collected in 2004. The interview texts were transcribed and interpreted using a phenomenological hermeneutic approach influenced by the philosophy of Ricoeur. One major theme was identified, experiencing confirmation, with six sub-themes: receiving explanations; a feeling of being understood; a feeling of safety; gaining strength and will-power; having possibilities and realizing their value. Close relatives served as tools for the person who was ill, facilitating better communication and an increased ability to do various things. Simultaneously, feelings of dependence on the close relatives were expressed. There were descriptions of loneliness and fear in the absence of close relatives and, in order to feel safe, the participants wanted their close relatives to stay near them. Close relatives are vital, as they are the ill person's motivation to stay alive and to continue the struggle. Their presence is of great importance for the ill person and must be facilitated by staff.

Simultaneous gene finding in multiple genomes.

PubMed

König, Stefanie; Romoth, Lars W; Gerischer, Lizzy; Stanke, Mario

2016-11-15

As the tree of life is populated with sequenced genomes ever more densely, the new challenge is the accurate and consistent annotation of entire clades of genomes. We address this problem with a new approach to comparative gene finding that takes a multiple genome alignment of closely related species and simultaneously predicts the location and structure of protein-coding genes in all input genomes, thereby exploiting negative selection and sequence conservation. The model prefers potential gene structures in the different genomes that are in agreement with each other, or-if not-where the exon gains and losses are plausible given the species tree. We formulate the multi-species gene finding problem as a binary labeling problem on a graph. The resulting optimization problem is NP hard, but can be efficiently approximated using a subgradient-based dual decomposition approach. The proposed method was tested on whole-genome alignments of 12 vertebrate and 12 Drosophila species. The accuracy was evaluated for human, mouse and Drosophila melanogaster and compared to competing methods. Results suggest that our method is well-suited for annotation of (a large number of) genomes of closely related species within a clade, in particular, when RNA-Seq data are available for many of the genomes. The transfer of existing annotations from one genome to another via the genome alignment is more accurate than previous approaches that are based on protein-spliced alignments, when the genomes are at close to medium distances. The method is implemented in C ++ as part of Augustus and available open source at http://bioinf.uni-greifswald.de/augustus/ CONTACT: stefaniekoenig@ymail.com or mario.stanke@uni-greifswald.deSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Small-scale swirl events in the quiet Sun chromosphere

NASA Astrophysics Data System (ADS)

Wedemeyer-Böhm, S.; Rouppe van der Voort, L.

2009-11-01

Context: Recent progress in instrumentation enables solar observations with high resolution simultaneously in the spatial, temporal, and spectral domains. Aims: We use such high-resolution observations to study small-scale structures and dynamics in the chromosphere of the quiet Sun. Methods: We analyse time series of spectral scans through the Ca ii 854.2 nm spectral line obtained with the CRISP instrument at the Swedish 1-m Solar Telescope. The targets are quiet Sun regions inside coronal holes close to disc-centre. Results: The line core maps exhibit relatively few fibrils compared to what is normally observed in quiet Sun regions outside coronal holes. The time series show a chaotic and dynamic scene that includes spatially confined “swirl” events. These events feature dark and bright rotating patches, which can consist of arcs, spiral arms, rings or ring fragments. The width of the fragments typically appears to be of the order of only 0.2 arcsec, which is close to the effective spatial resolution. They exhibit Doppler shifts of -2 to -4 km s-1 but sometimes up to -7 km s-1, indicating fast upflows. The diameter of a swirl is usually of the order of 2´´. At the location of these swirls, the line wing and wide-band maps show close groups of photospheric bright points that move with respect to each other. Conclusions: A likely explanation is that the relative motion of the bright points twists the associated magnetic field in the chromosphere above. Plasma or propagating waves may then spiral upwards guided by the magnetic flux structure, thereby producing the observed intensity signature of Doppler-shifted ring fragments. The movie is only available in electronic form at http://www.aanda.org Marie Curie Intra-European Fellow of the European Commission.

Measuring Adaptive Coping of Hospitalized Patients With a Severe Medical Condition: The Sickness Insight in Coping Questionnaire.

PubMed

Boezeman, Edwin J; Hofhuis, José G M; Hovingh, Aly; Cox, Christopher E; de Vries, Reinout E; Spronk, Peter E

2016-09-01

Adaptive coping strategies are associated with less psychological distress. However, there is no brief, specific, and validated instrument for assessing adaptive coping among seriously ill patients. Our objective was to examine the validity and patient-proxy agreement of a novel instrument, the Sickness Insight in Coping Questionnaire. A cross-sectional design which included two related studies. A single university-affiliated Dutch hospital. Hospitalized patients (study 1) and ICU-patients and proxies (study 2). None. Study 1 (n = 103 hospitalized patients) addressed the Sickness Insight in Coping Questionnaire's performance relative to questionnaires addressing similar content areas. Coping subscales of the BRIEF COPE, Illness Cognition Questionnaire, and Utrecht Coping List were used as comparator measures in testing the construct validity of the Sickness Insight in Coping Questionnaire-subscales (fighting spirit, toughness, redefinition, positivism, and non-acceptance). The Sickness Insight in Coping Questionnaire had good internal consistency (0.64 ≤ α ≤ 0.79), a clear initial factor structure, and fair convergent (0.24 ≤ r ≤ 0.50) and divergent (r, ≤ 0.12) construct validity. Study 2 examined the performance of the Sickness Insight in Coping Questionnaire among 100 ICU patients and their close family members. This study showed that the Sickness Insight in Coping Questionnaire has good structural validity (confirmatory factor analyses with Comparative Fit Index > 0.90 and Root Mean Square Error of Approximation < 0.08) and moderate (r, 0.37; non-acceptance) to strong (r, > 0.50; fighting spirit, toughness, redefinition, and positivism) patient-close proxy agreement. Overall, the Sickness Insight in Coping Questionnaire has good psychometric properties. ICU clinicians can use the Sickness Insight in Coping Questionnaire to gain insight in adaptive coping style of patients through ratings of patients or their close family members.

Large-scale properties of the interplanetary magnetic field

NASA Technical Reports Server (NTRS)

Schatten, K. H.

1972-01-01

Early theoretical work of Parker is presented along with the observational evidence supporting his Archimedes spiral model. Variations present in the interplanetary magnetic field from the spiral angle are related to structures in the solar wind. The causes of these structures are found to be either nonuniform radial solar wind flow or the time evolution of the photospheric field. Coronal magnetic models are related to the connection between the solar magnetic field and the interplanetary magnetic field. Direct extension of the solar field-magnetic nozzle controversy is discussed along with the coronal magnetic models. Effects of active regions on the interplanetary magnetic field is discussed with particular reference to the evolution of interplanetary sectors. Interplanetary magnetic field magnitude variations are shown throughout the solar cycle. The percentage of time the field magnitude is greater than 10 gamma is shown to closely parallel sunspot number. The sun's polar field influence on the interplanetary field and alternative views of the magnetic field structure out of the ecliptic plane are presented. In addition, a variety of significantly different interplanetary field structures are discussed.

Structural Efficiency of Percolated Landscapes in Flow Networks

PubMed Central

Serrano, M. Ángeles; De Los Rios, Paolo

2008-01-01

The large-scale structure of complex systems is intimately related to their functionality and evolution. In particular, global transport processes in flow networks rely on the presence of directed pathways from input to output nodes and edges, which organize in macroscopic connected components. However, the precise relation between such structures and functional or evolutionary aspects remains to be understood. Here, we investigate which are the constraints that the global structure of directed networks imposes on transport phenomena. We define quantitatively under minimal assumptions the structural efficiency of networks to determine how robust communication between the core and the peripheral components through interface edges could be. Furthermore, we assess that optimal topologies in terms of access to the core should look like “hairy balls” so to minimize bottleneck effects and the sensitivity to failures. We illustrate our investigation with the analysis of three real networks with very different purposes and shaped by very different dynamics and time-scales–the Internet customer-provider set of relationships, the nervous system of the worm Caenorhabditis elegans, and the metabolism of the bacterium Escherichia coli. Our findings prove that different global connectivity structures result in different levels of structural efficiency. In particular, biological networks seem to be close to the optimal layout. PMID:18985157

Random close packing of disks and spheres in confined geometries

NASA Astrophysics Data System (ADS)

Desmond, Kenneth W.; Weeks, Eric R.

2009-11-01

Studies of random close packing of spheres have advanced our knowledge about the structure of systems such as liquids, glasses, emulsions, granular media, and amorphous solids. In confined geometries, the structural properties of random-packed systems will change. To understand these changes, we study random close packing in finite-sized confined systems, in both two and three dimensions. Each packing consists of a 50-50 binary mixture with particle size ratio of 1.4. The presence of confining walls significantly lowers the overall maximum area fraction (or volume fraction in three dimensions). A simple model is presented, which quantifies the reduction in packing due to wall-induced structure. This wall-induced structure decays rapidly away from the wall, with characteristic length scales comparable to the small particle diameter.

Sexual dimorphism in bite performance drives morphological variation in chameleons.

PubMed

da Silva, Jessica M; Herrel, Anthony; Measey, G John; Tolley, Krystal A

2014-01-01

Phenotypic performance in different environments is central to understanding the evolutionary and ecological processes that drive adaptive divergence and, ultimately, speciation. Because habitat structure can affect an animal's foraging behaviour, anti-predator defences, and communication behaviour, it can influence both natural and sexual selection pressures. These selective pressures, in turn, act upon morphological traits to maximize an animal's performance. For performance traits involved in both social and ecological activities, such as bite force, natural and sexual selection often interact in complex ways, providing an opportunity to understand the adaptive significance of morphological variation with respect to habitat. Dwarf chameleons within the Bradypodion melanocephalum-Bradypodion thamnobates species complex have multiple phenotypic forms, each with a specific head morphology that could reflect its use of either open- or closed-canopy habitats. To determine whether these morphological differences represent adaptations to their habitats, we tested for differences in both absolute and relative bite performance. Only absolute differences were found between forms, with the closed-canopy forms biting harder than their open-canopy counterparts. In contrast, sexual dimorphism was found for both absolute and relative bite force, but the relative differences were limited to the closed-canopy forms. These results indicate that both natural and sexual selection are acting within both habitat types, but to varying degrees. Sexual selection seems to be the predominant force within the closed-canopy habitats, which are more protected from aerial predators, enabling chameleons to invest more in ornamentation for communication. In contrast, natural selection is likely to be the predominant force in the open-canopy habitats, inhibiting the development of conspicuous secondary sexual characteristics and, ultimately, enforcing their overall diminutive body size and constraining performance.

Sexual Dimorphism in Bite Performance Drives Morphological Variation in Chameleons

PubMed Central

da Silva, Jessica M.; Herrel, Anthony; Measey, G. John; Tolley, Krystal A.

2014-01-01

Phenotypic performance in different environments is central to understanding the evolutionary and ecological processes that drive adaptive divergence and, ultimately, speciation. Because habitat structure can affect an animal’s foraging behaviour, anti-predator defences, and communication behaviour, it can influence both natural and sexual selection pressures. These selective pressures, in turn, act upon morphological traits to maximize an animal’s performance. For performance traits involved in both social and ecological activities, such as bite force, natural and sexual selection often interact in complex ways, providing an opportunity to understand the adaptive significance of morphological variation with respect to habitat. Dwarf chameleons within the Bradypodion melanocephalum-Bradypodion thamnobates species complex have multiple phenotypic forms, each with a specific head morphology that could reflect its use of either open- or closed-canopy habitats. To determine whether these morphological differences represent adaptations to their habitats, we tested for differences in both absolute and relative bite performance. Only absolute differences were found between forms, with the closed-canopy forms biting harder than their open-canopy counterparts. In contrast, sexual dimorphism was found for both absolute and relative bite force, but the relative differences were limited to the closed-canopy forms. These results indicate that both natural and sexual selection are acting within both habitat types, but to varying degrees. Sexual selection seems to be the predominant force within the closed-canopy habitats, which are more protected from aerial predators, enabling chameleons to invest more in ornamentation for communication. In contrast, natural selection is likely to be the predominant force in the open-canopy habitats, inhibiting the development of conspicuous secondary sexual characteristics and, ultimately, enforcing their overall diminutive body size and constraining performance. PMID:24475183

Going that extra mile: individuals travel further to maintain face-to-face contact with highly related kin than with less related kin.

PubMed

Pollet, Thomas V; Roberts, Sam G B; Dunbar, Robin I M

2013-01-01

The theory of inclusive fitness has transformed our understanding of cooperation and altruism. However, the proximate psychological underpinnings of altruism are less well understood, and it has been argued that emotional closeness mediates the relationship between genetic relatedness and altruism. In this study, we use a real-life costly behaviour (travel time) to dissociate the effects of genetic relatedness from emotional closeness. Participants travelled further to see more closely related kin, as compared to more distantly related kin. For distantly related kin, the level of emotional closeness mediated this relationship--when emotional closeness was controlled for, there was no effect of genetic relatedness on travel time. However, participants were willing to travel further to visit parents, children and siblings as compared to more distantly related kin, even when emotional closeness was controlled for. This suggests that the mediating effect of emotional closeness on altruism varies with levels of genetic relatedness.

Groups of related belugas (Delphinapterus leucas) travel together during their seasonal migrations in and around Hudson Bay

PubMed Central

Colbeck, Gabriel J.; Duchesne, Pierre; Postma, Lianne D.; Lesage, Véronique; Hammill, Mike O.; Turgeon, Julie

2013-01-01

Social structure involving long-term associations with relatives should facilitate the learning of complex behaviours such as long-distance migration. In and around Hudson Bay (Canada), three stocks of beluga whales form a panmictic unit, but have different migratory behaviours associated with different summering areas. We analysed genetic variation at 13 microsatellite loci among 1524 belugas, to test hypotheses about social structure in belugas. We found significant proportions of mother–offspring pairs throughout the migratory cycle, but average relatedness extended beyond close kinship only during migration. Average relatedness was significantly above random expectations for pairs caught at the same site but on different days or months of a year, suggesting that belugas maintain associations with a network of relatives during migration. Pairs involving a female (female–female or male–female) were on average more related than pairs of males, and males seemed to disperse from their matrilineal group to associate with other mature males. Altogether, our results indicate that relatives other than strictly parents, and especially females, play a role in maintaining a social structure that could facilitate the learning of migration routes. Cultural conservatism may limit contributions from nearby summer stocks to endangered stocks such as the Eastern Hudson Bay beluga. PMID:23222451

Groups of related belugas (Delphinapterus leucas) travel together during their seasonal migrations in and around Hudson Bay.

PubMed

Colbeck, Gabriel J; Duchesne, Pierre; Postma, Lianne D; Lesage, Véronique; Hammill, Mike O; Turgeon, Julie

2013-02-07

Social structure involving long-term associations with relatives should facilitate the learning of complex behaviours such as long-distance migration. In and around Hudson Bay (Canada), three stocks of beluga whales form a panmictic unit, but have different migratory behaviours associated with different summering areas. We analysed genetic variation at 13 microsatellite loci among 1524 belugas, to test hypotheses about social structure in belugas. We found significant proportions of mother-offspring pairs throughout the migratory cycle, but average relatedness extended beyond close kinship only during migration. Average relatedness was significantly above random expectations for pairs caught at the same site but on different days or months of a year, suggesting that belugas maintain associations with a network of relatives during migration. Pairs involving a female (female-female or male-female) were on average more related than pairs of males, and males seemed to disperse from their matrilineal group to associate with other mature males. Altogether, our results indicate that relatives other than strictly parents, and especially females, play a role in maintaining a social structure that could facilitate the learning of migration routes. Cultural conservatism may limit contributions from nearby summer stocks to endangered stocks such as the Eastern Hudson Bay beluga.

In-situ observation of bubble trapping in polar firn

NASA Astrophysics Data System (ADS)

Florian Schaller, Christoph; Freitag, Johannes; Sowers, Todd; Vinther, Bo; Weinhart, Alexander; Eisen, Olaf

2017-04-01

The air trapped in polar ice cores is not a direct record of past atmospheric composition but is strongly influenced by the process of firnification as bubbles are only sealed at a certain point, when the respective horizontal layer reaches a so called "critical" porosity. In order to investigate this process, we performed high-resolution (approximately 25 μm) 3D-XCT measurements of the complete lock-in zone for two polar ice cores representing opposite extremes of the temperature and accumulation rate range: B53, close to Dome Fuji, East Antarctica and RECAP_S2, Renland, Greenland. For every 1m core segment, we scanned a minimum number of five sections of approximately 3.5cm height of the full core diameter with a focus on homogenous layers. This allows us to non-destructively deduce detailed profiles of open and closed porosity on a solid statistical basis. For each of the cores individually, we find that the trapping of bubbles in a single layer is solely determined by its total porosity and thereby independent of depth. We can confirm the existence of a distinct Schwander-type relation of closed and total porosity. Even though the two cores deviate from each other significantly in critical porosity, 0.0907 for B53 compared to 0.1025 for RECAP_S2, we observe many similarities. We hypothesize, that the determining factors of bubble trapping are the average size and variability of pore space structures. This could potentially allow the reconstruction of past close-off porosities from the remaining pore structures in deep ice, e.g. from bubble number densities.

Structures and dynamics in a two-dimensional dipolar dust particle system

NASA Astrophysics Data System (ADS)

Hou, X. N.; Liu, Y. H.; Kravchenko, O. V.; Lapushkina, T. A.; Azarova, O. A.; Chen, Z. Y.; Huang, F.

2018-05-01

The effects of electric dipole moment, the number of dipolar particles, and system temperature on the structures and dynamics of a dipolar dust particle system are studied by molecular dynamics simulations. The results show that the larger electric dipole moment is favorable for the formation of a long-chain structure, the larger number of dipolar dust particles promotes the formation of the multi-chain structure, and the higher system temperature can cause higher rotation frequency. The trajectories, mean square displacement (MSD), and the corresponding spectrum functions of the MSDs are also calculated to illustrate the dynamics of the dipolar dust particle system, which is also closely related to the growth of dust particles. Some simulations are qualitatively in agreement with our experiments and can provide a guide for the study on dust growth, especially on the large-sized particles.

Relationship of microstructure properties to oxygen impurities in nanocrystalline silicon photovoltaic materials

NASA Astrophysics Data System (ADS)

Xu, H.; Wen, C.; Liu, H.; Li, Z. P.; Shen, W. Z.

2013-03-01

We have fully investigated the correlation of microstructure properties and oxygen impurities in hydrogenated nanocrystalline silicon photovoltaic films. The achievement has been realized through a series of different hydrogen dilution ratio treatment by plasma enhanced chemical vapor deposition system. Raman scattering, x-ray diffraction, and ultraviolet-visible transmission techniques have been employed to characterize the physical structural characterization and to elucidate the structure evolution. The bonding configuration of the oxygen impurities was investigated by x-ray photoelectron spectroscopy and the Si-O stretching mode of infrared-transmission, indicating that the films were well oxidized in SiO2 form. Based on the consistence between the proposed structure factor and the oxygen content, we have demonstrated that there are two dominant disordered structure regions closely related to the post-oxidation contamination: plate-like configuration and clustered microvoids.

Probing Chemical Space with Alkaloid-Inspired Libraries

PubMed Central

McLeod, Michael C.; Singh, Gurpreet; Plampin, James N.; Rane, Digamber; Wang, Jenna L.; Day, Victor W.; Aubé, Jeffrey

2014-01-01

Screening of small molecule libraries is an important aspect of probe and drug discovery science. Numerous authors have suggested that bioactive natural products are attractive starting points for such libraries, due to their structural complexity and sp3-rich character. Here, we describe the construction of a screening library based on representative members of four families of biologically active alkaloids (Stemonaceae, the structurally related cyclindricine and lepadiformine families, lupin, and Amaryllidaceae). In each case, scaffolds were based on structures of the naturally occurring compounds or a close derivative. Scaffold preparation was pursued following the development of appropriate enabling chemical methods. Diversification provided 686 new compounds suitable for screening. The libraries thus prepared had structural characteristics, including sp3 content, comparable to a basis set of representative natural products and were highly rule-of-five compliant. PMID:24451589

Tuning the surface microstructure of titanate coatings on titanium implants for enhancing bioactivity of implants

PubMed Central

Wang, Hui; Lai, Yue-Kun; Zheng, Ru-Yue; Bian, Ye; Zhang, Ke-Qin; Lin, Chang-Jian

2015-01-01

Biological performance of artificial implant materials is closely related to their surface characteristics, such as microtopography, and composition. Therefore, convenient fabrication of artificial implant materials with a cell-friendly surface structure and suitable composition was of great significance for current tissue engineering. In this work, titanate materials with a nanotubular structure were successfully fabricated through a simple chemical treatment. Immersion test in a simulated body fluid and in vitro cell culture were used to evaluate the biological performance of the treated samples. The results demonstrate that the titanate layer with a nanotubular structure on Ti substrates can promote the apatite-inducing ability remarkably and greatly enhance cellular responses. This highlights the potential of such titanate biomaterials with the special nanoscale structure and effective surface composition for biomedical applications such as bone implants. PMID:26089665

Purification and Thermal Stability of Intact Bacillus subtilis Flagella

PubMed Central

Dimmitt, K.; Simon, M.

1971-01-01

Flagella were prepared and purified in a relatively intact form from bacterial lysates. Immunochemical tests showed that over 95% of the protein in the final preparation consisted of flagellar antigen. These flagella are more stable to thermal denaturation than flagella filaments obtained by shearing. Their thermal properties more closely resemble those of flagella in the native state on bacteria. The presence of the hook structure is responsible for this extra stability. Images PMID:4993323

High power microwave generator

DOEpatents

Ekdahl, Carl A.

1986-01-01

A microwave generator efficiently converts the energy of an intense relativistic electron beam (REB) into a high-power microwave emission using the Smith-Purcell effect which is related to Cerenkov radiation. Feedback for efficient beam bunching and high gain is obtained by placing a cylindrical Smith-Purcell transmission grating on the axis of a toroidal resonator. High efficiency results from the use of a thin cold annular highly-magnetized REB that is closely coupled to the resonant structure.

Programming Environments Based on Structured Editors: The MENTOR Experience,

DTIC Science & Technology

1980-07-01

ambitious plan has been actually implemented in MENTOR- PASCAL. There are niostly two reaons for this, which are actually cnmplementary aspects of...languages. As might be expecteo, these desig,, * r.t.. ia ar closely 8 related to those based on semantic considerationslO. We have good hope that the...d) it has reasonably good user interaction facilities: there are various debugging aids osuch as a trace package, an interrupt facility, and the user

High power microwave generator

DOEpatents

Ekdahl, C.A.

1983-12-29

A microwave generator efficiently converts the energy of an intense relativistic electron beam (REB) into a high-power microwave emission using the Smith-Purcell effect which is related to Cerenkov radiation. Feedback for efficient beam bunching and high gain is obtained by placing a cylindrical Smith-Purcell transmission grating on the axis of a toroidal resonator. High efficiency results from the use of a thin cold annular highly-magnetized REB that is closely coupled to the resonant structure.

The first crystal structures of a family 19 class IV chitinase: the enzyme from Norway spruce.

PubMed

Ubhayasekera, Wimal; Rawat, Reetika; Ho, Sharon Wing Tak; Wiweger, Malgorzata; Von Arnold, Sara; Chye, Mee-Len; Mowbray, Sherry L

2009-10-01

Chitinases help plants defend themselves against fungal attack, and play roles in other processes, including development. The catalytic modules of most plant chitinases belong to glycoside hydrolase family 19. We report here x-ray structures of such a module from a Norway spruce enzyme, the first for any family 19 class IV chitinase. The bi-lobed structure has a wide cleft lined by conserved residues; the most interesting for catalysis are Glu113, the proton donor, and Glu122, believed to be a general base that activate a catalytic water molecule. Comparisons to class I and II enzymes show that loop deletions in the class IV proteins make the catalytic cleft shorter and wider; from modeling studies, it is predicted that only three N-acetylglucosamine-binding subsites exist in class IV. Further, the structural comparisons suggest that the family 19 enzymes become more closed on substrate binding. Attempts to solve the structure of the complete protein including the associated chitin-binding module failed, however, modeling studies based on close relatives indicate that the binding module recognizes at most three N-acetylglucosamine units. The combined results suggest that the class IV enzymes are optimized for shorter substrates than the class I and II enzymes, or alternatively, that they are better suited for action on substrates where only small regions of chitin chain are accessible. Intact spruce chitinase is shown to possess antifungal activity, which requires the binding module; removing this module had no effect on measured chitinase activity.

The crystal chemistry of inorganic metal borohydrides and their relation to metal oxides.

PubMed

Černý, Radovan; Schouwink, Pascal

2015-12-01

The crystal structures of inorganic homoleptic metal borohydrides are analysed with respect to their structural prototypes found amongst metal oxides in the inorganic databases such as Pearson's Crystal Data [Villars & Cenzual (2015). Pearson's Crystal Data. Crystal Structure Database for Inorganic Compounds, Release 2014/2015, ASM International, Materials Park, Ohio, USA]. The coordination polyhedra around the cations and the borohydride anion are determined, and constitute the basis of the structural systematics underlying metal borohydride chemistry in various frameworks and variants of ionic packing, including complex anions and the packing of neutral molecules in the crystal. Underlying nets are determined by topology analysis using the program TOPOS [Blatov (2006). IUCr CompComm. Newsl. 7, 4-38]. It is found that the Pauling rules for ionic crystals apply to all non-molecular borohydride crystal structures, and that the latter can often be derived by simple deformation of the close-packed anionic lattices c.c.p. and h.c.p., by partially removing anions and filling tetrahedral or octahedral sites. The deviation from an ideal close packing is facilitated in metal borohydrides with respect to the oxide due to geometrical and electronic considerations of the BH4(-) anion (tetrahedral shape, polarizability). This review on crystal chemistry of borohydrides and their similarity to oxides is a contribution which should serve materials engineers as a roadmap to design new materials, synthetic chemists in their search for promising compounds to be prepared, and materials scientists in understanding the properties of novel materials.

Surface Structure and Wetting Characteristics of Collembola Cuticles

PubMed Central

Gundersen, Håkon; Leinaas, Hans Petter; Thaulow, Christian

2014-01-01

The cuticles of the arthropods Collembola (springtails) are known to be superhydrophobic, displaying such properties as water-repellence and plastron formation; overhanging surface structures have been suggested as the source of these properties. Superhydrophobicity is closely related to surface structuring and other surfaces with overhanging structures have been shown to possess robust superhydrophobic properties. In effort to correlate the wetting performance and surface structuring of the cuticles, from both a technical and evolutionary point of view, we investigated a selection of Collembola species including species from several families and covering habitats ranging from aquatic to very dry. The observed contact angles of wetting was in general larger than those predicted by the conventional models. Not all the studied Collembola were found to have superhydrophobic properties, indicating that superhydrophobicity is common, but not a universal trait in Collembola. Overhanging structures were found in some, but not all Collembola species with superhydrophobic cuticles; which leads to the conclusion that there is no direct link between overhanging surface structures and superhydrophobicity in Collembola. PMID:24498281

Low Pressure Greenhouse Concepts for Mars

NASA Technical Reports Server (NTRS)

Fowler, Philip A.; Wheeler, Raymond M.; Bucklin, Ray A.; Corey, Kenneth A.

2000-01-01

A project was initiated to begin testing some environmental limits for managing plant growth systems. These limits will help determine some of the concepts for building plant enclosures for use on Mars. In particular, this study focuses on the effects of reduced atmospheric pressures. Structural design is considered as it relates to the biological processes that would occur within that structure. The design must be closely tied to the functionality of the biological system and has a few primary concerns that need to be tested to resolve the question as to the path of the design. Early tests indicate that plants can survive and grow at low (greater than 76 mb) pressure.

A silicon micromachined resonant pressure sensor

NASA Astrophysics Data System (ADS)

Tang, Zhangyang; Fan, Shangchun; Cai, Chenguang

2009-09-01

This paper describes the design, fabrication and test of a silicon micromachined resonant pressure sensor. A square membrane and a doubly clamped resonant beam constitute a compound structure. The former senses the pressure directly, while the latter changes its resonant frequency according to deformation of the membrane. The final output relation between the resonant frequency and the applied pressure is deducted according to the structure mechanical properties. Sensors are fabricated by micromachining technology, and then sealed in vaccum. These sensors are tested by open-loop and close-loop system designed on purpose. The experiment results demonstrate that the sensor has a sensitivity of 49.8Hz/kPa and repeatability of 0.08%.

Relatively stable, large-amplitude Alfvenic waves seen at 2.5 and 5.0 AU

NASA Technical Reports Server (NTRS)

Mavromichalaki, H.; Moussas, X.; Quenby, J. J.; Valdes-Galicia, J. F.; Smith, E. J.

1988-01-01

Pioneer 11 and 10 observations of the wave structure seen in a corotating interaction region at 2.5 AU on day 284 of 1973 and 8 days later at 5 AU reveal large-amplitude Alfvenic structures with many detailed correlations seen between their features at the two radial distances. Hodogram analysis suggests the dominance of near plane polarized, transverse Alfvenic mode fluctuations with periods between 2 min and one hour or more. Some wave evolution close to the Corotating Interaction Region (CIR) shock is noticed, but waves towards the center of the compression seem to propagate with little damping between the spacecraft observation positions.

The self-assembling zwitterionic form of L-phenylalanine at neutral pH.

PubMed

Mossou, Estelle; Teixeira, Susana C M; Mitchell, Edward P; Mason, Sax A; Adler-Abramovich, Lihi; Gazit, Ehud; Forsyth, V Trevor

2014-03-01

The title zwitterion (2S)-2-azaniumyl-1-hydroxy-3-phenylpropan-1-olate, C9H11NO2, also known as L-phenylalanine, was characterized using synchrotron X-rays. It crystallized in the monoclinic space group P21 with four molecules in the asymmetric unit. The 0.62 Å resolution structure is assumed to be closely related to the fibrillar form of phenylalanine, as observed by electron microscopy and electron diffraction. The structure exists in a zwitterionic form in which π-π stacking and hydrogen-bonding interactions are believed to form the basis of the self-assembling properties.

The evolving market structures of gambling: case studies modelling the socioeconomic assignment of gaming machines in Melbourne and Sydney, Australia.

PubMed

Marshall, David C; Baker, Robert G V

2002-01-01

The expansion of gambling industries worldwide is intertwined with the growing government dependence on gambling revenue for fiscal assignments. In Australia, electronic gaming machines (EGMs) have dominated recent gambling industry growth. As EGMs have proliferated, growing recognition has emerged that EGM distribution closely reflects levels of socioeconomic disadvantage. More machines are located in less advantaged regions. This paper analyses time-series socioeconomic distributions of EGMs in Melbourne, Australia, an immature EGM market, and then compares the findings with the mature market in Sydney. Similar findings in both cities suggest that market assignment of EGMs transcends differences in historical and legislative environments. This indicates that similar underlying structures are evident in both markets. Modelling the spatial structures of gambling markets provides an opportunity to identify regions most at risk of gambling related problems. Subsequently, policies can be formulated which ensure fiscal revenue from gambling can be better targeted towards regions likely to be most afflicted by excessive gambling-related problems.

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

Longenecker, Kenton L.; Stamper, Geoffrey F.; Hajduk, Philip J.

In a broad genomics analysis to find novel protein targets for antibiotic discovery, MurF was identified as an essential gene product for Streptococcus pneumonia that catalyzes a critical reaction in the biosynthesis of the peptidoglycan in the formation of the cell wall. Lacking close relatives in mammalian biology, MurF presents attractive characteristics as a potential drug target. Initial screening of the Abbott small-molecule compound collection identified several compounds for further validation as pharmaceutical leads. Here we report the integrated efforts of NMR and X-ray crystallography, which reveal the multidomain structure of a MurF-inhibitor complex in a compact conformation that differsmore » dramatically from related structures. The lead molecule is bound in the substrate-binding region and induces domain closure, suggestive of the domain arrangement for the as yet unobserved transition state conformation for MurF enzymes. The results form a basis for directed optimization of the compound lead by structure-based design to explore the suitability of MurF as a pharmaceutical target.« less

Electron Diffraction Evidence for the Ordering of Excess Nickel Atoms by Relation to Stoichiometry in Nickel-Rich Beta'-Nial Formation of a Nickel-Aluminum (Ni2al) Superlattices

NASA Technical Reports Server (NTRS)

Reynaud, F.

1988-01-01

In electron diffraction patterns of nickel-rich beta-NiAl alloys, many anomalies are observed. One of these is the appearance of diffuse intensity maxima between the reflexions of the B2 structure. This is explained by the short-range ordering of the excess nickel atoms on the simple cubic sublattice occupied only by aluminum atoms in the stoichiometric, perfectly ordered NiAl alloy. After annealing Ni 37.5 atomic percent Al and Ni 37.75 atomic percent Al for 1 week at 300 and 400 C, the diffuse intensity maxima transformed into sharp superstructure reflexions. These reflexions are explained by the formation of the four possible variants of an ordered hexagonal superstructure corresponding to the Ni2Al composition. This structure is closely related to the Ni2Al3 structure (same space group) formed by the ordering of vacancies on the nickel sublattice in aluminum-rich beta-NiAl alloys.

The phylogenetic structure of plant-pollinator networks increases with habitat size and isolation.

PubMed

Aizen, Marcelo A; Gleiser, Gabriela; Sabatino, Malena; Gilarranz, Luis J; Bascompte, Jordi; Verdú, Miguel

2016-01-01

Similarity among species in traits related to ecological interactions is frequently associated with common ancestry. Thus, closely related species usually interact with ecologically similar partners, which can be reinforced by diverse co-evolutionary processes. The effect of habitat fragmentation on the phylogenetic signal in interspecific interactions and correspondence between plant and animal phylogenies is, however, unknown. Here, we address to what extent phylogenetic signal and co-phylogenetic congruence of plant-animal interactions depend on habitat size and isolation by analysing the phylogenetic structure of 12 pollination webs from isolated Pampean hills. Phylogenetic signal in interspecific interactions differed among webs, being stronger for flower-visiting insects than plants. Phylogenetic signal and overall co-phylogenetic congruence increased independently with hill size and isolation. We propose that habitat fragmentation would erode the phylogenetic structure of interaction webs. A decrease in phylogenetic signal and co-phylogenetic correspondence in plant-pollinator interactions could be associated with less reliable mutualism and erratic co-evolutionary change. © 2015 John Wiley & Sons Ltd/CNRS.

Structural organizations of yeast RNase P and RNase MRP holoenzymes as revealed by UV-crosslinking studies of RNA–protein interactions

PubMed Central

Khanova, Elena; Esakova, Olga; Perederina, Anna; Berezin, Igor; Krasilnikov, Andrey S.

2012-01-01

Eukaryotic ribonuclease (RNase) P and RNase MRP are closely related ribonucleoprotein complexes involved in the metabolism of various RNA molecules including tRNA, rRNA, and some mRNAs. While evolutionarily related to bacterial RNase P, eukaryotic enzymes of the RNase P/MRP family are much more complex. Saccharomyces cerevisiae RNase P consists of a catalytic RNA component and nine essential proteins; yeast RNase MRP has an RNA component resembling that in RNase P and 10 essential proteins, most of which are shared with RNase P. The structural organizations of eukaryotic RNases P/MRP are not clear. Here we present the results of RNA–protein UV crosslinking studies performed on RNase P and RNase MRP holoenzymes isolated from yeast. The results indicate locations of specific protein-binding sites in the RNA components of RNase P and RNase MRP and shed light on the structural organizations of these large ribonucleoprotein complexes. PMID:22332141

Structural organizations of yeast RNase P and RNase MRP holoenzymes as revealed by UV-crosslinking studies of RNA-protein interactions.

PubMed

Khanova, Elena; Esakova, Olga; Perederina, Anna; Berezin, Igor; Krasilnikov, Andrey S

2012-04-01

Eukaryotic ribonuclease (RNase) P and RNase MRP are closely related ribonucleoprotein complexes involved in the metabolism of various RNA molecules including tRNA, rRNA, and some mRNAs. While evolutionarily related to bacterial RNase P, eukaryotic enzymes of the RNase P/MRP family are much more complex. Saccharomyces cerevisiae RNase P consists of a catalytic RNA component and nine essential proteins; yeast RNase MRP has an RNA component resembling that in RNase P and 10 essential proteins, most of which are shared with RNase P. The structural organizations of eukaryotic RNases P/MRP are not clear. Here we present the results of RNA-protein UV crosslinking studies performed on RNase P and RNase MRP holoenzymes isolated from yeast. The results indicate locations of specific protein-binding sites in the RNA components of RNase P and RNase MRP and shed light on the structural organizations of these large ribonucleoprotein complexes.

A Near-Atomic Structure of the Dark Apoptosome Provides Insight into Assembly and Activation.

PubMed

Cheng, Tat Cheung; Akey, Ildikó V; Yuan, Shujun; Yu, Zhiheng; Ludtke, Steven J; Akey, Christopher W

2017-01-03

In Drosophila, the Apaf-1-related killer (Dark) forms an apoptosome that activates procaspases. To investigate function, we have determined a near-atomic structure of Dark double rings using cryo-electron microscopy. We then built a nearly complete model of the apoptosome that includes 7- and 8-blade β-propellers. We find that the preference for dATP during Dark assembly may be governed by Ser325, which is in close proximity to the 2' carbon of the deoxyribose ring. Interestingly, β-propellers in V-shaped domains of the Dark apoptosome are more widely separated, relative to these features in the Apaf-1 apoptosome. This wider spacing may be responsible for the lack of cytochrome c binding to β-propellers in the Dark apoptosome. Our structure also highlights the roles of two loss-of-function mutations that may block Dark assembly. Finally, the improved model provides a framework to understand apical procaspase activation in the intrinsic cell death pathway. Copyright © 2016 Elsevier Ltd. All rights reserved.

Thermodynamic behavior of glassy state of structurally related compounds.

PubMed

Kaushal, Aditya Mohan; Bansal, Arvind Kumar

2008-08-01

Thermodynamic properties of amorphous pharmaceutical forms are responsible for enhanced solubility as well as poor physical stability. The present study was designed to investigate the differences in thermodynamic parameters arising out of disparate molecular structures and associations for four structurally related pharmaceutical compounds--celecoxib, valdecoxib, rofecoxib, and etoricoxib. Conventional and modulated temperature differential scanning calorimetry were employed to study glass forming ability and thermodynamic behavior of the glassy state of model compounds. Glass transition temperature of four glassy compounds was in a close range of 327.6-331.8 K, however, other thermodynamic parameters varied considerably. Kauzmann temperature, strength parameter and fragility parameter showed rofecoxib glass to be most fragile of the four compounds. Glass forming ability of the compounds fared similar in the critical cooling rate experiments, suggesting that different factors were determining the glass forming ability and subsequent behavior of the compounds in glassy state. A comprehensive understanding of such thermodynamic facets of amorphous form would help in rationalizing the approaches towards development of stable glassy pharmaceuticals.

Shifts of microbial communities of wheat (Triticum aestivum L.) cultivation in a closed artificial ecosystem.

PubMed

Qin, Youcai; Fu, Yuming; Dong, Chen; Jia, Nannan; Liu, Hong

2016-05-01

The microbial communities of plant ecosystems are in relation to plant growing environment, but the alteration in biodiversity of rhizosphere and phyllosphere microbial communities in closed and controlled environments is unknown. The purpose of this study is to analyze the change regularity of microbial communities with wheat plants dependent-cultivated in a closed artificial ecosystem. The microbial community structures in closed-environment treatment plants were investigated by a culture-dependent approach, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), and Illumina Miseq high-throughput sequencing. The results indicated that the number of microbes decreased along with time, and the magnitude of bacteria, fungi, and actinomycetes were 10(7)-10(8), 10(5), and 10(3)-10(4) CFU/g (dry weight), respectively. The analysis of PCR-DGGE and Illumina Miseq revealed that the wheat leaf surface and near-root substrate had different microbial communities at different periods of wheat ecosystem development and showed that the relative highest diversity of microbial communities appeared at late and middle periods of the plant ecosystem, respectively. The results also indicated that the wheat leaf and substrate had different microbial community compositions, and the wheat substrate had higher richness of microbial community than the leaf. Flavobacterium, Pseudomonas, Paenibacillus, Enterobacter, Penicillium, Rhodotorula, Acremonium, and Alternaria were dominant in the wheat leaf samples, and Pedobacter, Flavobacterium, Halomonas, Marinobacter, Salinimicrobium, Lysobacter, Pseudomonas, Halobacillus, Xanthomonas, Acremonium, Monographella, and Penicillium were dominant populations in the wheat near-root substrate samples.

Complete Mitochondrial Genome Sequence of Acrida cinerea (Acrididae: Orthoptera) and Comparative Analysis of Mitochondrial Genomes in Orthoptera

PubMed Central

Liu, Nian; Huang, Yuan

2010-01-01

The complete 15,599-bp mitogenome of Acrida cinerea was determined and compared with that of the other 20 orthopterans. It displays characteristic gene content, genome organization, nucleotide composition, and codon usage found in other Caelifera mitogenomes. Comparison of 21 orthopteran sequences revealed that the tRNAs encoded by the H-strand appear more conserved than those by the L-stand. All tRNAs form the typical clover-leaf structure except trnS (agn), and most of the size variation among tRNAs stemmed from the length variation in the arm and loop of TΨC and the loop of DHU. The derived secondary structure models of the rrnS and rrnL from 21 orthoptera species closely resemble those from other insects on CRW except a considerably enlarged loop of helix 1399 of rrnS in Caelifera, which is a potentially autapomorphy of Caelifera. In the A+T-rich region, tandem repeats are not only conserved in the closely related mitogenome but also share some conserved motifs in the same subfamily. A stem-loop structure, 16 bp or longer, is likely to be involved in replication initiation in Caelifera and Grylloidea. A long T-stretch (>17 bp) with conserved stem-loop structure next to rrnS on the H-strand, bounded by a purine at either end, exists in the three species from Tettigoniidae. PMID:21197069

...And Kronos Ate His Sons

NASA Astrophysics Data System (ADS)

Vitiello, Giuseppe

In closed systems, energy is conserved. The origin of the time axis is completely arbitrary due to the invariance under continuous time-translations. The flowing of time swallows those fictitious origins one might assign on its axis, as Kronos ate his sons. Dissipation breaks such a scenario. It implies a non-forgettable origin of time. Open systems need their complement (their "double") in order to become, together, a closed system. Time emerges as an observable measured by the evolution of the open system complement, which acts as a clock. The conservation of the energy-momentum tensor in electrodynamics is considered and its relation with dissipative systems and self-similar fractal structures is discussed. The isomorphism with coherent states in quantum field theory (QFT) is established and the generator of transitions among unitarily inequivalent representations of the canonical commutation relations (CCR) is shown to provide sequences in time of phases, which defines the arrow of time. Merging properties of electrodynamics, fractal self-similarity, dissipation and coherent states point to an integrated vision of Nature.

High in Vivo Stability of 64Cu-Labeled Cross-Bridged Chelators Is a Crucial Factor in Improved Tumor Imaging of RGD Peptide Conjugates.

PubMed

Sarkar, Swarbhanu; Bhatt, Nikunj; Ha, Yeong Su; Huynh, Phuong Tu; Soni, Nisarg; Lee, Woonghee; Lee, Yong Jin; Kim, Jung Young; Pandya, Darpan N; An, Gwang Il; Lee, Kyo Chul; Chang, Yongmin; Yoo, Jeongsoo

2018-01-11

Although the importance of bifunctional chelators (BFCs) is well recognized, the chemophysical parameters of chelators that govern the biological behavior of the corresponding bioconjugates have not been clearly elucidated. Here, five BFCs closely related in structure were conjugated with a cyclic RGD peptide and radiolabeled with Cu-64 ions. Various biophysical and chemical properties of the Cu(II) complexes were analyzed with the aim of identifying correlations between individual factors and the biological behavior of the conjugates. Tumor uptake and body clearance of the 64 Cu-labeled bioconjugates were directly compared by animal PET imaging in animal models, which was further supported by biodistribution studies. Conjugates containing propylene cross-bridged chelators showed higher tumor uptake, while a closely related ethylene cross-bridged analogue exhibited rapid body clearance. High in vivo stability of the copper-chelator complex was strongly correlated with high tumor uptake, while the overall lipophilicity of the bioconjugate affected both tumor uptake and body clearance.